NCBI Conserved Domain Search

RNA recognition motif;

134-213

4.06e-10

RNA recognition motif;

Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 56.45 E-value: 4.06e-10

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437    134 NVYVSGLPPDITVDEFIQLMSKFGIIMRdpqteefkVKLYKDNQ-GNLKGDGLCCYLKRESVELALKLLDEDEIRGYKLH 212
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVES--------VRLVRDKEtGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLK 72


                   .
gi 21361437    213 V 213
Cdd:smart00360  73 V 73

RRM_1

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...

135-212

2.13e-08

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease.

Pssm-ID: 425453 [Multi-domain] Cd Length: 70 Bit Score: 51.46 E-value: 2.13e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 21361437   135 VYVSGLPPDITVDEFIQLMSKFGIIMRdpqteefkVKLYKDNQGNLKGDGLCCYLKRESVELALKLLDEDEIRGYKLH 212
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKS--------IRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

RRM_1

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...

288-343

1.99e-07

Pssm-ID: 425453 [Multi-domain] Cd Length: 70 Bit Score: 48.77 E-value: 1.99e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 21361437   288 REDLRVECSKFGQIRKLLLF---DRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQIT 343
Cdd:pfam00076  12 EEDLKDLFSKFGPIKSIRLVrdeTGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

RRM

RNA recognition motif;

289-343

1.96e-06

RNA recognition motif;

Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 46.05 E-value: 1.96e-06

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 21361437    289 EDLRVECSKFGQIRKL-LLFDRH---PDGVASVSFRDPEEADYCIQTLDGRWFGGRQIT 343
Cdd:smart00360  14 EELRELFSKFGKVESVrLVRDKEtgkSKGFAFVEFESEEDAEKALEALNGKELDGRPLK 72

2A1904

K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying ...

451-715

4.58e-06

K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying compounds]

Pssm-ID: 273344 [Multi-domain] Cd Length: 1096 Bit Score: 50.38 E-value: 4.58e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437    451 ESSPEKEAEEGCPEKESEEGCPKRGfEGSCSQKESEEGNPVRGSEEDSPKKESKKKTLKNDCEENGLAKESEDDlnkesE 530
Cdd:TIGR00927  639 EHTGERTGEEGERPTEAEGENGEES-GGEAEQEGETETKGENESEGEIPAERKGEQEGEGEIEAKEADHKGETE-----A 712

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437    531 EEVGPTKESEEDDSEKESDEDCSEKQSEDGSEREFEENGLEkDLDEEGSEKELHENVLDKELEENDSENSEFEDDGSEKV 610
Cdd:TIGR00927  713 EEVEHEGETEAEGTEDEGEIETGEEGEEVEDEGEGEAEGKH-EVETEGDRKETEHEGETEAEGKEDEDEGEIQAGEDGEM 791

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437    611 LDEEGSEREFDEDSDEKEEEEDTYEKVFDDESDEKEDEEYADEKGLEAADKkaEEGDADEKlfeesDDKEDEDADGKEVE 690
Cdd:TIGR00927  792 KGDEGAEGKVEHEGETEAGEKDEHEGQSETQADDTEVKDETGEQELNAENQ--GEAKQDEK-----GVDGGGGSDGGDSE 864

                          250       260
                   ....*....|....*....|....*
gi 21361437    691 DADEKLFEDDDSNEKLFDEEEDSSE 715
Cdd:TIGR00927  865 EEEEEEEEEEEEEEEEEEEEEEEEE 889

PHA03169

hypothetical protein; Provisional

403-603

7.16e-04

hypothetical protein; Provisional

Pssm-ID: 223003 [Multi-domain] Cd Length: 413 Bit Score: 42.65 E-value: 7.16e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437  403 SEHPSTSKMNAQETATGMAFEEPIDEKKFEKTEDGGEFEEGASENNAKESSPEkeaEEGCPEKESEEGCPKRGFEGSCSQ 482
Cdd:PHA03169  54 SGPQVRAVAEQGHRQTESDTETAEESRHGEKEERGQGGPSGSGSESVGSPTPS---PSGSAEELASGLSPENTSGSSPES 130

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437  483 KESEEGNPVRGSEED--SPKKESKKKTLKNDCEENGLAKESEDdlnkESEEEVGPTKESEEDDSEKESDEDCSEKQSE-D 559
Cdd:PHA03169 131 PASHSPPPSPPSHPGphEPAPPESHNPSPNQQPSSFLQPSHED----SPEEPEPPTSEPEPDSPGPPQSETPTSSPPPqS 206

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 21361437  560 GSEREFEENGLEKDLDEEGSEKELHENvlDKELEENDSENSEFE 603
Cdd:PHA03169 207 PPDEPGEPQSPTPQQAPSPNTQQAVEH--EDEPTEPEREGPPFP 248

Name

Accession

Description

Interval

E-value

RRM1_TatSF1_like

cd12281

RNA recognition motif 1 (RRM1) found in HIV Tat-specific factor 1 (Tat-SF1) and similar ...

132-222

7.15e-51

Pssm-ID: 409723 [Multi-domain] Cd Length: 92 Bit Score: 172.35 E-value: 7.15e-51

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437 132 NTNVYVSGLPPDITVDEFIQLMSKFGIIMRDPQTEEFKVKLYKDNQGNLKGDGLCCYLKRESVELALKLLDEDEI-RGYK 210
Cdd:cd12281   1 NTNVYVSGLPLDITVEEFVELFSKCGIIMEDPETGEPKIKLYRDENGNLKGDALCCYLKEESVELALQLLDGTEIgRGYK 80

                        90
                ....*....|..
gi 21361437 211 LHVEVAKFQLKG 222
Cdd:cd12281  81 IHVERAKFELKG 92

RRM2_TatSF1_like

cd12282

RNA recognition motif 2 (RRM2) found in HIV Tat-specific factor 1 (Tat-SF1) and similar ...

263-353

8.36e-50

Pssm-ID: 409724 [Multi-domain] Cd Length: 91 Bit Score: 169.34 E-value: 8.36e-50

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437 263 ERVVIIKNMFHPMDFEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQI 342
Cdd:cd12282   1 EKVVILKNMFHPKEFEEDPELINEIKEDLREECEKFGQVKKVVVFDRHPDGVASVKFKEPEEADKCIQALNGRWFAGRKL 80

                        90
                ....*....|.
gi 21361437 343 TAQAWDGTTDY 353
Cdd:cd12282  81 EAETWDGKTDY 91

RRM3_RBM39_like

cd12285

RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 39 (RBM39) and similar ...

264-348

1.09e-25

RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 39 (RBM39) and similar proteins; This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs.

Pssm-ID: 409727 [Multi-domain] Cd Length: 85 Bit Score: 101.09 E-value: 1.09e-25

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437 264 RVVIIKNMFHPMDFEDDPLvLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQIT 343
Cdd:cd12285   2 RCVILKNMFDPAEETEDNW-DDEIKEDVIEECSKYGPVLHIYVDKNSPQGNVYVKFKTIEAAQKCVQAMNGRWFDGRQIT 80


                ....*
gi 21361437 344 AQAWD 348
Cdd:cd12285  81 AAYVP 85

RRM_SF

cd00590

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...

135-214

4.67e-12

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

Pssm-ID: 409669 [Multi-domain] Cd Length: 72 Bit Score: 61.92 E-value: 4.67e-12

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437 135 VYVSGLPPDITVDEFIQLMSKFGIIMRdpqteefkVKLYKDNQGNLKGDGLCCYLKRESVELALKLLDEDEIRGYKLHVE 214
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVS--------VRIVRDRDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72

RRM3_UHM_PUF60

cd12648

RNA recognition motif 3 (RRM3) found in UHM domain of poly(U)-binding-splicing factor PUF60 ...

264-350

6.49e-12

RNA recognition motif 3 (RRM3) found in UHM domain of poly(U)-binding-splicing factor PUF60 and similar proteins; This subgroup corresponds to the RRM3 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1), an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. The research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition.

Pssm-ID: 410052 [Multi-domain] Cd Length: 98 Bit Score: 62.43 E-value: 6.49e-12

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437 264 RVVIIKNMFHPMDFEDDplvlneIREDLRVECSKFGQIRKLLLF------DRHPDGVAS--VSFRDPEEADYCIQTLDGR 335
Cdd:cd12648   2 RVMVLRNMVGPEDIDDD------LEGEVTEECGKFGAVNRVIIYqekqgeEEDAEIIVKifVEFSMPSEAEKAIQALNGR 75

                        90
                ....*....|....*
gi 21361437 336 WFGGRQITAQAWDGT 350
Cdd:cd12648  76 WFGGRKVVAELYDQT 90

RRM_FET

cd12280

RNA recognition motif (RRM) found in the FET family of RNA-binding proteins; This subfamily ...

135-214

8.04e-12

RNA recognition motif (RRM) found in the FET family of RNA-binding proteins; This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15.

Pssm-ID: 409722 [Multi-domain] Cd Length: 82 Bit Score: 61.66 E-value: 8.04e-12

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437 135 VYVSGLPPDITVDEFIQLMSKFGIIMRDPQTEEFKVKLYKD-NQGNLKGDGLCCYLKRESVELALKLLDEDEIRGYKLHV 213
Cdd:cd12280   1 IFVSGLPPDVTIDELADLFGQIGIIKRYKDTWPPKIKIYTDkETGKPKGEATLTYEDPSAAKAAIEWFNGKEFRGNKIKV 80


                .
gi 21361437 214 E 214
Cdd:cd12280  81 S 81

RRM3_U2AF65

cd12232

RNA recognition motif 3 (RRM3) found in U2 large nuclear ribonucleoprotein auxiliary factor ...

264-345

1.09e-11

RNA recognition motif 3 (RRM3) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins; This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs.

Pssm-ID: 409679 [Multi-domain] Cd Length: 89 Bit Score: 61.45 E-value: 1.09e-11

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437 264 RVVIIKNMFHPMDFEDDPLVlNEIREDLRVECSKFGQIRKLLLFDRHPDGVAS-------VSFRDPEEADYCIQTLDGRW 336
Cdd:cd12232   2 RVLCLLNMVTPEELEDDEEY-EEILEDVKEECSKYGKVLSVVIPRPEAEGVDVpgvgkvfVEFEDVEDAQKAQKALAGRK 80


                ....*....
gi 21361437 337 FGGRQITAQ 345
Cdd:cd12232  81 FDGRTVVAS 89

RRM_UHM_SPF45_PUF60

cd12374

RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar ...

264-348

4.06e-11

RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins; This subfamily corresponds to the RRM found in UHM domain of 45 kDa-splicing factor (SPF45 or RBM17), poly(U)-binding-splicing factor PUF60 (FIR or Hfp or RoBP1 or Siah-BP1), and similar proteins. SPF45 is an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155. PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RRMs and a C-terminal UHM domain.

Pssm-ID: 409809 [Multi-domain] Cd Length: 85 Bit Score: 59.54 E-value: 4.06e-11

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437 264 RVVIIKNMFHPMDFEDDplvlneIREDLRVECSKFGQIRKLLLfdrHPDGVAS--------VSFRDPEEADYCIQTLDGR 335
Cdd:cd12374   2 KILVLRNMVGPGEIDED------LKDEIKEECSKYGKVLNVII---HEVASSEaddavrvfVEFEDADEAIKAFRALNGR 72

                        90
                ....*....|...
gi 21361437 336 WFGGRQITAQAWD 348
Cdd:cd12374  73 FFGGRKVKARFYD 85

half-pint

TIGR01645

poly-U binding splicing factor, half-pint family; The proteins represented by this model ...

259-348

1.32e-10

Pssm-ID: 130706 [Multi-domain] Cd Length: 612 Bit Score: 64.71 E-value: 1.32e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437   259 RMRHERVVIIKNMFHPMDFEDDplvlneIREDLRVECSKFGQIRKLLLFDRHPDGVAS--------VSFRDPEEADYCIQ 330
Cdd:TIGR01645 510 RTNRSNVIVLRNMVTPQDIDEF------LEGEIREECGKFGVVDRVIINFEKQGEEEDaeiivkifVEFSDSMEVDRAKA 583

                          90
                  ....*....|....*...
gi 21361437   331 TLDGRWFGGRQITAQAWD 348
Cdd:TIGR01645 584 ALDGRFFGGRTVVAEAYD 601

PABP-1234

TIGR01628

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...

133-340

2.46e-10

Pssm-ID: 130689 [Multi-domain] Cd Length: 562 Bit Score: 63.67 E-value: 2.46e-10

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437   133 TNVYVSGLPPDITVDEFIQLMSKFGIIMrdpqteefKVKLYKDNQGNLKGDGLCCYLKRESVELALKLLDEDEI----RG 208
Cdd:TIGR01628 179 TNLYVKNLDPSVNEDKLRELFAKFGEIT--------SAAVMKDGSGRSRGFAFVNFEKHEDAAKAVEEMNGKKIglakEG 250

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437   209 YKLHveVAKFQLKGEYDAskkkkkckdykkKLSMQQKQLdwRPERragpsRMRHERVVI-IKNMfhpmdfedDPLVLNei 287
Cdd:TIGR01628 251 KKLY--VGRAQKRAEREA------------ELRRKFEEL--QQER-----KMKAQGVNLyVKNL--------DDTVTD-- 299

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 21361437   288 rEDLRVECSKFGQIR--KLLLFD-RHPDGVASVSFRDPEEADYCIQTLDGRWFGGR 340
Cdd:TIGR01628 300 -EKLRELFSECGEITsaKVMLDEkGVSRGFGFVCFSNPEEANRAVTEMHGRMLGGK 354

RRM

RNA recognition motif;

134-213

4.06e-10

RNA recognition motif;

Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 56.45 E-value: 4.06e-10

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437    134 NVYVSGLPPDITVDEFIQLMSKFGIIMRdpqteefkVKLYKDNQ-GNLKGDGLCCYLKRESVELALKLLDEDEIRGYKLH 212
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVES--------VRLVRDKEtGKSKGFAFVEFESEEDAEKALEALNGKELDGRPLK 72


                   .
gi 21361437    213 V 213
Cdd:smart00360  73 V 73

RRM_SF

cd00590

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...

288-345

1.21e-09

Pssm-ID: 409669 [Multi-domain] Cd Length: 72 Bit Score: 54.98 E-value: 1.21e-09

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 21361437 288 REDLRVECSKFGQIRKLLLF---DRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQ 345
Cdd:cd00590  12 EEDLRELFSKFGEVVSVRIVrdrDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72

SF-CC1

TIGR01622

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors ...

264-344

1.22e-09

splicing factor, CC1-like family; This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed.

Pssm-ID: 273721 [Multi-domain] Cd Length: 494 Bit Score: 61.47 E-value: 1.22e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437   264 RVVIIKNMFHPMDfEDDPLVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQIT 343
Cdd:TIGR01622 400 RCLVLSNMFDPAT-EEEPNWDKEIEDDVREECSKYGGVVHIYVDDKNSAGDIYLKFDSVQAAEAAIKALNGRYFGGKMIT 478


                  .
gi 21361437   344 A 344
Cdd:TIGR01622 479 A 479

U2AF_lg

TIGR01642

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of ...

100-344

3.73e-09

U2 snRNP auxilliary factor, large subunit, splicing factor; These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi.

Pssm-ID: 273727 [Multi-domain] Cd Length: 509 Bit Score: 59.91 E-value: 3.73e-09

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437   100 PPQEKAPEPTDARK----KGEKRKAESGWFHVEEDRntnVYVSGLPPDITVDEFIQLMSKFGIIMrdpqteefKVKLYKD 175
Cdd:TIGR01642 262 PVPQITPEVSQKNPddnaKNVEKLVNSTTVLDSKDR---IYIGNLPLYLGEDQIKELLESFGDLK--------AFNLIKD 330

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437   176 -NQGNLKGDGLCCYLKRESVELALKLLDEDEIRGYKLHVEVAKFQLK-GEYDASKKKKKCKDYKKKLSMQQKQLDWRPER 253
Cdd:TIGR01642 331 iATGLSKGYAFCEYKDPSVTDVAIAALNGKDTGDNKLHVQRACVGANqATIDTSNGMAPVTLLAKALSQSILQIGGKPTK 410

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437   254 ragpsrmrherVVIIKNMFHPMDFEDDPlVLNEIREDLRVECSKFGQIRKLLLFDRHPDGVAS-------VSFRDPEEAD 326
Cdd:TIGR01642 411 -----------VVQLTNLVTGDDLMDDE-EYEEIYEDVKTEFSKYGPLINIVIPRPNGDRNSTpgvgkvfLEYADVRSAE 478

                         250
                  ....*....|....*...
gi 21361437   327 YCIQTLDGRWFGGRQITA 344
Cdd:TIGR01642 479 KAMEGMNGRKFNDRVVVA 496

RRM_1

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...

135-212

2.13e-08

Pssm-ID: 425453 [Multi-domain] Cd Length: 70 Bit Score: 51.46 E-value: 2.13e-08

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 21361437   135 VYVSGLPPDITVDEFIQLMSKFGIIMRdpqteefkVKLYKDNQGNLKGDGLCCYLKRESVELALKLLDEDEIRGYKLH 212
Cdd:pfam00076   1 LFVGNLPPDTTEEDLKDLFSKFGPIKS--------IRLVRDETGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

RRM_UHM_SPF45

cd12647

RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar ...

264-348

2.70e-08

RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins; This subgroup corresponds to the RRM of SPF45, also termed RNA-binding motif protein 17 (RBM17), an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155.

Pssm-ID: 410051 [Multi-domain] Cd Length: 95 Bit Score: 51.90 E-value: 2.70e-08

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437 264 RVVIIKNMFHPMDFEDDplvlneIREDLRVECSKFGQIRKLLLFD--RHPDGVAS---VSFRDPEEADYCIQTLDGRWFG 338
Cdd:cd12647   3 KVVLLRNMVGPGEVDED------LEPEVKEECEKYGKVTKVVIFEipGAPDDEAVrifVEFERVESAIKAVVDLNGRFFG 76

                        90
                ....*....|
gi 21361437 339 GRQITAQAWD 348
Cdd:cd12647  77 GRTVKASFYD 86

RRM_U2AF35_like

cd12287

RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF ...

285-345

6.00e-08

RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35) and similar proteins; This subfamily corresponds to the RRM in U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF) which has been implicated in the recruitment of U2 snRNP to pre-mRNAs. It is a highly conserved heterodimer composed of large and small subunits; this family includes the small subunit of U2AF (U2AF35 or U2AF1) and U2AF 35 kDa subunit B (U2AF35B or C3H60). U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF (U2AF65 or U2AF2). Although the biological role of U2AF35B remains unclear, it shows high sequence homolgy to U2AF35, which contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR) -rich segment interrupted by glycines. In contrast to U2AF35, U2AF35B has a plant-specific conserved C-terminal region containing SERE motif(s), which may have an important function specific to higher plants.

Pssm-ID: 409729 [Multi-domain] Cd Length: 101 Bit Score: 51.11 E-value: 6.00e-08

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 21361437 285 NEIREDLRVECSKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQ 345
Cdd:cd12287  35 DEFYEDVFLELSRFGEIEDLVVCSNlndHLLGNVYVKFESEEDAEAALQALNGRYYAGRPLYPE 98

RRM_SARFH

cd12534

RNA recognition motif (RRM) found in Drosophila melanogaster RNA-binding protein cabeza and ...

135-216

9.96e-08

RNA recognition motif (RRM) found in Drosophila melanogaster RNA-binding protein cabeza and similar proteins; This subgroup corresponds to the RRM in cabeza, also termed P19, or sarcoma-associated RNA-binding fly homolog (SARFH). It is a putative homolog of human RNA-binding proteins FUS (also termed TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1), TAF15 (also termed hTAFII68 or TAF2N or RPB56), and belongs to the of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a nuclear RNA binding protein that may play an important role in the regulation of RNA metabolism during fly development. Cabeza contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 240978 [Multi-domain] Cd Length: 83 Bit Score: 50.11 E-value: 9.96e-08

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437 135 VYVSGLPPDITVDEFIQLMSKFGIIMRDPQTEEFKVKLYKDNQ-GNLKGDGLCCYLKRESVELALKLLDEDEIRGYKLHV 213
Cdd:cd12534   1 VFVSNLPPNTTEQDLAEHFGSIGIIKIDKKTGKPKIWLYKDKDtGEPKGEATVTYDDPHAASAAIEWFNNKDFMGNTIKV 80


                ...
gi 21361437 214 EVA 216
Cdd:cd12534  81 SLA 83

RRM_1

RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...

288-343

1.99e-07

Pssm-ID: 425453 [Multi-domain] Cd Length: 70 Bit Score: 48.77 E-value: 1.99e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 21361437   288 REDLRVECSKFGQIRKLLLF---DRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQIT 343
Cdd:pfam00076  12 EEDLKDLFSKFGPIKSIRLVrdeTGRSKGFAFVEFEDEEDAEKAIEALNGKELGGRELK 70

RRM3_I_PABPs

cd12380

RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This ...

133-213

2.17e-07

RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.

Pssm-ID: 409814 [Multi-domain] Cd Length: 80 Bit Score: 48.71 E-value: 2.17e-07

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437 133 TNVYVSGLPPDITVDEFIQLMSKFGIIMrdpqteefKVKLYKDNQGNLKGDGLCCYLKRESVELALKLLDEDEIRGYKLH 212
Cdd:cd12380   2 TNVYVKNFGEDVDDDELKELFEKYGKIT--------SAKVMKDDSGKSKGFGFVNFENHEAAQKAVEELNGKELNGKKLY 73


                .
gi 21361437 213 V 213
Cdd:cd12380  74 V 74

RRM

RNA recognition motif;

289-343

1.96e-06

RNA recognition motif;

Pssm-ID: 214636 [Multi-domain] Cd Length: 73 Bit Score: 46.05 E-value: 1.96e-06

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 21361437    289 EDLRVECSKFGQIRKL-LLFDRH---PDGVASVSFRDPEEADYCIQTLDGRWFGGRQIT 343
Cdd:smart00360  14 EELRELFSKFGKVESVrLVRDKEtgkSKGFAFVEFESEEDAEKALEALNGKELDGRPLK 72

RRM1_MSSP

cd12243

RNA recognition motif 1 (RRM1) found in the c-myc gene single-strand binding proteins (MSSP) ...

133-201

2.76e-06

RNA recognition motif 1 (RRM1) found in the c-myc gene single-strand binding proteins (MSSP) family; This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot.

Pssm-ID: 409689 [Multi-domain] Cd Length: 71 Bit Score: 45.38 E-value: 2.76e-06

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437 133 TNVYVSGLPPDITVDEFIQLMSKFGIIMrdpqteefKVKLYKDNQGNL-KGDGLCCYLKRESVELALKLL 201
Cdd:cd12243   1 TNVYIRGLPPNTTDEDLLLLCQSFGKII--------STKAIIDKQTNKcKGYGFVDFDSPEAALKAIEGL 62

2A1904

K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying ...

451-715

4.58e-06

K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying compounds]

Pssm-ID: 273344 [Multi-domain] Cd Length: 1096 Bit Score: 50.38 E-value: 4.58e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437    451 ESSPEKEAEEGCPEKESEEGCPKRGfEGSCSQKESEEGNPVRGSEEDSPKKESKKKTLKNDCEENGLAKESEDDlnkesE 530
Cdd:TIGR00927  639 EHTGERTGEEGERPTEAEGENGEES-GGEAEQEGETETKGENESEGEIPAERKGEQEGEGEIEAKEADHKGETE-----A 712

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437    531 EEVGPTKESEEDDSEKESDEDCSEKQSEDGSEREFEENGLEkDLDEEGSEKELHENVLDKELEENDSENSEFEDDGSEKV 610
Cdd:TIGR00927  713 EEVEHEGETEAEGTEDEGEIETGEEGEEVEDEGEGEAEGKH-EVETEGDRKETEHEGETEAEGKEDEDEGEIQAGEDGEM 791

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437    611 LDEEGSEREFDEDSDEKEEEEDTYEKVFDDESDEKEDEEYADEKGLEAADKkaEEGDADEKlfeesDDKEDEDADGKEVE 690
Cdd:TIGR00927  792 KGDEGAEGKVEHEGETEAGEKDEHEGQSETQADDTEVKDETGEQELNAENQ--GEAKQDEK-----GVDGGGGSDGGDSE 864

                          250       260
                   ....*....|....*....|....*
gi 21361437    691 DADEKLFEDDDSNEKLFDEEEDSSE 715
Cdd:TIGR00927  865 EEEEEEEEEEEEEEEEEEEEEEEEE 889

RRM_SR140

cd12223

RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This ...

133-217

8.24e-06

RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain).

Pssm-ID: 409670 [Multi-domain] Cd Length: 84 Bit Score: 44.59 E-value: 8.24e-06

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437 133 TNVYVSGLPPDITVDEFIQLMSKFGI-----IMRdPQTEEFKVKlykdnqgnlkgDGLC---CYLKRESVELALKLLDED 204
Cdd:cd12223   2 TNLYVGNLPPSVTEEVLLREFGRFGPlasvkIMW-PRTEEERRR-----------NRNCgfvAFMSRADAERAMRELNGK 69

                        90
                ....*....|...
gi 21361437 205 EIRGYKLHVEVAK 217
Cdd:cd12223  70 DVMGYELKLGWGK 82

RRM_SRSF10_SRSF12

cd12312

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and ...

289-345

2.65e-05

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins; This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.

Pssm-ID: 240758 [Multi-domain] Cd Length: 84 Bit Score: 43.13 E-value: 2.65e-05

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 21361437 289 EDLRVECSKFGQIRK----LLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQ 345
Cdd:cd12312  15 DDLRREFGRYGPIVDvyipLDFYTRRPRGFAYIQFEDVRDAEDALYYLDRTRFLGREIEIQ 75

RRM_SRSF10

cd12559

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 10 (SRSF10) and ...

283-349

2.72e-05

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins; This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.

Pssm-ID: 409975 [Multi-domain] Cd Length: 95 Bit Score: 43.51 E-value: 2.72e-05

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 21361437 283 VLNEIR-EDLRVECSKFGQIRKLLL----FDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDG 349
Cdd:cd12559  13 VADDTRsEDLRREFGRYGPIVDVYVpldfYTRRPRGFAYVQFEDVRDAEDALHNLDRKWICGRQIEIQFAQG 84

RRM_Set1

cd12304

RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases; This ...

284-345

6.38e-05

RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases; This subfamily corresponds to the RRM of the Set1-like family of histone-lysine N-methyltransferases which includes Set1A and Set1B that are ubiquitously expressed vertebrates histone methyltransferases exhibiting high homology to yeast Set1. Set1A and Set1B proteins exhibit a largely non-overlapping subnuclear distribution in euchromatic nuclear speckles, strongly suggesting that they bind to a unique set of target genes and thus make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. With the exception of the catalytic component, the subunit composition of the Set1A and Set1B histone methyltransferase complexes are identical. Each complex contains six human homologs of the yeast Set1/COMPASS complex, including Set1A or Set1B, Ash2 (homologous to yeast Bre2), CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). The genomic targeting of these complexes is determined by the identity of the catalytic subunit present in each histone methyltransferase complex. Thus, the Set1A and Set1B complexes may exhibit both overlapping and non-redundant properties. Both Set1A and Set1B contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo.

Pssm-ID: 409745 [Multi-domain] Cd Length: 93 Bit Score: 42.34 E-value: 6.38e-05

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 21361437 284 LNE-IRED-LRVECSKFGQIRKLLLFdRHPD-----GVASVSFRDPEEADYCIQTLDGRWFGGRQITAQ 345
Cdd:cd12304  10 LNDnINEGfLKDMCKKYGEVEEVKIY-FHPKtgkhlGLARVVFDTTKGAKDCVEKLNQTSVMGNIIHVF 77

RRM_eIF3G_like

cd12408

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G ...

288-335

7.43e-05

RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins; This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus.

Pssm-ID: 409842 [Multi-domain] Cd Length: 76 Bit Score: 41.73 E-value: 7.43e-05

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 21361437 288 REDLRVECSKFGQIRKLLL-FDRH---PDGVASVSFRDPEEADYCIQTLDGR 335
Cdd:cd12408  13 EEDLRELFRPFGPISRVYLaKDKEtgqSKGFAFVTFETREDAERAIEKLNGF 64

RRM_SRSF3_like

cd12373

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and ...

288-343

8.58e-05

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins; This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.

Pssm-ID: 409808 [Multi-domain] Cd Length: 73 Bit Score: 41.46 E-value: 8.58e-05

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 21361437 288 REDLRVECSKFGQIRKLLLfDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQIT 343
Cdd:cd12373  13 KRELEDAFEKYGPLRNVWV-ARNPPGFAFVEFEDPRDAEDAVRALDGRRICGSRVR 67

RRM2_RAVER

cd12389

RNA recognition motif 2 (RRM2) found in ribonucleoprotein PTB-binding raver-1, raver-2 and ...

137-213

1.17e-04

RNA recognition motif 2 (RRM2) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins; This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only.

Pssm-ID: 409823 [Multi-domain] Cd Length: 77 Bit Score: 41.15 E-value: 1.17e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 21361437 137 VSGLPPDITVDEFIQLMSKFGIIMRDpqteeFKVklYKDNQGNLKGDGLCCYLKRESVELALKLLDEDEIRGYKLHV 213
Cdd:cd12389   4 VTNLPLSFTEEQFEELVRPYGNVERC-----FLV--YSEVTGESKGYGFVEYTSKESAIRAKNQLHGRQIGGRALQV 73

RRM_RBM25

cd12446

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 25 and similar proteins; ...

133-215

1.28e-04

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 25 and similar proteins; This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor.

Pssm-ID: 409880 [Multi-domain] Cd Length: 83 Bit Score: 40.97 E-value: 1.28e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437 133 TNVYVSGLPPDITvDEFI-QLMSKFGIIMRdpqteefkVKLYKDNQGNLKGDGLCCYLKRESVELALKLLDEDEIRGYKL 211
Cdd:cd12446   1 TTVFVGNIPDDVS-DDFIrQLLEKCGKVLS--------WKRVQDPSGKLKAFGFCEFEDPEGALRALRLLNGLELGGKKL 71


                ....
gi 21361437 212 HVEV 215
Cdd:cd12446  72 LVKV 75

RRM_CNOT4

cd12438

RNA recognition motif (RRM) found in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) ...

297-353

1.55e-04

RNA recognition motif (RRM) found in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins; This subfamily corresponds to the RRM of NOT4, also termed CCR4-associated factor 4, or E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4Hp, a component of the CCR4-NOT complex, a global negative regulator of RNA polymerase II transcription. NOT4 functions as an ubiquitin-protein ligase (E3). It contains an N-terminal C4C4 type RING finger motif, followed by a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RING fingers may interact with a subset of ubiquitin-conjugating enzymes (E2s), including UbcH5B, and mediate protein-protein interactions. T

Pssm-ID: 409872 [Multi-domain] Cd Length: 98 Bit Score: 41.36 E-value: 1.55e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 21361437 297 KFGQIRKLLLFDRHPDGV-------ASVSFRDPEEADYCIQTLDGRWFGGRQITAQAwdGTTDY 353
Cdd:cd12438  31 QYGKIKKIVINRSTSYAGsqgpsasAYVTYSRKEDALRAIQAVDGFVLDGRTLKASF--GTTKY 92

RRM3_RBM19_RRM2_MRD1

cd12316

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition ...

289-340

1.56e-04

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1); This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events.

Pssm-ID: 409755 [Multi-domain] Cd Length: 74 Bit Score: 40.79 E-value: 1.56e-04

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 21361437 289 EDLRVECSKFGQIRKL-LLFDR---HPDGVASVSFRDPEEADYCIQTLDGRWFGGR 340
Cdd:cd12316  14 DELRELFEAFGKISEVhIPLDKqtkRSKGFAFVLFVIPEDAVKAYQELDGSIFQGR 69

RRM2_Hu_like

cd12376

RNA recognition motif 2 (RRM2) found in the Hu proteins family, Drosophila sex-lethal (SXL), ...

133-202

1.73e-04

RNA recognition motif 2 (RRM2) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins; This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts.

Pssm-ID: 240822 [Multi-domain] Cd Length: 79 Bit Score: 40.69 E-value: 1.73e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 21361437 133 TNVYVSGLPPDITVDEFIQLMSKFGI-----IMRDPQTeefkvklykdnqGNLKGDGLCCYLKRESVELALKLLD 202
Cdd:cd12376   1 ANLYVSGLPKTMTQKELEQLFSQYGRiitsrILRDQLT------------GVSRGVGFIRFDKRIEAEEAIKGLN 63

RRM_SAFB_like

cd12417

RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This ...

289-344

1.88e-04

RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM.

Pssm-ID: 409851 [Multi-domain] Cd Length: 74 Bit Score: 40.32 E-value: 1.88e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437 289 EDLRVECSKFGQIR--KLLLFDRHPDGV--ASVSFRDPEEADYCIQTLDGRWFGGRQITA 344
Cdd:cd12417  14 ADLKKIFSKYGKVVsaKVVTSARTPGSRcyGYVTMASVEEADLCIKSLNKTELHGRVITV 73

2A1904

K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying ...

403-705

1.92e-04

K+-dependent Na+/Ca+ exchanger; [Transport and binding proteins, Cations and iron carrying compounds]

Pssm-ID: 273344 [Multi-domain] Cd Length: 1096 Bit Score: 44.99 E-value: 1.92e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437    403 SEHPSTSKMNAQETATGMAFEEPIDEKKFEKTEDGGEFEEGASENNAKESSPEKEAE-EGCPEKESEEGCPKRgfEGSCS 481
Cdd:TIGR00927  636 AEAEHTGERTGEEGERPTEAEGENGEESGGEAEQEGETETKGENESEGEIPAERKGEqEGEGEIEAKEADHKG--ETEAE 713

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437    482 QKESEEGNPVRGSEEDSpkkeskkktlknDCEENGLAKESEDDLNKESEEEVGPTKESEEDDSEKESDEDCSEKQSEDGS 561
Cdd:TIGR00927  714 EVEHEGETEAEGTEDEG------------EIETGEEGEEVEDEGEGEAEGKHEVETEGDRKETEHEGETEAEGKEDEDEG 781

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437    562 EREFEENGLEKDldEEGSEKELHENVLDKELEENDSENSEFEDDGSEKVLDEEGSEREFDEDSDEKEEeedtyekvfdde 641
Cdd:TIGR00927  782 EIQAGEDGEMKG--DEGAEGKVEHEGETEAGEKDEHEGQSETQADDTEVKDETGEQELNAENQGEAKQ------------ 847

                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 21361437    642 sdekedeeyaDEKGLEAaDKKAEEGDADEKlfeesddkEDEDADGKEVEDADEKLFEDDDSNEK 705
Cdd:TIGR00927  848 ----------DEKGVDG-GGGSDGGDSEEE--------EEEEEEEEEEEEEEEEEEEEEEENEE 892

RRM2_PTBP1_like

cd12693

RNA recognition motif 2 (RRM2) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) ...

266-335

3.00e-04

RNA recognition motif 2 (RRM2) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins; This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).

Pssm-ID: 410093 [Multi-domain] Cd Length: 96 Bit Score: 40.41 E-value: 3.00e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437 266 VIIKNMFHPMDFEddplVLNEIredlrveCSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGR 335
Cdd:cd12693   6 VIVENLFYPVTLD----VLHQI-------FSKFGTVLKIITFTKNNQFQALIQFADAVSAQAAKLSLDGQ 64

RRM_SRSF12

cd12560

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 12 (SRSF12) and ...

289-349

3.32e-04

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins; This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.

Pssm-ID: 409976 [Multi-domain] Cd Length: 84 Bit Score: 39.98 E-value: 3.32e-04

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 21361437 289 EDLRVECSKFGQIRKLLL----FDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQAWDG 349
Cdd:cd12560  15 EDLRREFGRYGPIVDVYIpldfYNRRPRGFAYIQFEDVRDAEDALYNLNRKWVCGRQIEIQFAQG 79

RRM_EWS

cd12533

RNA recognition motif (RRM) found in vertebrate Ewing Sarcoma Protein (EWS); This subgroup ...

135-213

4.74e-04

RNA recognition motif (RRM) found in vertebrate Ewing Sarcoma Protein (EWS); This subgroup corresponds to the RRM of EWS, also termed Ewing sarcoma breakpoint region 1 protein, a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multifunctional protein and may play roles in transcription and RNA processing. EWS is involved in transcriptional regulation by interacting with the preinitiation complex TFIID and the RNA polymerase II (RNAPII) complexes. It is also associated with splicing factors, such as the U1 snRNP protein U1C, suggesting its implication in pre-mRNA splicing. Additionally, EWS has been shown to regulate DNA damage-induced alternative splicing (AS). Like other members in the FET family, EWS contains an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. EWS specifically binds to poly G and poly U RNA. It also binds to the proximal-element DNA of the macrophage-specific promoter of the CSF-1 receptor gene.

Pssm-ID: 409950 [Multi-domain] Cd Length: 84 Bit Score: 39.44 E-value: 4.74e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437 135 VYVSGLPPDITVDEFIQLMSKFGIIMRDPQTEEFKVKLYKDNQ-GNLKGDGLCCYLKRESVELALKLLDEDEIRGYKLHV 213
Cdd:cd12533   3 IYVQGLNENVTLEELADFFKHCGVVKINKRTGQPMINIYTDKEtGKPKGDATVSYEDPPAAKAAVEWFDGKDFQGNKLKV 82

hnRNP-R-Q

TIGR01648

heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the ...

123-211

5.66e-04

heterogeneous nuclear ribonucleoprotein R, Q family; Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q, and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain.

Pssm-ID: 273732 [Multi-domain] Cd Length: 578 Bit Score: 43.45 E-value: 5.66e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437   123 GWFHVEEDRNTNVYVSGLPPDITVDEFIQLMSKFGIImrdpqteeFKVKLYKDNQGNLKGDGLCCYLKRESVELALKLLD 202
Cdd:TIGR01648  49 GWSGVQPGRGCEVFVGKIPRDLYEDELVPLFEKAGPI--------YELRLMMDFSGQNRGYAFVTFCGKEEAKEAVKLLN 120


                  ....*....
gi 21361437   203 EDEIRGYKL 211
Cdd:TIGR01648 121 NYEIRPGRL 129

RRM_U2AF35B

cd12539

RNA recognition motif (RRM) found in splicing factor U2AF 35 kDa subunit B (U2AF35B); This ...

276-345

6.86e-04

RNA recognition motif (RRM) found in splicing factor U2AF 35 kDa subunit B (U2AF35B); This subgroup corresponds to the RRM of U2AF35B, also termed zinc finger CCCH domain-containing protein 60 (C3H60), which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. Members in this family are mainly found in plant. They show high sequence homology to vertebrates U2AF35 that directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. U2AF35B contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich domain. In contrast to U2AF35, U2AF35B has a plant-specific conserved C-terminal region containing SERE motif(s), which may have an important function specific to higher plants.

Pssm-ID: 409955 [Multi-domain] Cd Length: 102 Bit Score: 39.69 E-value: 6.86e-04

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 21361437 276 DFEDdplvlneIREDLRVECSKFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITAQ 345
Cdd:cd12539  34 HFED-------FYEDVFEELSKFGEVEALNVCDNlgdHMVGNVYVKFRDEEHAAAALKALQGRFYAGRPIIVE 99

PHA03169

hypothetical protein; Provisional

403-603

7.16e-04

hypothetical protein; Provisional

Pssm-ID: 223003 [Multi-domain] Cd Length: 413 Bit Score: 42.65 E-value: 7.16e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437  403 SEHPSTSKMNAQETATGMAFEEPIDEKKFEKTEDGGEFEEGASENNAKESSPEkeaEEGCPEKESEEGCPKRGFEGSCSQ 482
Cdd:PHA03169  54 SGPQVRAVAEQGHRQTESDTETAEESRHGEKEERGQGGPSGSGSESVGSPTPS---PSGSAEELASGLSPENTSGSSPES 130

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437  483 KESEEGNPVRGSEED--SPKKESKKKTLKNDCEENGLAKESEDdlnkESEEEVGPTKESEEDDSEKESDEDCSEKQSE-D 559
Cdd:PHA03169 131 PASHSPPPSPPSHPGphEPAPPESHNPSPNQQPSSFLQPSHED----SPEEPEPPTSEPEPDSPGPPQSETPTSSPPPqS 206

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 21361437  560 GSEREFEENGLEKDLDEEGSEKELHENvlDKELEENDSENSEFE 603
Cdd:PHA03169 207 PPDEPGEPQSPTPQQAPSPNTQQAVEH--EDEPTEPEREGPPFP 248

RRM1_hnRNPR_like

cd12249

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) ...

135-215

8.00e-04

RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins; This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs.

Pssm-ID: 409695 [Multi-domain] Cd Length: 78 Bit Score: 38.72 E-value: 8.00e-04

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437 135 VYVSGLPPDITVDEFIQLMSKFGIImrdpqteeFKVKLYKDNQGNLKGDGLCCYLKRESVELALKLLDEDEIRGYKlHVE 214
Cdd:cd12249   4 VFVGKIPRDVFEDELVPLFEKCGKI--------YELRLMMDFSGLNRGYAFVTYTNKEAAQRAVKTLNNYEIRPGK-LLG 74


                .
gi 21361437 215 V 215
Cdd:cd12249  75 V 75

RRM_RBM18

cd12355

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...

296-342

1.42e-03

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear.

Pssm-ID: 409791 [Multi-domain] Cd Length: 80 Bit Score: 38.05 E-value: 1.42e-03

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 21361437 296 SKFGQIRKL-LLFDR------HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQI 342
Cdd:cd12355  21 SKYGKIKKFdFLFHKtgplkgQPRGYCFVTFETKEEAEKAIECLNGKLALGKKL 74

RRM4_I_PABPs

cd12381

RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily ...

132-216

1.56e-03

RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins; This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions.

Pssm-ID: 409815 [Multi-domain] Cd Length: 79 Bit Score: 38.02 E-value: 1.56e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437 132 NTNVYVSGLPPDITVDEFIQLMSKFGIIMRdpqteefkVKLYKDNQGNLKGDGLCCYLKRESVELALKLLDEDEIRGYKL 211
Cdd:cd12381   1 GVNLYVKNLDDTIDDEKLREEFSPFGTITS--------AKVMTDEGGRSKGFGFVCFSSPEEATKAVTEMNGRIIGGKPL 72


                ....*
gi 21361437 212 HVEVA 216
Cdd:cd12381  73 YVALA 77

RRM2_PTBP1_hnRNPL_like

cd12422

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), ...

266-335

2.10e-03

RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins; This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs.

Pssm-ID: 409856 [Multi-domain] Cd Length: 85 Bit Score: 37.55 E-value: 2.10e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437 266 VIIKNMFHPMDFEddplVLNEIredlrveCSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGR 335
Cdd:cd12422   4 VTVTNLLYPVTVD----VLHQV-------FSPYGAVEKIVIFEKGTGVQALVQFDSVESAEAAKKALNGR 62

RRM2_Hu

cd12652

RNA recognition motif 2 (RRM2) found in the Hu proteins family; This subfamily corresponds to ...

134-201

2.13e-03

RNA recognition motif 2 (RRM2) found in the Hu proteins family; This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions.

Pssm-ID: 410055 [Multi-domain] Cd Length: 79 Bit Score: 37.69 E-value: 2.13e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 21361437 134 NVYVSGLPPDITVDEFIQLMSKFGIIMRDpqteefkvKLYKDNQGNL-KGDGLCCYLKRESVELALKLL 201
Cdd:cd12652   2 NLYVSGLPKTMTQKELEQLFSQFGRIITS--------RILCDNVTGLsRGVGFIRFDKRVEAERAIKAL 62

RRM2_TIA1_like

cd12353

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and ...

289-342

2.16e-03

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR; This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains.

Pssm-ID: 409789 [Multi-domain] Cd Length: 75 Bit Score: 37.37 E-value: 2.16e-03

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 21361437 289 EDLRVECSKFGQIRKL-LLFDRH---PDGVASVSFRDPEEADYCIQTLDGRWFGGRQI 342
Cdd:cd12353  14 EDLKEAFAPFGEISDArVVKDTQtgkSKGYGFVSFVKKEDAENAIQGMNGQWLGGRNI 71

RRM1_ACF

cd12486

RNA recognition motif 1 (RRM1) found in vertebrate APOBEC-1 complementation factor (ACF); This ...

135-211

2.34e-03

RNA recognition motif 1 (RRM1) found in vertebrate APOBEC-1 complementation factor (ACF); This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1.

Pssm-ID: 409912 [Multi-domain] Cd Length: 78 Bit Score: 37.65 E-value: 2.34e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 21361437 135 VYVSGLPPDITVDEFIQLMSKFGIImrdpqteeFKVKLYKDNQGNLKGDGLCCYLKRESVELALKLLDEDEIRGYKL 211
Cdd:cd12486   4 IFIGKLPRDLFEDELVPLCEKIGKI--------YEMRMMMDFNGNNRGYAFVTFSNKQEARNAIKQLNNYEIRNGRL 72

RRM_DAZL_BOULE

cd12412

RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and ...

135-213

2.67e-03

RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE; This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis.

Pssm-ID: 409846 [Multi-domain] Cd Length: 81 Bit Score: 37.21 E-value: 2.67e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 21361437 135 VYVSGLPPDITVDEFIQLMSKFGIIMrdpqteefKVKLYKDNQGNLKGDGLCCYLKRESVELALKLLDEDEIRGYKLHV 213
Cdd:cd12412   5 IFVGGIDWDTTEEELREFFSKFGKVK--------DVKIIKDRAGVSKGYGFVTFETQEDAEKIQKWGANLVFKGKKLNV 75

RRM2_RBM34

cd12395

RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; ...

135-214

2.84e-03

RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins; This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein.

Pssm-ID: 409829 [Multi-domain] Cd Length: 73 Bit Score: 37.09 E-value: 2.84e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437 135 VYVSGLPPDITVDEFIQLMSKFGIIMRdpqteefkVKLYKDNQGNL-KGDGLCCYLKRESVELALKlLDEDEIRGYKLHV 213
Cdd:cd12395   2 VFVGNLPFDIEEEELRKHFEDCGDVEA--------VRIVRDRETGIgKGFGYVLFKDKDSVDLALK-LNGSKLRGRKLRV 72


                .
gi 21361437 214 E 214
Cdd:cd12395  73 K 73

RRM_CSTF2_RNA15_like

cd12398

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ...

135-216

3.15e-03

RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins; This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs.

Pssm-ID: 409832 [Multi-domain] Cd Length: 77 Bit Score: 37.11 E-value: 3.15e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437 135 VYVSGLPPDITVDEFIQLMSKFGIIMrdpqteefKVKLYKDNQ-GNLKGDGLCCYLKRESVELALKLLDEDEIRGYKLHV 213
Cdd:cd12398   3 VFVGNIPYDATEEQLKEIFSEVGPVV--------SFRLVTDREtGKPKGYGFCEFRDAETALSAVRNLNGYELNGRPLRV 74


                ...
gi 21361437 214 EVA 216
Cdd:cd12398  75 DFA 77

RRM2_SXL

cd12651

RNA recognition motif 2 (RRM2) found in Drosophila sex-lethal (SXL) and similar proteins; This ...

131-202

3.53e-03

RNA recognition motif 2 (RRM2) found in Drosophila sex-lethal (SXL) and similar proteins; This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts.

Pssm-ID: 410054 [Multi-domain] Cd Length: 81 Bit Score: 37.18 E-value: 3.53e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 21361437 131 RNTNVYVSGLPPDITVDEFIQLMSKFGIIMrdpqteefKVKLYKDN-QGNLKGDGLCCYLKRESVELALKLLD 202
Cdd:cd12651   1 KDTNLYVTNLPRTITEDELDTIFGAYGNIV--------QKNLLRDKlTGRPRGVAFVRYDKREEAQAAISALN 65

RRM_ZCRB1

cd12393

RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing ...

135-211

3.75e-03

RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins; This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains.

Pssm-ID: 409827 [Multi-domain] Cd Length: 76 Bit Score: 36.88 E-value: 3.75e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437 135 VYVSGLPPDITVDEFIQLMSKFG-----IIMRDPQTEEFkvklykdnqgnlKGDGLCCYLKRESVELALKLLDEDEIRGY 209
Cdd:cd12393   4 VYVSNLPFSLTNNDLHQIFSKYGkvvkvTILKDKETRKS------------KGVAFVLFLDRESAHNAVRAMNNKELFGR 71


                ..
gi 21361437 210 KL 211
Cdd:cd12393  72 TL 73

RRM3_TIA1_like

cd12354

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and ...

133-197

3.93e-03

RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1; This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3.

Pssm-ID: 409790 [Multi-domain] Cd Length: 71 Bit Score: 36.49 E-value: 3.93e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 21361437 133 TNVYVSGLPPDITVDEFIQLMSKFGIIMrdpqteefKVKLYKDnqgnlKGdglCCYLKRESVELA 197
Cdd:cd12354   1 TTVYVGNITKGLTEALLQQTFSPFGQIL--------EVRVFPD-----KG---YAFIRFDSHEAA 49

RRM3_RBM28_like

cd12415

RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; ...

289-342

4.43e-03

RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.

Pssm-ID: 409849 [Multi-domain] Cd Length: 83 Bit Score: 36.81 E-value: 4.43e-03

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 21361437 289 EDLRVECSKFGQIRKLLL-FDR---HPDGVASVSFRDPEEADYCIQT------LDGRWFGGRQI 342
Cdd:cd12415  15 EDLKEFFSKFGEVKYARIvLDKdtgHSKGTAFVQFKTKESADKCIEAandeseDGGLVLDGRKL 78

RRM3_Prp24

cd12298

RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...

264-343

4.68e-03

RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.

Pssm-ID: 409739 [Multi-domain] Cd Length: 78 Bit Score: 36.47 E-value: 4.68e-03

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 21361437 264 RVVIIKNMfhpmDFEddplvLNEirEDLRVECSKFGQIRKLLL-------FDRHPDGVASVSFRDPEEADYCIQtLDGRW 336
Cdd:cd12298   1 REIRVRNL----DFE-----LDE--EALRGIFEKFGEIESINIpkkqknrKGRHNNGFAFVTFEDADSAESALQ-LNGTL 68


                ....*..
gi 21361437 337 FGGRQIT 343
Cdd:cd12298  69 LDNRKIS 75

RRM3_HRB1_GBP2

cd21607

RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein HRB1, ...

310-342

4.82e-03

RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins; The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the third RRM motif.

Pssm-ID: 410186 [Multi-domain] Cd Length: 79 Bit Score: 36.53 E-value: 4.82e-03

                        10        20        30
                ....*....|....*....|....*....|...
gi 21361437 310 HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQI 342
Cdd:cd21607  41 DPTGSAVVEYENLDDADVCISKLNNYNYGGCDL 73

RRM3_RBM19

cd12567

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and similar proteins; ...

289-340

6.87e-03

RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

Pssm-ID: 409983 [Multi-domain] Cd Length: 79 Bit Score: 36.22 E-value: 6.87e-03

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 21361437 289 EDLRVECSKFGQIRKLLL----FDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGR 340
Cdd:cd12567  17 EDLEKLFSKYGPLSEVHFpidsLTKKPKGFAFVTYMIPEHAVKAYAELDGTVFQGR 72

RRM3_Nop4p

cd12676

RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; ...

263-330

8.66e-03

RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins; This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).

Pssm-ID: 410077 [Multi-domain] Cd Length: 107 Bit Score: 36.64 E-value: 8.66e-03

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 21361437 263 ERVVIIKNMfhPMDFEDDplvlneireDLRVECSKFGQIR-KLLLFDR---HPDGVASVSFRDPEEADYCIQ 330
Cdd:cd12676   1 GRTLFVRNL--PFDATED---------ELYSHFSQFGPLKyARVVKDPatgRSKGTAFVKFKNKEDADNCLS 61

RRM_1

smart00361

RNA recognition motif;

294-344

8.70e-03

RNA recognition motif;

Pssm-ID: 214637 [Multi-domain] Cd Length: 70 Bit Score: 35.46 E-value: 8.70e-03

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 21361437    294 ECSKFGQIRKLLLF-------DRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 344
Cdd:smart00361  12 EEEYFGEVGKINKIyiddvgyENHKRGNVYITFERSEDAARAIVDLNGRYFDGRLVKA 69

2A1904