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Conserved domains on  [gi|1078654864|gb|AOW01979|]
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hypothetical protein YALI1_B26763g [Yarrowia lipolytica]

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RRM1_RBM26_like cd12257
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar ...
176-247 1.62e-31

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins; This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear.


:

Pssm-ID: 409702 [Multi-domain]  Cd Length: 72  Bit Score: 115.74  E-value: 1.62e-31
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1078654864 176 NRKLVVEKIPDDYCSEQAVRDFFSKFGTLNSVKVNFAGKLAEIEFSTTAEAKNAYKSPETIFDNRFVKVYWR 247
Cdd:cd12257     1 KTTLEVRNIPPELNNITKLREHFSKFGTIVNIQVNYNPESALVQFSTSEEANKAYRSPEAVFNNRFIKVFWH 72
RRM_AtRDRP1_like cd21612
RNA recognition motif (RRM) found in Arabidopsis thaliana RNA-dependent RNA polymerase 1 ...
397-464 1.14e-23

RNA recognition motif (RRM) found in Arabidopsis thaliana RNA-dependent RNA polymerase 1 (AtRDRP1) and similar proteins; AtRDRP1, also called RNA-directed RNA polymerase 1, is an RNA-dependent direct polymerase involved in antiviral silencing. It is required for the biogenesis of viral secondary siRNAs, process that follows the production of primary siRNAs derived from viral RNA replication. Members in this family contain an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


:

Pssm-ID: 410191  Cd Length: 67  Bit Score: 94.07  E-value: 1.14e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1078654864 397 KDVLISPVTaDKQEHIRAHLVSVGEYSNVAQASGDSVVVSFPDRRAAEKFFYGSADIPDVGKVDKQWF 464
Cdd:cd21612     1 KCVRHVPNS-EKQEELKKFLEQVGTYYAIAKKSTDDVIVSFSTRAAAEKLFYGVEDVPKVGKVEMNWV 67
Radial_spoke_3 super family cl25553
Radial spoke protein 3; This family consists of several radial spoke protein 3 (RSP3) ...
255-298 2.67e-03

Radial spoke protein 3; This family consists of several radial spoke protein 3 (RSP3) sequences. Eukaryotic cilia and flagella present in diverse types of cells perform motile, sensory, and developmental functions in organizms from protists to humans. They are centred by precisely organized, microtubule-based structures, the axonemes. The axoneme consists of two central singlet microtubules, called the central pair, and nine outer doublet microtubules. These structures are well-conserved during evolution. The outer doublet microtubules, each composed of A and B sub-fibres, are connected to each other by nexin links, while the central pair is held at the centre of the axoneme by radial spokes. The radial spokes are T-shaped structures extending from the A-tubule of each outer doublet microtubule to the centre of the axoneme. Radial spoke protein 3 (RSP3), is present at the proximal end of the spoke stalk and helps in anchoring the radial spoke to the outer doublet. It is thought that radial spokes regulate the activity of inner arm dynein through protein phosphorylation and dephosphorylation.


The actual alignment was detected with superfamily member pfam06098:

Pssm-ID: 461827  Cd Length: 286  Bit Score: 39.54  E-value: 2.67e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1078654864 255 ENEVAEQQRLQEERQAAFEEKEQRRKEHLEKmtgiLAQKKQLLE 298
Cdd:pfam06098 170 NAELAEVQRLEEQERRLREEKERRIAQQREA----LKKEKETAE 209
 
Name Accession Description Interval E-value
RRM1_RBM26_like cd12257
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar ...
176-247 1.62e-31

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins; This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear.


Pssm-ID: 409702 [Multi-domain]  Cd Length: 72  Bit Score: 115.74  E-value: 1.62e-31
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1078654864 176 NRKLVVEKIPDDYCSEQAVRDFFSKFGTLNSVKVNFAGKLAEIEFSTTAEAKNAYKSPETIFDNRFVKVYWR 247
Cdd:cd12257     1 KTTLEVRNIPPELNNITKLREHFSKFGTIVNIQVNYNPESALVQFSTSEEANKAYRSPEAVFNNRFIKVFWH 72
RRM_AtRDRP1_like cd21612
RNA recognition motif (RRM) found in Arabidopsis thaliana RNA-dependent RNA polymerase 1 ...
397-464 1.14e-23

RNA recognition motif (RRM) found in Arabidopsis thaliana RNA-dependent RNA polymerase 1 (AtRDRP1) and similar proteins; AtRDRP1, also called RNA-directed RNA polymerase 1, is an RNA-dependent direct polymerase involved in antiviral silencing. It is required for the biogenesis of viral secondary siRNAs, process that follows the production of primary siRNAs derived from viral RNA replication. Members in this family contain an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410191  Cd Length: 67  Bit Score: 94.07  E-value: 1.14e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1078654864 397 KDVLISPVTaDKQEHIRAHLVSVGEYSNVAQASGDSVVVSFPDRRAAEKFFYGSADIPDVGKVDKQWF 464
Cdd:cd21612     1 KCVRHVPNS-EKQEELKKFLEQVGTYYAIAKKSTDDVIVSFSTRAAAEKLFYGVEDVPKVGKVEMNWV 67
RRM smart00360
RNA recognition motif;
178-244 1.25e-06

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 46.05  E-value: 1.25e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1078654864  178 KLVVEKIPDDyCSEQAVRDFFSKFGTLNSVKV---NFAGKL---AEIEFSTTAEAKNAYKS-PETIFDNRFVKV 244
Cdd:smart00360   1 TLFVGNLPPD-TTEEELRELFSKFGKVESVRLvrdKETGKSkgfAFVEFESEEDAEKALEAlNGKELDGRPLKV 73
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
179-243 1.35e-03

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: 37.21  E-value: 1.35e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1078654864 179 LVVEKIPDDyCSEQAVRDFFSKFGTLNSVKV-----NFAGKLAEIEFSTTAEAKNAYKS-PETIFDNRFVK 243
Cdd:pfam00076   1 LFVGNLPPD-TTEEDLKDLFSKFGPIKSIRLvrdetGRSKGFAFVEFEDEEDAEKAIEAlNGKELGGRELK 70
Radial_spoke_3 pfam06098
Radial spoke protein 3; This family consists of several radial spoke protein 3 (RSP3) ...
255-298 2.67e-03

Radial spoke protein 3; This family consists of several radial spoke protein 3 (RSP3) sequences. Eukaryotic cilia and flagella present in diverse types of cells perform motile, sensory, and developmental functions in organizms from protists to humans. They are centred by precisely organized, microtubule-based structures, the axonemes. The axoneme consists of two central singlet microtubules, called the central pair, and nine outer doublet microtubules. These structures are well-conserved during evolution. The outer doublet microtubules, each composed of A and B sub-fibres, are connected to each other by nexin links, while the central pair is held at the centre of the axoneme by radial spokes. The radial spokes are T-shaped structures extending from the A-tubule of each outer doublet microtubule to the centre of the axoneme. Radial spoke protein 3 (RSP3), is present at the proximal end of the spoke stalk and helps in anchoring the radial spoke to the outer doublet. It is thought that radial spokes regulate the activity of inner arm dynein through protein phosphorylation and dephosphorylation.


Pssm-ID: 461827  Cd Length: 286  Bit Score: 39.54  E-value: 2.67e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1078654864 255 ENEVAEQQRLQEERQAAFEEKEQRRKEHLEKmtgiLAQKKQLLE 298
Cdd:pfam06098 170 NAELAEVQRLEEQERRLREEKERRIAQQREA----LKKEKETAE 209
 
Name Accession Description Interval E-value
RRM1_RBM26_like cd12257
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar ...
176-247 1.62e-31

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins; This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear.


Pssm-ID: 409702 [Multi-domain]  Cd Length: 72  Bit Score: 115.74  E-value: 1.62e-31
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1078654864 176 NRKLVVEKIPDDYCSEQAVRDFFSKFGTLNSVKVNFAGKLAEIEFSTTAEAKNAYKSPETIFDNRFVKVYWR 247
Cdd:cd12257     1 KTTLEVRNIPPELNNITKLREHFSKFGTIVNIQVNYNPESALVQFSTSEEANKAYRSPEAVFNNRFIKVFWH 72
RRM_AtRDRP1_like cd21612
RNA recognition motif (RRM) found in Arabidopsis thaliana RNA-dependent RNA polymerase 1 ...
397-464 1.14e-23

RNA recognition motif (RRM) found in Arabidopsis thaliana RNA-dependent RNA polymerase 1 (AtRDRP1) and similar proteins; AtRDRP1, also called RNA-directed RNA polymerase 1, is an RNA-dependent direct polymerase involved in antiviral silencing. It is required for the biogenesis of viral secondary siRNAs, process that follows the production of primary siRNAs derived from viral RNA replication. Members in this family contain an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 410191  Cd Length: 67  Bit Score: 94.07  E-value: 1.14e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1078654864 397 KDVLISPVTaDKQEHIRAHLVSVGEYSNVAQASGDSVVVSFPDRRAAEKFFYGSADIPDVGKVDKQWF 464
Cdd:cd21612     1 KCVRHVPNS-EKQEELKKFLEQVGTYYAIAKKSTDDVIVSFSTRAAAEKLFYGVEDVPKVGKVEMNWV 67
RRM_RBM27 cd12517
RNA recognition motif (RRM) found in vertebrate RNA-binding protein 27 (RBM27); This subgroup ...
176-248 1.98e-13

RNA recognition motif (RRM) found in vertebrate RNA-binding protein 27 (RBM27); This subgroup corresponds to the RRM of RBM27 which contains a single RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although the specific function of the RRM in RBM27 remains unclear, it shows high sequence similarity with RRM1of RBM26, which functions as a cutaneous lymphoma (CL)-associated antigen.


Pssm-ID: 409939 [Multi-domain]  Cd Length: 76  Bit Score: 65.45  E-value: 1.98e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1078654864 176 NRKLVVEKIPDDYCSEQAVRDFFSKFGTLNSVKVNFAG--KLAEIEFSTTAEAKNAYKSPETIFDNRFVKVYWRK 248
Cdd:cd12517     1 NTKLEVRKIPQELNNITQLNEHFSKFGTIVNIQVAFGGdpEAALIQYTTNEEARRAISSTEAVLNNRFIRVLWHR 75
RRM1_RBM26 cd12516
RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26); This ...
176-248 6.29e-13

RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26); This subgroup corresponds to the RRM1 of RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, which represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions.


Pssm-ID: 409938 [Multi-domain]  Cd Length: 76  Bit Score: 63.88  E-value: 6.29e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1078654864 176 NRKLVVEKIPDDYCSEQAVRDFFSKFGTLNSVKVNFAG--KLAEIEFSTTAEAKNAYKSPETIFDNRFVKVYWRK 248
Cdd:cd12516     1 NTKLELRKVPPELNNISKLNEHFSKFGTIVNLQVAYQGdpEGALIQFATHEEAKRAISSTEAVLNNRFIKVYWHR 75
RRM smart00360
RNA recognition motif;
178-244 1.25e-06

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 46.05  E-value: 1.25e-06
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1078654864  178 KLVVEKIPDDyCSEQAVRDFFSKFGTLNSVKV---NFAGKL---AEIEFSTTAEAKNAYKS-PETIFDNRFVKV 244
Cdd:smart00360   1 TLFVGNLPPD-TTEEELRELFSKFGKVESVRLvrdKETGKSkgfAFVEFESEEDAEKALEAlNGKELDGRPLKV 73
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
179-244 2.91e-06

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: 44.97  E-value: 2.91e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1078654864 179 LVVEKIPDDyCSEQAVRDFFSKFGTLNSVKV--NFAGKL---AEIEFSTTAEAKNAYKS-PETIFDNRFVKV 244
Cdd:cd00590     1 LFVGNLPPD-TTEEDLRELFSKFGEVVSVRIvrDRDGKSkgfAFVEFESPEDAEKALEAlNGTELGGRPLKV 71
RRM2_La_like cd12292
RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 ...
178-240 8.19e-05

RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 or PIP7S) and similar proteins; This subfamily corresponds to the RRM2 of La and LARP7. La is a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. LARP7 is an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. It is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP), intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. LARP7 plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. Both La and LARP7 contain an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409734 [Multi-domain]  Cd Length: 74  Bit Score: 40.77  E-value: 8.19e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1078654864 178 KLVVEKIPDDYCSEQaVRDFFSKFGTLNSVKVNFAGKLAEIEFSTTAEAKNAYKSPETIFDNR 240
Cdd:cd12292     3 ILKITGIGPSVSRDD-LKELFKQFGEVEYVDFTPGDDEGHVRFKTSEAAQKARDAYTGKLELN 64
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
177-245 1.91e-04

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: 39.94  E-value: 1.91e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1078654864 177 RKLVVEKIpDDYCSEQAVRDFFSKFGTLNSVKV---------NFAGKLAEIEFSTTAEAKNAYKSPETIFDNRFVKVY 245
Cdd:cd12298     1 REIRVRNL-DFELDEEALRGIFEKFGEIESINIpkkqknrkgRHNNGFAFVTFEDADSAESALQLNGTLLDNRKISVS 77
RRM2_RBM28_like cd12414
RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
178-246 6.05e-04

RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM2 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: 409848 [Multi-domain]  Cd Length: 76  Bit Score: 38.30  E-value: 6.05e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1078654864 178 KLVVEKIPDDyCSEQAVRDFFSKFGTLNSVKV--NFAGKL---AEIEFSTTAEAKNAYK-SPETIFDNRFVKVYW 246
Cdd:cd12414     1 RLIVRNLPFK-CTEDDLKKLFSKFGKVLEVTIpkKPDGKLrgfAFVQFTNVADAAKAIKgMNGKKIKGRPVAVDW 74
RRM_1 pfam00076
RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain); The RRM motif is probably diagnostic ...
179-243 1.35e-03

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: 37.21  E-value: 1.35e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1078654864 179 LVVEKIPDDyCSEQAVRDFFSKFGTLNSVKV-----NFAGKLAEIEFSTTAEAKNAYKS-PETIFDNRFVK 243
Cdd:pfam00076   1 LFVGNLPPD-TTEEDLKDLFSKFGPIKSIRLvrdetGRSKGFAFVEFEDEEDAEKAIEAlNGKELGGRELK 70
RRM_MCM3A_like cd12443
RNA recognition motif (RRM) found in 80 kDa MCM3-associated protein (Map80) and similar ...
179-248 1.45e-03

RNA recognition motif (RRM) found in 80 kDa MCM3-associated protein (Map80) and similar proteins; This subfamily corresponds to the RRM of Map80, also termed germinal center-associated nuclear protein (GANP), involved in the nuclear localization pathway of MCM3, a protein necessary for the initiation of DNA replication and also involves in controls that ensure DNA replication is initiated once per cell cycle. Map80 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409877 [Multi-domain]  Cd Length: 75  Bit Score: 37.30  E-value: 1.45e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1078654864 179 LVVEKIPDDYCSEQAVRDFFSKFGTLNSVKVNFAGKLAEIEFSTTAEAKNAYKSPETIFDN-RFVKVYWRK 248
Cdd:cd12443     3 IVCKNIPEELNDKEILRRHFSKFGKVARVFCNPRKNLAIVHFKDHESAALAKKKGKLLSKGgKPIEIFWSS 73
RRM1_Prp24 cd12296
RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
180-229 2.36e-03

RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM1 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: 409737 [Multi-domain]  Cd Length: 71  Bit Score: 36.48  E-value: 2.36e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1078654864 180 VVEKIPDDYcSEQAVRDFFSKFGTLNSVKVN--FAGKLAEIEFSTTAEAKNA 229
Cdd:cd12296     4 LVKNLPKSI-TENKIRQFFKDCGEIREVKILesGNGLVAVIEFETEDEALAA 54
Radial_spoke_3 pfam06098
Radial spoke protein 3; This family consists of several radial spoke protein 3 (RSP3) ...
255-298 2.67e-03

Radial spoke protein 3; This family consists of several radial spoke protein 3 (RSP3) sequences. Eukaryotic cilia and flagella present in diverse types of cells perform motile, sensory, and developmental functions in organizms from protists to humans. They are centred by precisely organized, microtubule-based structures, the axonemes. The axoneme consists of two central singlet microtubules, called the central pair, and nine outer doublet microtubules. These structures are well-conserved during evolution. The outer doublet microtubules, each composed of A and B sub-fibres, are connected to each other by nexin links, while the central pair is held at the centre of the axoneme by radial spokes. The radial spokes are T-shaped structures extending from the A-tubule of each outer doublet microtubule to the centre of the axoneme. Radial spoke protein 3 (RSP3), is present at the proximal end of the spoke stalk and helps in anchoring the radial spoke to the outer doublet. It is thought that radial spokes regulate the activity of inner arm dynein through protein phosphorylation and dephosphorylation.


Pssm-ID: 461827  Cd Length: 286  Bit Score: 39.54  E-value: 2.67e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1078654864 255 ENEVAEQQRLQEERQAAFEEKEQRRKEHLEKmtgiLAQKKQLLE 298
Cdd:pfam06098 170 NAELAEVQRLEEQERRLREEKERRIAQQREA----LKKEKETAE 209
RRM1_RBM19 cd12564
RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
178-243 3.40e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), 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: 409980 [Multi-domain]  Cd Length: 76  Bit Score: 36.52  E-value: 3.40e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1078654864 178 KLVVEKIPDDyCSEQAVRDFFSKFGTLNSVKVNFA--GK---LAEIEFSTTAEAKNAYKSpetiFDNRFVK 243
Cdd:cd12564     2 RLIVKNLPSS-ITEDRLRKLFSAFGTITDVQLKYTkdGKfrrFGFVGFKSEEEAQKALKH----FNNSFID 67
RRM3_MRD1 cd12568
RNA recognition motif 3 (RRM3) found in yeast multiple RNA-binding domain-containing protein 1 ...
190-232 5.24e-03

RNA recognition motif 3 (RRM3) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins; This subgroup corresponds to the RRM3 of MRD1 which 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). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events.


Pssm-ID: 241012 [Multi-domain]  Cd Length: 72  Bit Score: 35.83  E-value: 5.24e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1078654864 190 SEQAVRDFFSKFGTLNSVKVNFAGKLAEIEFSTTAEAKNAYKS 232
Cdd:cd12568    13 TAEELRDLFEPHGKLTRVLMPPAGTIAIVEFANPQQARLAFKA 55
RRM6_RBM19 cd12571
RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19) and similar proteins; ...
178-232 6.61e-03

RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19) and similar proteins; This subgroup corresponds to the RRM6 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: 409985 [Multi-domain]  Cd Length: 79  Bit Score: 35.48  E-value: 6.61e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1078654864 178 KLVVEKIPDDyCSEQAVRDFFSKFGTLNSVKV--NFAGK-----LAEIEFSTTAEAKNAYKS 232
Cdd:cd12571     2 KILVRNIPFQ-ATVKEVRELFSTFGELKTVRLpkKMGGTgqhrgFGFVDFITKQDAKRAFDA 62
RBD_RRM1_NPL3 cd12340
RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; ...
178-232 9.64e-03

RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins; This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues.


Pssm-ID: 409777 [Multi-domain]  Cd Length: 69  Bit Score: 34.68  E-value: 9.64e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1078654864 178 KLVVEKIPDDyCSEQAVRDFFSKFGTLNSVKVNFAGKLAEIEFSTTAEAKNAYKS 232
Cdd:cd12340     1 RLFVRPFPPD-TSESAIREIFSPYGPVKEVKMLSDSNFAFVEFEELEDAIRAKDS 54
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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