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Conserved domains on  [gi|1721935850|ref|XP_030212583|]
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regulation of nuclear pre-mRNA domain-containing protein 1B [Gadus morhua]

Protein Classification

VHS_ENTH_ANTH and CREPT domain-containing protein( domain architecture ID 10914520)

VHS_ENTH_ANTH and CREPT domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CREPT pfam16566
Cell-cycle alteration and expression-elevated protein in tumour; CREPT (Cell-cycle alteration ...
 189-335 2.24e-82

Cell-cycle alteration and expression-elevated protein in tumour; CREPT (Cell-cycle alteration and expression-elevated protein in tumour) is a family of eukaryotic transcriptional regulators that ptromote the binding of RNA-polymerase to the CYCLIN D1, CCDN1, promoter and other genes involved in the cell-cycle. It promotes the formation of a chromatin loop in the CYCLIN D1 gene, and is preferentially expressed in a range of different human tumours.


:

Pssm-ID: 465181 [Multi-domain]  Cd Length: 147  Bit Score: 246.38  E-value: 2.24e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721935850 189 EELVKALQDLENAASGDAAVRQKIASLPQEVQDVSLLEKITDKEAADRLSKTVDEACLLLAEYNGRLAAELEDRRQLARM 268
Cdd:pfam16566   1 EELIKALQDLENSASSDAAVRERIASLPPEVSDVSLLSKIQDKESAERLLKQVNEACELLAEYNGRLAAELEDRKKVAQM 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1721935850 269 LTDYISSQKNALGEREKKLEEFKQKLARVTTVRKELKSHIQSLPDLSLLPNVTGGLAPLPSAGDLFS 335
Cdd:pfam16566  81 LRDFLQLQKELLAQAEERLEEYKEKLEKVSQVRKELKSHIQSLPDLTLLPDVTGGLAPLPSAGDLFS 147
VHS_ENTH_ANTH super family cl02544
VHS, ENTH and ANTH domain superfamily; This superfamily is composed of proteins containing a ...
 3-131 2.09e-80

VHS, ENTH and ANTH domain superfamily; This superfamily is composed of proteins containing a VHS, CID, ENTH, or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The CTD-Interacting Domain (CID) is present in several RNA-processing factors and binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase II (RNAP II or Pol II). The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-Terminal Homology (ANTH) domain. VHS, ENTH, and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH and ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH domain-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the Trans-Golgi Network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding.


The actual alignment was detected with superfamily member cd17012:

Pssm-ID: 470608  Cd Length: 129  Bit Score: 240.68  E-value: 2.09e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721935850   3 SFSESALEKKLSELSNSQQSVQTLSLWIIHHRKHSPLIVKVWHRELKKAKTSRKLTFLYLANDVIQNSKKKGPEFAKDFE 82
Cdd:cd17012     1 SFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSSRKLTFLYLANDVIQNSKRKGPEFTREFE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1721935850  83 TVLVDACSHVAREADGSCKKPMERLLNIWKERALYRADFIQQLKLAIED 131
Cdd:cd17012    81 SVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGDFIQQLKLSIED 129
 
Name Accession Description Interval E-value
CREPT pfam16566
Cell-cycle alteration and expression-elevated protein in tumour; CREPT (Cell-cycle alteration ...
 189-335 2.24e-82

Cell-cycle alteration and expression-elevated protein in tumour; CREPT (Cell-cycle alteration and expression-elevated protein in tumour) is a family of eukaryotic transcriptional regulators that ptromote the binding of RNA-polymerase to the CYCLIN D1, CCDN1, promoter and other genes involved in the cell-cycle. It promotes the formation of a chromatin loop in the CYCLIN D1 gene, and is preferentially expressed in a range of different human tumours.


Pssm-ID: 465181 [Multi-domain]  Cd Length: 147  Bit Score: 246.38  E-value: 2.24e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721935850 189 EELVKALQDLENAASGDAAVRQKIASLPQEVQDVSLLEKITDKEAADRLSKTVDEACLLLAEYNGRLAAELEDRRQLARM 268
Cdd:pfam16566   1 EELIKALQDLENSASSDAAVRERIASLPPEVSDVSLLSKIQDKESAERLLKQVNEACELLAEYNGRLAAELEDRKKVAQM 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1721935850 269 LTDYISSQKNALGEREKKLEEFKQKLARVTTVRKELKSHIQSLPDLSLLPNVTGGLAPLPSAGDLFS 335
Cdd:pfam16566  81 LRDFLQLQKELLAQAEERLEEYKEKLEKVSQVRKELKSHIQSLPDLTLLPDVTGGLAPLPSAGDLFS 147
CID_RPRD1B cd17012
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1B; ...
 3-131 2.09e-80

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1B; Regulation of nuclear pre-mRNA domain-containing protein 1B (RPRD1B) is also called Cell cycle-related and expression-elevated protein in tumor (CREPT). RPRD1B is a CID (CTD-Interacting Domain) containing protein that co-purifies with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. RPRD1B form homodimers and heterodimers with RPRD1A through their coiled-coil domains. Both RPRD1A and RPRD1B associate directly with RPAP2 phosphatase and serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2. RPRD1B is highly expressed during tumorigenesis and in endometrial cancer, has been shown to promote tumor growth by accelerating the cell cycle. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340809  Cd Length: 129  Bit Score: 240.68  E-value: 2.09e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721935850   3 SFSESALEKKLSELSNSQQSVQTLSLWIIHHRKHSPLIVKVWHRELKKAKTSRKLTFLYLANDVIQNSKKKGPEFAKDFE 82
Cdd:cd17012     1 SFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSSRKLTFLYLANDVIQNSKRKGPEFTREFE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1721935850  83 TVLVDACSHVAREADGSCKKPMERLLNIWKERALYRADFIQQLKLAIED 131
Cdd:cd17012    81 SVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGDFIQQLKLSIED 129
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 7-122 4.03e-48

CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase II. This domain is known as the CTD-interacting domain (CID).


Pssm-ID: 461442  Cd Length: 117  Bit Score: 157.76  E-value: 4.03e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721935850   7 SALEKKLSELSNSQQSVQTLSLWIIHHRKHSPLIVKVWHRELKKAKTSRKLTFLYLANDVIQNSKKKG-PEFAKDFETVL 85
Cdd:pfam04818   1 EALEKKLSSLNNSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSRKKGkSEFADAFEPVL 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1721935850  86 VDACSHVAREADGSCKKPMERLLNIWKERALYRADFI 122
Cdd:pfam04818  81 PEAFASAYKKCDEKLKKKLERLLNIWEERNVFSPEVI 117
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
8-126 7.15e-38

domain present in proteins, which are involved in regulation of nuclear pre-mRNA;


Pssm-ID: 214731  Cd Length: 124  Bit Score: 131.24  E-value: 7.15e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721935850    8 ALEKKLSELSNSQQSVQTLSLWIIHHRKHSPLIVKVWHRELKKAKTSRKLTFLYLANDVIQNSK-KKGPEFAKDFETVLV 86
Cdd:smart00582   1 AFEQKLESLNNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKrKYGSEFGDELGPVFQ 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1721935850   87 DACSHVAREADGSCKKPMERLLNIWKERALYRADFIQQLK 126
Cdd:smart00582  81 DALRRVLGAAPEELKKKIRRLLNIWEERGIFPPEVLRPLR 120
 
Name Accession Description Interval E-value
CREPT pfam16566
Cell-cycle alteration and expression-elevated protein in tumour; CREPT (Cell-cycle alteration ...
 189-335 2.24e-82

Cell-cycle alteration and expression-elevated protein in tumour; CREPT (Cell-cycle alteration and expression-elevated protein in tumour) is a family of eukaryotic transcriptional regulators that ptromote the binding of RNA-polymerase to the CYCLIN D1, CCDN1, promoter and other genes involved in the cell-cycle. It promotes the formation of a chromatin loop in the CYCLIN D1 gene, and is preferentially expressed in a range of different human tumours.


Pssm-ID: 465181 [Multi-domain]  Cd Length: 147  Bit Score: 246.38  E-value: 2.24e-82
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721935850 189 EELVKALQDLENAASGDAAVRQKIASLPQEVQDVSLLEKITDKEAADRLSKTVDEACLLLAEYNGRLAAELEDRRQLARM 268
Cdd:pfam16566   1 EELIKALQDLENSASSDAAVRERIASLPPEVSDVSLLSKIQDKESAERLLKQVNEACELLAEYNGRLAAELEDRKKVAQM 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1721935850 269 LTDYISSQKNALGEREKKLEEFKQKLARVTTVRKELKSHIQSLPDLSLLPNVTGGLAPLPSAGDLFS 335
Cdd:pfam16566  81 LRDFLQLQKELLAQAEERLEEYKEKLEKVSQVRKELKSHIQSLPDLTLLPDVTGGLAPLPSAGDLFS 147
CID_RPRD1B cd17012
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1B; ...
 3-131 2.09e-80

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1B; Regulation of nuclear pre-mRNA domain-containing protein 1B (RPRD1B) is also called Cell cycle-related and expression-elevated protein in tumor (CREPT). RPRD1B is a CID (CTD-Interacting Domain) containing protein that co-purifies with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. RPRD1B form homodimers and heterodimers with RPRD1A through their coiled-coil domains. Both RPRD1A and RPRD1B associate directly with RPAP2 phosphatase and serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2. RPRD1B is highly expressed during tumorigenesis and in endometrial cancer, has been shown to promote tumor growth by accelerating the cell cycle. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340809  Cd Length: 129  Bit Score: 240.68  E-value: 2.09e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721935850   3 SFSESALEKKLSELSNSQQSVQTLSLWIIHHRKHSPLIVKVWHRELKKAKTSRKLTFLYLANDVIQNSKKKGPEFAKDFE 82
Cdd:cd17012     1 SFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSSRKLTFLYLANDVIQNSKRKGPEFTREFE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1721935850  83 TVLVDACSHVAREADGSCKKPMERLLNIWKERALYRADFIQQLKLAIED 131
Cdd:cd17012    81 SVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGDFIQQLKLSIED 129
CID_RPRD1 cd17002
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1 and ...
 4-128 5.33e-73

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1 and similar proteins; This subfamily contains Regulation of nuclear pre-mRNA domain-containing proteins 1A (RPRD1A) and 1B (RPRD1B) from jawed vertebrates, CID domain-containing protein 1 (CIDS1 or cids-1) from Caenorhabditis elegans, and similar proteins. RPRD1A and RPRD1B are CID (CTD-Interacting Domain) containing proteins that co-purify with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. RPRD1A and RPRD1B form homodimers and heterodimers through their coiled-coil domains. Both associate directly with RPAP2 phosphatase and serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2. The function of CIDS1 is not yet known. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340799  Cd Length: 128  Bit Score: 221.75  E-value: 5.33e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721935850   4 FSESALEKKLSELSNSQQSVQTLSLWIIHHRKHSPLIVKVWHRELKKAKTSRKLTFLYLANDVIQNSKKKGPEFAKDFET 83
Cdd:cd17002     1 FSEAALEKKLAELSNSQQSIQTLSLWLIHHRKHAKTIVRVWLKELRKEKPSKKLTLLYLANDVIQNSRKKGPEFTKEFAP 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1721935850  84 VLVDACSHVAREADGSCKKPMERLLNIWKERALYRADFIQQLKLA 128
Cdd:cd17002    81 VLEDAFKHVAKLTDSEVLKALERILNIWKERQVYEKDFIEQLRAA 125
CID_RPRD1A cd17011
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A; ...
 4-129 1.25e-67

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A; Regulation of nuclear pre-mRNA domain-containing protein 1A (RPRD1A) is also called Cyclin-dependent kinase inhibitor 2B-related protein or p15INK4B-related protein (P15RS). RPRD1A is a CID (CTD-Interacting Domain) containing protein that co-purifies with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. RPRD1A form homodimers and heterodimers with RPRD1B through their coiled-coil domains. Both RPRD1A and RPRD1B associate directly with RPAP2 phosphatase and serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340808  Cd Length: 128  Bit Score: 208.36  E-value: 1.25e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721935850   4 FSESALEKKLSELSNSQQSVQTLSLWIIHHRKHSPLIVKVWHRELKKAKTSRKLTFLYLANDVIQNSKKKGPEFAKDFET 83
Cdd:cd17011     1 FSEAALEKKLSELSNSQQSVQTLSLWLIHHRKHSRPIVTVWERELRKAKPNRKLTFLYLANDVIQNSKRKGPEFTKDFAP 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1721935850  84 VLVDACSHVAREADGSCKKPMERLLNIWKERALYRADFIQQLKLAI 129
Cdd:cd17011    81 VIVEAFKHVSSETDESCKKHLGRVLSIWEERSVYENDVLEQLKQAL 126
CID_RPRD_like cd16981
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; ...
 6-126 3.06e-56

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; This family is composed of Regulation of nuclear pre-mRNA domain-containing proteins 1A (RPRD1A), 1B (RPRD1B), 2 (RPRD2), yeast Rtt103, and similar proteins. RPRD1A, RPRD1B, and RPRD2 are CID (CTD-Interacting Domain) containing proteins that co-purify with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. Yeast transcription termination factor Rtt103 is a CID containing protein that functions in DNA damage response. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340778  Cd Length: 125  Bit Score: 178.93  E-value: 3.06e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721935850   6 ESALEKKLSELSNSQQSVQTLSLWIIHHRKHSPLIVKVWHRELKKAKTSRKLTFLYLANDVIQNSKKKG-PEFAKDFETV 84
Cdd:cd16981     1 EEALEKKLRSLNNTQQSIQTLSLWCLFHKKHAKQIVKIWLKELKKAKPERKLTLLYLANDVLQNSRRKGaPEFVEAFKKV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1721935850  85 LVDACSHVAREADGSCKKPMERLLNIWKERALYRADFIQQLK 126
Cdd:cd16981    81 LPEALALVRSEGDESVRKKVLRVLNIWEERNVFGSEFLAELR 122
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 7-122 4.03e-48

CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase II. This domain is known as the CTD-interacting domain (CID).


Pssm-ID: 461442  Cd Length: 117  Bit Score: 157.76  E-value: 4.03e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721935850   7 SALEKKLSELSNSQQSVQTLSLWIIHHRKHSPLIVKVWHRELKKAKTSRKLTFLYLANDVIQNSKKKG-PEFAKDFETVL 85
Cdd:pfam04818   1 EALEKKLSSLNNSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSRKKGkSEFADAFEPVL 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1721935850  86 VDACSHVAREADGSCKKPMERLLNIWKERALYRADFI 122
Cdd:pfam04818  81 PEAFASAYKKCDEKLKKKLERLLNIWEERNVFSPEVI 117
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
8-126 7.15e-38

domain present in proteins, which are involved in regulation of nuclear pre-mRNA;


Pssm-ID: 214731  Cd Length: 124  Bit Score: 131.24  E-value: 7.15e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721935850    8 ALEKKLSELSNSQQSVQTLSLWIIHHRKHSPLIVKVWHRELKKAKTSRKLTFLYLANDVIQNSK-KKGPEFAKDFETVLV 86
Cdd:smart00582   1 AFEQKLESLNNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKrKYGSEFGDELGPVFQ 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 1721935850   87 DACSHVAREADGSCKKPMERLLNIWKERALYRADFIQQLK 126
Cdd:smart00582  81 DALRRVLGAAPEELKKKIRRLLNIWEERGIFPPEVLRPLR 120
CID cd03562
CID (CTD-Interacting Domain) family; The CTD-Interacting Domain (CID) is present in several ...
 8-126 4.30e-37

CID (CTD-Interacting Domain) family; The CTD-Interacting Domain (CID) is present in several eukaryotic RNA-processing factors including yeast proteins, Pcf11 and Nrd1, and vertebrate proteins, CTD-associated factors 8 (SCAF8) and Regulation of nuclear pre-mRNA domain-containing proteins (such as RPRD1 and RPRD2). Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340766  Cd Length: 123  Bit Score: 129.56  E-value: 4.30e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721935850   8 ALEKKLSELSN-SQQSVQTLSLWIIHHRKHSPLIVKVWHRELKKAKTSRKLTFLYLANDVIQNSKKKGPEFAKDFETVLV 86
Cdd:cd03562     2 AFNSKLEELSDlSQQSITTLTKWAIHHIKHSRPIVTVIEREIRKCKPNRKLTFLYLIDSIIRNSKRKGPEFTKDFSPVIV 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1721935850  87 DACSHVAREADGSCKKPMERLLNIWKERALYRADFIQQLK 126
Cdd:cd03562    82 ELFKHVYSETDEDCKKKLGRVLSIWEERNVFENSVLEQLK 121
CID_Rtt103 cd17003
CID (CTD-Interacting Domain) of yeast transcription termination factor Rtt103 and similar ...
 6-129 1.76e-29

CID (CTD-Interacting Domain) of yeast transcription termination factor Rtt103 and similar proteins; Yeast transcription termination factor Rtt103 is a CID (CTD-Interacting Domain) containing protein that functions in DNA damage response. It associates with sites of DNA breaks and is essential for recovery from DNA double strand breaks in the chromosome. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). Rtt103 CID preferentially interacts with CTD phosphorylated at Ser2. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340800  Cd Length: 127  Bit Score: 109.62  E-value: 1.76e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721935850   6 ESALEKKLSELSNSQQSVQTLSLWIIHHRKHSPLIVKVWHRELKKA--KTSRKLTFLYLANDVIQNSK-KKGPEFAKDFE 82
Cdd:cd17003     1 EEQFISKLNALNETQESIVSISQWVLFHYRHADEIAEIWSDYLLKSsvNSRRKLLLIYLANDVVQQAKaKKKTEFIDAFS 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1721935850  83 TVLVDACSHVAREADGSCKKPMERLLNIWKERALYRADFIQQLKLAI 129
Cdd:cd17003    81 KVLPEVLEKIYPSLPSDIKKKIKRVVNVWKQRQIFSKDVIDDIEERL 127
CID_RPRD2 cd17001
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 2; ...
 6-129 7.62e-24

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 2; Regulation of nuclear pre-mRNA domain-containing protein 2 (RPRD2) is a CID (CTD-Interacting Domain) domain containing protein that co-purifies with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340798  Cd Length: 125  Bit Score: 94.60  E-value: 7.62e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721935850   6 ESALEKKLSELSNSQQSVQTLSLWIIHHRKHSPLIVKVWHRELKKAKTSRKLTFLYLANDVIQNSKKKGP-EFAKDFETV 84
Cdd:cd17001     3 ESSLDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAiVFRESFAEV 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1721935850  85 LVDACSHVareADGSCKKPMERLLNIWKERALYRADFIQQLKLAI 129
Cdd:cd17001    83 LPEAAALV---KDASVSKSVERIFKIWEERNVYPEETIAALKEAL 124
CID_Pcf11 cd16982
CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied ...
 10-113 3.65e-08

CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied protein is Saccharomyces cerevisiae Pcf11, also called protein 1 of CF I, an essential subunit of the cleavage factor IA (CFIA) complex which is required for polyadenylation-dependent pre-mRNA 3'-end processing and RNA polymerase (Pol) II (RNAP II) transcription termination. Human Pcf11, also referred to as pre-mRNA cleavage complex 2 protein Pcf11, has been shown to enhance degradation of RNAP II-associated nascent RNA and transcriptional termination. The family also includes plant PCFS4 (Pcf11-similar-4 protein or Polyadenylation and cleavage factor homolog 4) and Caenorhabditis elegans Polyadenylation and cleavage factor homolog 11. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. Pcf11 CID preferentially interacts with CTD phosphorylated at Ser2. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340779  Cd Length: 127  Bit Score: 51.41  E-value: 3.65e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721935850  10 EKKLSELS-NSQQSVQTLSLWIIHHRKHSPLIVKVWHRELKKAKTSRKLTFLYLAnDVIqnSKKKGPEFAKDFETVLVDA 88
Cdd:cd16982     5 RSALAELTfNSKPIINNLTMLAEENIQAAQAIVEAIEERIRKVPPEQKLPALYLL-DSI--VKNVGGPYTSLFSPNLVDL 81

                          90       100
                  ....*....|....*....|....*
gi 1721935850  89 CSHVAREADGSCKKPMERLLNIWKE 113
Cdd:cd16982    82 FLDAYRLVDEKTRKKLEKLLNTWKT 106
CID_SCAF8_like cd16983
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins; ...
 7-126 4.23e-07

CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins; This subfamily includes SR-related and CTD-associated factors 8 (SCAF8) and 4 (SCAF4), and similar proteins. SCAF4 is also called Splicing factor arginine serine rich 15 (SFRS15). Members may play roles in mRNA processing. Both SCAF4 and SCAF8 contains a CTD-interacting domain (CID) at the amino terminus and a Ser/Arg-rich domain followed by an RNA recognition motif. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340780  Cd Length: 131  Bit Score: 48.38  E-value: 4.23e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721935850   7 SALEKKLSELSNSQQSV-----QTLSLWIIHHRKHSPLIVKVWHRELKKAKTSRKLTFLYLANDVIQNSKKK-GPE---F 77
Cdd:cd16983     1 EEFNKELSSLLDSKPPVskskiNAITKLAIKAIKFYKHVVQSVEKFIQKCKPEYKLPGLYVIDSIIRQSRHQyGKEkdvY 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1721935850  78 AKDFETVLVDACSHV--AREADgscKKPMERLLNIWKERALYRADFIQQLK 126
Cdd:cd16983    81 APRFAKNLSKTFLNLlkCPEKD---KPKVKRVLNLWQKNGVFPKEIIQPLL 128
CID_SCAF8 cd17004
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8; SR-related and ...
 31-125 6.24e-04

CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8; SR-related and CTD-associated factor 8 (SCAF8) is also called CDC5L complex-associated protein 7 (CCAP7) or RNA-binding motif protein 16 (RBM16). It may play a role in mRNA processing. SCAF8 contains a CTD-interacting domain (CID) at the amino terminus and a Ser/Arg-rich domain followed by an RNA recognition motif. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340801  Cd Length: 131  Bit Score: 39.24  E-value: 6.24e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721935850  31 IHHRKHsplIVKVWHRELKKAKTSRKLTFLYLANDVIQNSKKK-GPE---FAKDFETVLVDACSHVAReADGSCKKPMER 106
Cdd:cd17004    33 IKFYKH---VVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQfGQEkdvFAPRFSNNIISTFQNLYR-CPGDDKSKIVR 108

                          90
                  ....*....|....*....
gi 1721935850 107 LLNIWKERALYRADFIQQL 125
Cdd:cd17004   109 VLNLWQKNNVFKSEIIQPL 127
CID_SFRS15_SCAF4 cd17005
CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15; Splicing factor ...
 35-125 8.52e-03

CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15; Splicing factor arginine serine rich 15 (SFRS15) is also called CTD-binding SR-like protein RA4 or SR-related and CTD-associated factor 4 (SCAF4). It may act to physically and functionally link transcription and pre-mRNA processing. SFRS15/SCAF4 contains a CTD-interacting domain (CID) at the amino terminus and a Ser/Arg-rich domain followed by an RNA recognition motif. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340802  Cd Length: 131  Bit Score: 36.10  E-value: 8.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1721935850  35 KHsplIVKVWHRELKKAKTSRKLTFLYLANDVIQNSKKK--------GPEFAKDFETVLvdacsHVAREADGSCKKPMER 106
Cdd:cd17005    37 KH---VVQIVEKFIKKCKPEYKVPGLYVIDSIVRQSRHQfgadkdvfGPRFSKNITATF-----QYLYLCPSEDKSKIVR 108

                          90
                  ....*....|....*....
gi 1721935850 107 LLNIWKERALYRADFIQQL 125
Cdd:cd17005   109 VLNLWQKNGVFKIEIIQPL 127
 
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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