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Conserved domains on  [gi|597955332|ref|NP_001278064|]
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regulation of nuclear pre-mRNA domain-containing protein 1B isoform c [Mus musculus]

Protein Classification

VHS/ENTH/ANTH domain-containing protein( domain architecture ID 13017728)

VHS (Vps27/Hrs/STAM) /ENTH (Epsin N-Terminal Homology) /ANTH (AP180 N-Terminal Homology) domain-containing protein similar to Homo sapiens ADP-ribosylation factor-binding protein GGA3 that plays a role in protein sorting and trafficking between the trans-Golgi network (TGN) and endosomes

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CID_RPRD1B cd17012
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1B; ...
 3-131 2.65e-86

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: 254.16  E-value: 2.65e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 597955332   3 SFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRKGPEFTREFE 82
Cdd:cd17012    1 SFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSSRKLTFLYLANDVIQNSKRKGPEFTREFE 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 597955332  83 SVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFIQQLKLSMED 131
Cdd:cd17012   81 SVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGDFIQQLKLSIED 129
CREPT super family cl24960
Cell-cycle alteration and expression-elevated protein in tumour; CREPT (Cell-cycle alteration ...
 178-287 1.10e-49

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.


The actual alignment was detected with superfamily member pfam16566:

Pssm-ID: 465181 [Multi-domain]  Cd Length: 147  Bit Score: 161.25  E-value: 1.10e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 597955332  178 EELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARM 257
Cdd:pfam16566   1 EELIKALQDLENSASSDAAVRERIASLPPEVSDVSLLSKIQDKESAERLLKQVNEACELLAEYNGRLAAELEDRKKVAQM 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 597955332  258 LVEYTQNQKEVLSEKEKKLERLTQQLQPCS 287
Cdd:pfam16566  81 LRDFLQLQKELLAQAEERLEEYKEKLEKVS 110
 
Name Accession Description Interval E-value
CID_RPRD1B cd17012
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1B; ...
 3-131 2.65e-86

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: 254.16  E-value: 2.65e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 597955332   3 SFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRKGPEFTREFE 82
Cdd:cd17012    1 SFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSSRKLTFLYLANDVIQNSKRKGPEFTREFE 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 597955332  83 SVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFIQQLKLSMED 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 1.66e-50

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: 162.38  E-value: 1.66e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 597955332    7 SALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRKG-PEFTREFESVL 85
Cdd:pfam04818   1 EALEKKLSSLNNSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSRKKGkSEFADAFEPVL 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 597955332   86 VDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFI 122
Cdd:pfam04818  81 PEAFASAYKKCDEKLKKKLERLLNIWEERNVFSPEVI 117
CREPT pfam16566
Cell-cycle alteration and expression-elevated protein in tumour; CREPT (Cell-cycle alteration ...
 178-287 1.10e-49

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: 161.25  E-value: 1.10e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 597955332  178 EELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARM 257
Cdd:pfam16566   1 EELIKALQDLENSASSDAAVRERIASLPPEVSDVSLLSKIQDKESAERLLKQVNEACELLAEYNGRLAAELEDRKKVAQM 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 597955332  258 LVEYTQNQKEVLSEKEKKLERLTQQLQPCS 287
Cdd:pfam16566  81 LRDFLQLQKELLAQAEERLEEYKEKLEKVS 110
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
8-126 3.59e-46

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 151.66  E-value: 3.59e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 597955332     8 ALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRK-GPEFTREFESVLV 86
Cdd:smart00582   1 AFEQKLESLNNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKRKyGSEFGDELGPVFQ 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 597955332    87 DAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFIQQLK 126
Cdd:smart00582  81 DALRRVLGAAPEELKKKIRRLLNIWEERGIFPPEVLRPLR 120
 
Name Accession Description Interval E-value
CID_RPRD1B cd17012
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1B; ...
 3-131 2.65e-86

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: 254.16  E-value: 2.65e-86
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 597955332   3 SFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRKGPEFTREFE 82
Cdd:cd17012    1 SFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSSRKLTFLYLANDVIQNSKRKGPEFTREFE 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 597955332  83 SVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFIQQLKLSMED 131
Cdd:cd17012   81 SVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGDFIQQLKLSIED 129
CID_RPRD1 cd17002
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1 and ...
 4-130 1.23e-77

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: 232.15  E-value: 1.23e-77
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 597955332   4 FSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRKGPEFTREFES 83
Cdd:cd17002    1 FSEAALEKKLAELSNSQQSIQTLSLWLIHHRKHAKTIVRVWLKELRKEKPSKKLTLLYLANDVIQNSRKKGPEFTKEFAP 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 597955332  84 VLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFIQQLKLSME 130
Cdd:cd17002   81 VLEDAFKHVAKLTDSEVLKALERILNIWKERQVYEKDFIEQLRAALR 127
CID_RPRD1A cd17011
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A; ...
 4-129 3.17e-70

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: 213.36  E-value: 3.17e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 597955332   4 FSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRKGPEFTREFES 83
Cdd:cd17011    1 FSEAALEKKLSELSNSQQSVQTLSLWLIHHRKHSRPIVTVWERELRKAKPNRKLTFLYLANDVIQNSKRKGPEFTKDFAP 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 597955332  84 VLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFIQQLKLSM 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 1.33e-59

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: 185.86  E-value: 1.33e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 597955332   6 ESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRKG-PEFTREFESV 84
Cdd:cd16981    1 EEALEKKLRSLNNTQQSIQTLSLWCLFHKKHAKQIVKIWLKELKKAKPERKLTLLYLANDVLQNSRRKGaPEFVEAFKKV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 597955332  85 LVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFIQQLK 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 1.66e-50

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: 162.38  E-value: 1.66e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 597955332    7 SALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRKG-PEFTREFESVL 85
Cdd:pfam04818   1 EALEKKLSSLNNSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSRKKGkSEFADAFEPVL 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 597955332   86 VDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFI 122
Cdd:pfam04818  81 PEAFASAYKKCDEKLKKKLERLLNIWEERNVFSPEVI 117
CREPT pfam16566
Cell-cycle alteration and expression-elevated protein in tumour; CREPT (Cell-cycle alteration ...
 178-287 1.10e-49

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: 161.25  E-value: 1.10e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 597955332  178 EELIKALQDLENAASGDATVRQKIASLPQEVQDVSLLEKITDKEAAERLSKTVDEACLLLAEYNGRLAAELEDRRQLARM 257
Cdd:pfam16566   1 EELIKALQDLENSASSDAAVRERIASLPPEVSDVSLLSKIQDKESAERLLKQVNEACELLAEYNGRLAAELEDRKKVAQM 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 597955332  258 LVEYTQNQKEVLSEKEKKLERLTQQLQPCS 287
Cdd:pfam16566  81 LRDFLQLQKELLAQAEERLEEYKEKLEKVS 110
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
8-126 3.59e-46

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 151.66  E-value: 3.59e-46
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 597955332     8 ALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRK-GPEFTREFESVLV 86
Cdd:smart00582   1 AFEQKLESLNNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKRKyGSEFGDELGPVFQ 80

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 597955332    87 DAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFIQQLK 126
Cdd:smart00582  81 DALRRVLGAAPEELKKKIRRLLNIWEERGIFPPEVLRPLR 120
CID cd03562
CID (CTD-Interacting Domain) family; The CTD-Interacting Domain (CID) is present in several ...
 8-126 1.12e-42

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: 142.66  E-value: 1.12e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 597955332   8 ALEKKLSELSN-SQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRKGPEFTREFESVLV 86
Cdd:cd03562    2 AFNSKLEELSDlSQQSITTLTKWAIHHIKHSRPIVTVIEREIRKCKPNRKLTFLYLIDSIIRNSKRKGPEFTKDFSPVIV 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 597955332  87 DAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFIQQLK 126
Cdd:cd03562   82 ELFKHVYSETDEDCKKKLGRVLSIWEERNVFENSVLEQLK 121
CID_Rtt103 cd17003
CID (CTD-Interacting Domain) of yeast transcription termination factor Rtt103 and similar ...
 6-126 7.16e-31

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: 112.32  E-value: 7.16e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 597955332   6 ESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKA--KSNRKLTFLYLANDVIQNSKRKG-PEFTREFE 82
Cdd:cd17003    1 EEQFISKLNALNETQESIVSISQWVLFHYRHADEIAEIWSDYLLKSsvNSRRKLLLIYLANDVVQQAKAKKkTEFIDAFS 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 597955332  83 SVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGEFIQQLK 126
Cdd:cd17003   81 KVLPEVLEKIYPSLPSDIKKKIKRVVNVWKQRQIFSKDVIDDIE 124
CID_RPRD2 cd17001
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 2; ...
 6-129 1.11e-26

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: 101.14  E-value: 1.11e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 597955332   6 ESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRKGPEFTRE-FESV 84
Cdd:cd17001    3 ESSLDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAIVFREsFAEV 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 597955332  85 LVDAFSHVareADEGCKKPLERLLNIWQERSVYGGEFIQQLKLSM 129
Cdd:cd17001   83 LPEAAALV---KDASVSKSVERIFKIWEERNVYPEETIAALKEAL 124
CID_SCAF8_like cd16983
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins; ...
 7-126 1.30e-11

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: 60.70  E-value: 1.30e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 597955332   7 SALEKKLSELSNSQQSV-----QTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRK-GPE---F 77
Cdd:cd16983    1 EEFNKELSSLLDSKPPVskskiNAITKLAIKAIKFYKHVVQSVEKFIQKCKPEYKLPGLYVIDSIIRQSRHQyGKEkdvY 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 597955332  78 TREFESVLVDAFSHVaREADEGCKKPLERLLNIWQERSVYGGEFIQQLK 126
Cdd:cd16983   81 APRFAKNLSKTFLNL-LKCPEKDKPKVKRVLNLWQKNGVFPKEIIQPLL 128
CID_Pcf11 cd16982
CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied ...
 10-115 3.89e-10

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: 56.81  E-value: 3.89e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 597955332  10 EKKLSELS-NSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSNRKLTFLYLAnDVIqnSKRKGPEFTREFESVLVDA 88
Cdd:cd16982    5 RSALAELTfNSKPIINNLTMLAEENIQAAQAIVEAIEERIRKVPPEQKLPALYLL-DSI--VKNVGGPYTSLFSPNLVDL 81

                         90       100
                 ....*....|....*....|....*..
gi 597955332  89 FSHVAREADEGCKKPLERLLNIWQERS 115
Cdd:cd16982   82 FLDAYRLVDEKTRKKLEKLLNTWKTVF 108
CID_SCAF8 cd17004
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8; SR-related and ...
 31-125 1.50e-05

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: 43.87  E-value: 1.50e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 597955332  31 IHHRKHagpIVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRK-GPE---FTREFESVLVDAFSHVAR-EADEgcKKPLE 105
Cdd:cd17004   33 IKFYKH---VVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQfGQEkdvFAPRFSNNIISTFQNLYRcPGDD--KSKIV 107

                         90       100
                 ....*....|....*....|
gi 597955332 106 RLLNIWQERSVYGGEFIQQL 125
Cdd:cd17004  108 RVLNLWQKNNVFKSEIIQPL 127
CagA_N pfam18971
CagA protein; The Helicobacter pylori type IV secretion effector CagA is a major bacterial ...
 1-277 9.01e-05

CagA protein; The Helicobacter pylori type IV secretion effector CagA is a major bacterial virulence determinant and critical for gastric carcinogenesis. X-ray crystallographic analysis of the N-terminal CagA fragment (residues 1-876) revealed that the region has a structure comprised of three discrete domains. Domain I constitutes a mobile CagA N terminus, while Domain II tethers CagA to the plasma membrane by interacting with membrane phosphatidylserine. Domain III interacts intramolecularly with the intrinsically disordered C-terminal region, and this interaction potentiates the pathogenic scaffold/hub function of CagA.


Pssm-ID: 408741 [Multi-domain]  Cd Length: 876  Bit Score: 43.99  E-value: 9.01e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 597955332    1 MSSFSESALEKKLSELSNS-QQSVQTLSLWLIHHRKHAGPIVSvWHRELRKAKSNRKLTFLYLANDVIQNSKRKGPEFTR 79
Cdd:pfam18971 553 ITSFVRRNLENKLTAKGLSlQEANKLIKDFLSSNKELAGKALN-FNKAVAEAKSTGNYDEVKKAQKDLEKSLRKREHLEK 631

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 597955332   80 EFESVL---------VDAFSHVAREADEgckkpLERLLNIWQERSVYGGEFIQQLKLSMEDSKSPPPKAAEEKKSLKRTF 150
Cdd:pfam18971 632 EVEKKLesksgnknkMEAKAQANSQKDE-----IFALINKEANRDARAIAYTQNLKGIKRELSDKLEKISKDLKDFSKSF 706

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 597955332  151 QQIQEEEDDDYPGSY--------SPQDPSAGPLL---TEELIKALQDLENAASGD-ATVRQKIASLPQEVQDVSLLEKIT 218
Cdd:pfam18971 707 DEFKNGKNKDFSKAEetlkalkgSVKDLGINPEWiskVENLNAALNEFKNGKNKDfSKVTQAKSDLENSVKDVIINQKVT 786

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 597955332  219 DKeaAERLSKTVDeaclllaeyngrLAAELEDRRQLARMLVEYTQNQKEVLSEKEKKLE 277
Cdd:pfam18971 787 DK--VDNLNQAVS------------VAKAMGDFSRVEQVLADLKNFSKEQLAQQAQKNE 831
CID_SFRS15_SCAF4 cd17005
CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15; Splicing factor ...
 40-125 1.98e-04

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: 40.72  E-value: 1.98e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 597955332  40 IVSVWHRELRKAKSNRKLTFLYLANDVIQNSKRK--------GPEFTREFESVLVDAFshvarEADEGCKKPLERLLNIW 111
Cdd:cd17005   39 VVQIVEKFIKKCKPEYKVPGLYVIDSIVRQSRHQfgadkdvfGPRFSKNITATFQYLY-----LCPSEDKSKIVRVLNLW 113

                         90
                 ....*....|....
gi 597955332 112 QERSVYGGEFIQQL 125
Cdd:cd17005  114 QKNGVFKIEIIQPL 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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