NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|19114598|ref|NP_593686|]
View 

putative cleavage and polyadenylation specificity factor [Schizosaccharomyces pombe]

Protein Classification

CTD-interacting domain-containing protein( domain architecture ID 13015791)

CTD-interacting domain (CID)-containing protein similar to Caenorhabditis elegans polyadenylation and cleavage factor homolog 11 (Pcf11)

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
CID_Pcf11 cd16982
CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied ...
 7-134 1.12e-55

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: 184.69  E-value: 1.12e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114598   7 DYLSALEDLTFNSKPIIHTLTYIAQENEPYAISIVNAIEKHIQKCPPNCKLPALYLLDSISKNLGAPYTYFFGLHLFSTF 86
Cdd:cd16982   3 EYRSALAELTFNSKPIINNLTMLAEENIQAAQAIVEAIEERIRKVPPEQKLPALYLLDSIVKNVGGPYTSLFSPNLVDLF 82

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 19114598  87 MSAYTVVEPRLRLKLDQLLATWKQRPPNSSslePVFSPIVTAKIENAL 134
Cdd:cd16982  83 LDAYRLVDEKTRKKLEKLLNTWKTVFPNGK---LLFPDEVLNKIERAL 127
 
Name Accession Description Interval E-value
CID_Pcf11 cd16982
CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied ...
 7-134 1.12e-55

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: 184.69  E-value: 1.12e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114598   7 DYLSALEDLTFNSKPIIHTLTYIAQENEPYAISIVNAIEKHIQKCPPNCKLPALYLLDSISKNLGAPYTYFFGLHLFSTF 86
Cdd:cd16982   3 EYRSALAELTFNSKPIINNLTMLAEENIQAAQAIVEAIEERIRKVPPEQKLPALYLLDSIVKNVGGPYTSLFSPNLVDLF 82

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 19114598  87 MSAYTVVEPRLRLKLDQLLATWKQRPPNSSslePVFSPIVTAKIENAL 134
Cdd:cd16982  83 LDAYRLVDEKTRKKLEKLLNTWKTVFPNGK---LLFPDEVLNKIERAL 127
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
7-135 2.17e-23

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 95.81  E-value: 2.17e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114598      7 DYLSALEDLTfNSKPIIHTLTYIAQENEPYAISIVNAIEKHIQKCPPNCKLPALYLLDSISKNLGAPYTYFFGLHLFSTF 86
Cdd:smart00582   1 AFEQKLESLN-NSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKRKYGSEFGDELGPVF 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 19114598     87 MSAYT-VVEP---RLRLKLDQLLATWKQRppnssslePVFSPIVTAKIENALL 135
Cdd:smart00582  80 QDALRrVLGAapeELKKKIRRLLNIWEER--------GIFPPEVLRPLREKLN 124
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 10-111 1.42e-11

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: 61.84  E-value: 1.42e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114598    10 SALEDLTfNSKPIIHTLTYIAQENEPYAISIVNAIEKHIQKCPPNCKLPALYLLDSI---SKNLGAPytYF---FGLHLF 83
Cdd:pfam04818   5 KKLSSLN-NSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVlqnSRKKGKS--EFadaFEPVLP 81

                          90       100
                  ....*....|....*....|....*...
gi 19114598    84 STFMSAYTVVEPRLRLKLDQLLATWKQR 111
Cdd:pfam04818  82 EAFASAYKKCDEKLKKKLERLLNIWEER 109
 
Name Accession Description Interval E-value
CID_Pcf11 cd16982
CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied ...
 7-134 1.12e-55

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: 184.69  E-value: 1.12e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114598   7 DYLSALEDLTFNSKPIIHTLTYIAQENEPYAISIVNAIEKHIQKCPPNCKLPALYLLDSISKNLGAPYTYFFGLHLFSTF 86
Cdd:cd16982   3 EYRSALAELTFNSKPIINNLTMLAEENIQAAQAIVEAIEERIRKVPPEQKLPALYLLDSIVKNVGGPYTSLFSPNLVDLF 82

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 19114598  87 MSAYTVVEPRLRLKLDQLLATWKQRPPNSSslePVFSPIVTAKIENAL 134
Cdd:cd16982  83 LDAYRLVDEKTRKKLEKLLNTWKTVFPNGK---LLFPDEVLNKIERAL 127
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
7-135 2.17e-23

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 95.81  E-value: 2.17e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114598      7 DYLSALEDLTfNSKPIIHTLTYIAQENEPYAISIVNAIEKHIQKCPPNCKLPALYLLDSISKNLGAPYTYFFGLHLFSTF 86
Cdd:smart00582   1 AFEQKLESLN-NSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKRKYGSEFGDELGPVF 79

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|...
gi 19114598     87 MSAYT-VVEP---RLRLKLDQLLATWKQRppnssslePVFSPIVTAKIENALL 135
Cdd:smart00582  80 QDALRrVLGAapeELKKKIRRLLNIWEER--------GIFPPEVLRPLREKLN 124
CID cd03562
CID (CTD-Interacting Domain) family; The CTD-Interacting Domain (CID) is present in several ...
 7-111 2.71e-20

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: 86.80  E-value: 2.71e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114598   7 DYLSALEDLTFNSKPIIHTLTYIAQENEPYAISIVNAIEKHIQKCPPNCKLPALYLLDSISKNL---GAPYTYFFGLHLF 83
Cdd:cd03562   2 AFNSKLEELSDLSQQSITTLTKWAIHHIKHSRPIVTVIEREIRKCKPNRKLTFLYLIDSIIRNSkrkGPEFTKDFSPVIV 81

                        90       100
                ....*....|....*....|....*...
gi 19114598  84 STFMSAYTVVEPRLRLKLDQLLATWKQR 111
Cdd:cd03562  82 ELFKHVYSETDEDCKKKLGRVLSIWEER 109
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 10-111 1.42e-11

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: 61.84  E-value: 1.42e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114598    10 SALEDLTfNSKPIIHTLTYIAQENEPYAISIVNAIEKHIQKCPPNCKLPALYLLDSI---SKNLGAPytYF---FGLHLF 83
Cdd:pfam04818   5 KKLSSLN-NSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVlqnSRKKGKS--EFadaFEPVLP 81

                          90       100
                  ....*....|....*....|....*...
gi 19114598    84 STFMSAYTVVEPRLRLKLDQLLATWKQR 111
Cdd:pfam04818  82 EAFASAYKKCDEKLKKKLERLLNIWEER 109
CID_SCAF8_like cd16983
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins; ...
 9-88 1.43e-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: 50.69  E-value: 1.43e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114598   9 LSALEDLtfnSKPI----IHTLTYIAQENEPYAISIVNAIEKHIQKCPPNCKLPALYLLDSISKN----LGA---PYTYF 77
Cdd:cd16983   7 LSSLLDS---KPPVskskINAITKLAIKAIKFYKHVVQSVEKFIQKCKPEYKLPGLYVIDSIIRQsrhqYGKekdVYAPR 83

                        90
                ....*....|.
gi 19114598  78 FGLHLFSTFMS 88
Cdd:cd16983  84 FAKNLSKTFLN 94
VHS_ENTH_ANTH cd00197
VHS, ENTH and ANTH domain superfamily; This superfamily is composed of proteins containing a ...
 12-108 1.01e-06

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.


Pssm-ID: 340764  Cd Length: 115  Bit Score: 47.80  E-value: 1.01e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114598  12 LEDLTFN-----SKPIIHTLTYIAQENEPYAISIVNAIEKHIQKCPPNCKLPALYLLDSISKNLGAPYTYFFGLHLFSTF 86
Cdd:cd00197   5 VEKATSNenmgpDWPLIMEICDLINETNVGPKEAVDAIKKRINNKNPHVVLKALTLLEYCVKNCGERFHQEVASNDFAVE 84

                        90       100
                ....*....|....*....|....*....
gi 19114598  87 MSA-------YTVVEPRLRLKLDQLLATW 108
Cdd:cd00197  85 LLKfdksgllGDDVSTNVREKAIELVQLW 113
CID_RPRD1A cd17011
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A; ...
 12-111 1.05e-04

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: 42.34  E-value: 1.05e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114598  12 LEDLTfNSKPIIHTLTYIAQENEPYAISIVNAIEKHIQKCPPNCKLPALYLLDSI---SKNLGAPYTYFFGLHLFSTFMS 88
Cdd:cd17011  10 LSELS-NSQQSVQTLSLWLIHHRKHSRPIVTVWERELRKAKPNRKLTFLYLANDViqnSKRKGPEFTKDFAPVIVEAFKH 88

                        90       100
                ....*....|....*....|...
gi 19114598  89 AYTVVEPRLRLKLDQLLATWKQR 111
Cdd:cd17011  89 VSSETDESCKKHLGRVLSIWEER 111
CID_SCAF8 cd17004
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8; SR-related and ...
 40-90 1.42e-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: 41.94  E-value: 1.42e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 19114598  40 IVNAIEKHIQKCPPNCKLPALYLLDSI----------SKNLGAPYtyfFGLHLFSTFMSAY 90
Cdd:cd17004  39 VVQSVEKFIQKCKPEYKVPGLYVIDSIvrqsrhqfgqEKDVFAPR---FSNNIISTFQNLY 96
CID_Nrd1_like cd16984
CID (CTD-Interacting Domain) of Nrd1 and similar proteins; This subfamily includes ...
 5-68 3.64e-04

CID (CTD-Interacting Domain) of Nrd1 and similar proteins; This subfamily includes Saccharomyces cerevisiae protein Nrd1, Schizosaccharomyces pombe Rpb7-binding protein Seb1, and similar proteins. Nrd1 cooperates with Nab3 and Sen1, also called the Nrd1-Nab3-Sen1 (NNS) complex, to terminate the transcription by RNA polymerase (Pol) II (RNAPII) of many noncoding RNAs (ncRNAs), including small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), and cryptic unstable transcripts (CUTs). Schizosaccharomyces pombe Seb1 does not function in an NNS-like termination pathway but promotes polyadenylation site selection of coding and noncoding genes. It cotranscriptionally controls alternative polyadenylation. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. Nrd1 CID preferentially interacts with CTD phosphorylated at Ser5. 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: 340781  Cd Length: 145  Bit Score: 41.05  E-value: 3.64e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114598   5 ELDylSALEDLTfNSKPI------IHTLTYIAQENEPYAISIVNAIEKHIQKCPPNCKLPALYLLDSISK 68
Cdd:cd16984   2 EFE--ATLKSLQ-ALKPPgvsgskIKKLTDIAVDNVQSESQIVSKLYRYFKKAPPTHKLGVLYVVDSVVR 68
CID_SFRS15_SCAF4 cd17005
CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15; Splicing factor ...
 40-78 3.03e-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: 38.41  E-value: 3.03e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19114598  40 IVNAIEKHIQKCPPNCKLPALYLLDSI-------------------SKNLGAPYTYFF 78
Cdd:cd17005  39 VVQIVEKFIKKCKPEYKVPGLYVIDSIvrqsrhqfgadkdvfgprfSKNITATFQYLY 96
CID_RPRD1B cd17012
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1B; ...
 18-111 4.56e-03

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: 37.68  E-value: 4.56e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114598  18 NSKPIIHTLTYIAQENEPYAISIVNAIEKHIQKCPPNCKLPALYLLDSI---SKNLGAPYTYFFGLHLFSTFMSAYTVVE 94
Cdd:cd17012  16 NSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSSRKLTFLYLANDViqnSKRKGPEFTREFESVLVDAFSHVAREAD 95

                        90
                ....*....|....*..
gi 19114598  95 PRLRLKLDQLLATWKQR 111
Cdd:cd17012  96 EGCKKPLERLLNIWQER 112
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH