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Conserved domains on  [gi|665408545|ref|NP_001286046|]
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uncharacterized protein Dmel_CG15160, isoform B [Drosophila melanogaster]

Protein Classification

CID of regulation of nuclear pre-mRNA domain-containing protein( domain architecture ID 13015623)

CID (CTD-Interacting Domain) of regulation of nuclear pre-mRNA domain-containing protein, such as RPRD1A, RPRD1B, and RPRD2, which co-purify with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CID_RPRD_like cd16981
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; ...
 7-127 3.56e-51

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: 174.69  E-value: 3.56e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408545   7 EELFETRLEALKDTQEGIQQMSNWCLQHRSNHKKIIQCWLNVFKRVRVDHRLVLFYLANDVIQYSKRKRY-EFVECWATA 85
Cdd:cd16981    1 EEALEKKLRSLNNTQQSIQTLSLWCLFHKKHAKQIVKIWLKELKKAKPERKLTLLYLANDVLQNSRRKGApEFVEAFKKV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 665408545  86 LQRATTMVR---DERVKDKILRIFKIWEQREIYNEEYLSDLSGLL 127
Cdd:cd16981   81 LPEALALVRsegDESVRKKVLRVLNIWEERNVFGSEFLAELRAIL 125
 
Name Accession Description Interval E-value
CID_RPRD_like cd16981
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; ...
 7-127 3.56e-51

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: 174.69  E-value: 3.56e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408545   7 EELFETRLEALKDTQEGIQQMSNWCLQHRSNHKKIIQCWLNVFKRVRVDHRLVLFYLANDVIQYSKRKRY-EFVECWATA 85
Cdd:cd16981    1 EEALEKKLRSLNNTQQSIQTLSLWCLFHKKHAKQIVKIWLKELKKAKPERKLTLLYLANDVLQNSRRKGApEFVEAFKKV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 665408545  86 LQRATTMVR---DERVKDKILRIFKIWEQREIYNEEYLSDLSGLL 127
Cdd:cd16981   81 LPEALALVRsegDESVRKKVLRVLNIWEERNVFGSEFLAELRAIL 125
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
10-128 5.15e-43

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 152.05  E-value: 5.15e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408545    10 FETRLEALKDTQEGIQQMSNWCLQHRSNHKKIIQCWLNVFKRVRVDHRLVLFYLANDVIQYSKRK-RYEFVECWATALQR 88
Cdd:smart00582   2 FEQKLESLNNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKRKyGSEFGDELGPVFQD 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 665408545    89 ATTMVR---DERVKDKILRIFKIWEQREIYNEEYLSDLSGLLN 128
Cdd:smart00582  82 ALRRVLgaaPEELKKKIRRLLNIWEERGIFPPEVLRPLREKLN 124
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 8-120 1.04e-38

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: 139.65  E-value: 1.04e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408545    8 ELFETRLEALKDTQEGIQQMSNWCLQHRSNHKKIIQCWLNVFKRVRVDHRLVLFYLANDVIQYSKRKR-YEFVECWATAL 86
Cdd:pfam04818   1 EALEKKLSSLNNSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSRKKGkSEFADAFEPVL 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 665408545   87 QRATTMV---RDERVKDKILRIFKIWEQREIYNEEYL 120
Cdd:pfam04818  81 PEAFASAykkCDEKLKKKLERLLNIWEERNVFSPEVI 117
 
Name Accession Description Interval E-value
CID_RPRD_like cd16981
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; ...
 7-127 3.56e-51

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: 174.69  E-value: 3.56e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408545   7 EELFETRLEALKDTQEGIQQMSNWCLQHRSNHKKIIQCWLNVFKRVRVDHRLVLFYLANDVIQYSKRKRY-EFVECWATA 85
Cdd:cd16981    1 EEALEKKLRSLNNTQQSIQTLSLWCLFHKKHAKQIVKIWLKELKKAKPERKLTLLYLANDVLQNSRRKGApEFVEAFKKV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 665408545  86 LQRATTMVR---DERVKDKILRIFKIWEQREIYNEEYLSDLSGLL 127
Cdd:cd16981   81 LPEALALVRsegDESVRKKVLRVLNIWEERNVFGSEFLAELRAIL 125
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
10-128 5.15e-43

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 152.05  E-value: 5.15e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408545    10 FETRLEALKDTQEGIQQMSNWCLQHRSNHKKIIQCWLNVFKRVRVDHRLVLFYLANDVIQYSKRK-RYEFVECWATALQR 88
Cdd:smart00582   2 FEQKLESLNNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKRKyGSEFGDELGPVFQD 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 665408545    89 ATTMVR---DERVKDKILRIFKIWEQREIYNEEYLSDLSGLLN 128
Cdd:smart00582  82 ALRRVLgaaPEELKKKIRRLLNIWEERGIFPPEVLRPLREKLN 124
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 8-120 1.04e-38

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: 139.65  E-value: 1.04e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408545    8 ELFETRLEALKDTQEGIQQMSNWCLQHRSNHKKIIQCWLNVFKRVRVDHRLVLFYLANDVIQYSKRKR-YEFVECWATAL 86
Cdd:pfam04818   1 EALEKKLSSLNNSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSRKKGkSEFADAFEPVL 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 665408545   87 QRATTMV---RDERVKDKILRIFKIWEQREIYNEEYL 120
Cdd:pfam04818  81 PEAFASAykkCDEKLKKKLERLLNIWEERNVFSPEVI 117
CID_RPRD1 cd17002
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1 and ...
 5-128 7.35e-32

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: 120.44  E-value: 7.35e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408545   5 FDEELFETRLEALKDTQEGIQQMSNWCLQHRSNHKKIIQCWLNVFKRVRVDHRLVLFYLANDVIQYSKRKRYEFVECWAT 84
Cdd:cd17002    1 FSEAALEKKLAELSNSQQSIQTLSLWLIHHRKHAKTIVRVWLKELRKEKPSKKLTLLYLANDVIQNSRKKGPEFTKEFAP 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 665408545  85 ALQRATTMV---RDERVKDKILRIFKIWEQREIYNEEYLSDLSGLLN 128
Cdd:cd17002   81 VLEDAFKHVaklTDSEVLKALERILNIWKERQVYEKDFIEQLRAALR 127
CID_RPRD2 cd17001
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 2; ...
 7-128 1.77e-30

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: 116.55  E-value: 1.77e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408545   7 EELFETRLEALKDTQEGIQQMSNWCLQHRSNHKKIIQCWLNVFKRVRVDHRLVLFYLANDVIQYSKRKR-YEFVECWATA 85
Cdd:cd17001    3 ESSLDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNaIVFRESFAEV 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 665408545  86 LQRATTMVRDERVKDKILRIFKIWEQREIYNEEYLSDLSGLLN 128
Cdd:cd17001   83 LPEAAALVKDASVSKSVERIFKIWEERNVYPEETIAALKEALS 125
CID_Rtt103 cd17003
CID (CTD-Interacting Domain) of yeast transcription termination factor Rtt103 and similar ...
 7-123 5.88e-25

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: 100.76  E-value: 5.88e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408545   7 EELFETRLEALKDTQEGIQQMSNWCLQHRSNHKKIIQCWLNVFKRVRVDHR--LVLFYLANDVIQYSKRKR-YEFVECWA 83
Cdd:cd17003    1 EEQFISKLNALNETQESIVSISQWVLFHYRHADEIAEIWSDYLLKSSVNSRrkLLLIYLANDVVQQAKAKKkTEFIDAFS 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 665408545  84 TALQRATTMVR---DERVKDKILRIFKIWEQREIYNEEYLSDL 123
Cdd:cd17003   81 KVLPEVLEKIYpslPSDIKKKIKRVVNVWKQRQIFSKDVIDDI 123
CID_RPRD1A cd17011
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A; ...
 5-127 3.29e-24

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: 98.58  E-value: 3.29e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408545   5 FDEELFETRLEALKDTQEGIQQMSNWCLQHRSNHKKIIQCWLNVFKRVRVDHRLVLFYLANDVIQYSKRKRYEFVECWAT 84
Cdd:cd17011    1 FSEAALEKKLSELSNSQQSVQTLSLWLIHHRKHSRPIVTVWERELRKAKPNRKLTFLYLANDVIQNSKRKGPEFTKDFAP 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 665408545  85 ALQRATTMVR---DERVKDKILRIFKIWEQREIYNEEYLSDLSGLL 127
Cdd:cd17011   81 VIVEAFKHVSsetDESCKKHLGRVLSIWEERSVYENDVLEQLKQAL 126
CID_RPRD1B cd17012
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1B; ...
 4-123 2.60e-20

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: 87.37  E-value: 2.60e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408545   4 TFDEELFETRLEALKDTQEGIQQMSNWCLQHRSNHKKIIQCWLNVFKRVRVDHRLVLFYLANDVIQYSKRKRYEFVECWA 83
Cdd:cd17012    1 SFSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSSRKLTFLYLANDVIQNSKRKGPEFTREFE 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 665408545  84 TALQRATTMVR---DERVKDKILRIFKIWEQREIYNEEYLSDL 123
Cdd:cd17012   81 SVLVDAFSHVAreaDEGCKKPLERLLNIWQERSVYGGDFIQQL 123
CID cd03562
CID (CTD-Interacting Domain) family; The CTD-Interacting Domain (CID) is present in several ...
 10-123 1.10e-15

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: 74.09  E-value: 1.10e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408545  10 FETRLEALKD-TQEGIQQMSNWCLQHRSNHKKIIQCWLNVFKRVRVDHRLVLFYLANDVIQYSKRKRYEFVECWATALQR 88
Cdd:cd03562    3 FNSKLEELSDlSQQSITTLTKWAIHHIKHSRPIVTVIEREIRKCKPNRKLTFLYLIDSIIRNSKRKGPEFTKDFSPVIVE 82

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 665408545  89 A---TTMVRDERVKDKILRIFKIWEQREIYNEEYLSDL 123
Cdd:cd03562   83 LfkhVYSETDEDCKKKLGRVLSIWEERNVFENSVLEQL 120
CID_SCAF8_like cd16983
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins; ...
 8-123 1.59e-04

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: 42.21  E-value: 1.59e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408545   8 ELFETRLEALKDTQEG-----IQQMSNWCLQHRSNHKKIIQCWLNVFKRVRVDHRLVLFYLANDVIQYSKRK-------- 74
Cdd:cd16983    1 EEFNKELSSLLDSKPPvskskINAITKLAIKAIKFYKHVVQSVEKFIQKCKPEYKLPGLYVIDSIIRQSRHQygkekdvy 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 665408545  75 --RYEFVECwATALQRATTMVRDervKDKILRIFKIWEQREIYNEEYLSDL 123
Cdd:cd16983   81 apRFAKNLS-KTFLNLLKCPEKD---KPKVKRVLNLWQKNGVFPKEIIQPL 127
CID_Nrd1_like cd16984
CID (CTD-Interacting Domain) of Nrd1 and similar proteins; This subfamily includes ...
 8-127 4.46e-03

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: 38.35  E-value: 4.46e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 665408545   8 ELFETRLEALKDTQE-GIQQ-----MSNWCLQHRSNHKKIIQCWLNVFKRVRVDHRLVLFYLANDVI-QY--SKRKRYEF 78
Cdd:cd16984    1 EEFEATLKSLQALKPpGVSGskikkLTDIAVDNVQSESQIVSKLYRYFKKAPPTHKLGVLYVVDSVVrAWidQAKKNGQS 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 665408545  79 VEC------WATALQRAT----TMVRD------ERVKDKILRIFKIWEQREIYNEEYLSDLSGLL 127
Cdd:cd16984   81 IDSsapdgtFAAGVYKITelieSLMNDaiqsapEDQKEKIKKLVDIWEKGNTFPAEMLNSIKQKL 145
 
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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