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Conserved domains on  [gi|190016443|pdb|3D9O|B]
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Chain B, RNA-binding protein 16

Protein Classification

CID_SCAF8 domain-containing protein( domain architecture ID 13017452)

CID_SCAF8 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CID_SCAF8 cd17004
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8; SR-related and ...
 5-135 8.86e-92

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: 261.89  E-value: 8.86e-92
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3D9O_B        5 KTFNSELYSL*D*KPPISKAK*TQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVF 84
Cdd:cd17004   1 KTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVF 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
3D9O_B       85 APRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLD*A 135
Cdd:cd17004  81 APRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLDMA 131
 
Name Accession Description Interval E-value
CID_SCAF8 cd17004
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8; SR-related and ...
 5-135 8.86e-92

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: 261.89  E-value: 8.86e-92
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3D9O_B        5 KTFNSELYSL*D*KPPISKAK*TQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVF 84
Cdd:cd17004   1 KTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVF 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
3D9O_B       85 APRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLD*A 135
Cdd:cd17004  81 APRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLDMA 131
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 5-128 4.74e-31

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: 107.68  E-value: 4.74e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3D9O_B          5 KTFNSELYSL*D*kppiSKAK*TQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEkdvF 84
Cdd:pfam04818   1 EALEKKLSSLNN-----SQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSRKKGKSE---F 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
3D9O_B         85 APRFSNNIISTFQNLYR-CPGDDKSKIVRVLNLWQKNNVFKSEII 128
Cdd:pfam04818  73 ADAFEPVLPEAFASAYKkCDEKLKKKLERLLNIWEERNVFSPEVI 117
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
6-131 5.24e-31

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 107.75  E-value: 5.24e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3D9O_B           6 TFNSELYSL*d*kppISKAK*TQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFG-QEKDVF 84
Cdd:smart00582   1 AFEQKLESLN-----NSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKRKYGsEFGDEL 75

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
3D9O_B          85 APRFSNNIISTFQNLYRcpgDDKSKIVRVLNLWQKNNVFKSEIIQPL 131
Cdd:smart00582  76 GPVFQDALRRVLGAAPE---ELKKKIRRLLNIWEERGIFPPEVLRPL 119
 
Name Accession Description Interval E-value
CID_SCAF8 cd17004
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8; SR-related and ...
 5-135 8.86e-92

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: 261.89  E-value: 8.86e-92
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3D9O_B        5 KTFNSELYSL*D*KPPISKAK*TQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVF 84
Cdd:cd17004   1 KTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVF 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
3D9O_B       85 APRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLD*A 135
Cdd:cd17004  81 APRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLDMA 131
CID_SCAF8_like cd16983
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins; ...
 5-135 1.77e-77

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: 225.57  E-value: 1.77e-77
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3D9O_B        5 KTFNSELYSL*D*KPPISKAK*TQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVF 84
Cdd:cd16983   1 EEFNKELSSLLDSKPPVSKSKINAITKLAIKAIKFYKHVVQSVEKFIQKCKPEYKLPGLYVIDSIIRQSRHQYGKEKDVY 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
3D9O_B       85 APRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLD*A 135
Cdd:cd16983  81 APRFAKNLSKTFLNLLKCPEKDKPKVKRVLNLWQKNGVFPKEIIQPLLDAA 131
CID_SFRS15_SCAF4 cd17005
CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15; Splicing factor ...
 7-135 1.05e-75

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: 221.38  E-value: 1.05e-75
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3D9O_B        7 FNSELYSL*D*KPPISKAK*TQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEKDVFAP 86
Cdd:cd17005   3 FNQELFSLMDMKPPISRAKMILITKAAIKAIKLYKHVVQIVEKFIKKCKPEYKVPGLYVIDSIVRQSRHQFGADKDVFGP 82

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
3D9O_B       87 RFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLD*A 135
Cdd:cd17005  83 RFSKNITATFQYLYLCPSEDKSKIVRVLNLWQKNGVFKIEIIQPLLDMA 131
CID cd03562
CID (CTD-Interacting Domain) family; The CTD-Interacting Domain (CID) is present in several ...
 5-133 8.45e-52

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: 160.38  E-value: 8.45e-52
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3D9O_B        5 KTFNSELYSL*D*kppiSKAK*TQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQfgqeKDVF 84
Cdd:cd03562   1 KAFNSKLEELSDL----SQQSITTLTKWAIHHIKHSRPIVTVIEREIRKCKPNRKLTFLYLIDSIIRNSKRK----GPEF 72

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|
3D9O_B       85 APRFSNNIISTFQNLYR-CPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLD 133
Cdd:cd03562  73 TKDFSPVIVELFKHVYSeTDEDCKKKLGRVLSIWEERNVFENSVLEQLKQ 122
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 5-128 4.74e-31

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: 107.68  E-value: 4.74e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3D9O_B          5 KTFNSELYSL*D*kppiSKAK*TQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEkdvF 84
Cdd:pfam04818   1 EALEKKLSSLNN-----SQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSRKKGKSE---F 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
3D9O_B         85 APRFSNNIISTFQNLYR-CPGDDKSKIVRVLNLWQKNNVFKSEII 128
Cdd:pfam04818  73 ADAFEPVLPEAFASAYKkCDEKLKKKLERLLNIWEERNVFSPEVI 117
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
6-131 5.24e-31

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 107.75  E-value: 5.24e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3D9O_B           6 TFNSELYSL*d*kppISKAK*TQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFG-QEKDVF 84
Cdd:smart00582   1 AFEQKLESLN-----NSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKRKYGsEFGDEL 75

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*..
3D9O_B          85 APRFSNNIISTFQNLYRcpgDDKSKIVRVLNLWQKNNVFKSEIIQPL 131
Cdd:smart00582  76 GPVFQDALRRVLGAAPE---ELKKKIRRLLNIWEERGIFPPEVLRPL 119
CID_Nrd1_like cd16984
CID (CTD-Interacting Domain) of Nrd1 and similar proteins; This subfamily includes ...
 7-131 3.31e-17

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: 73.02  E-value: 3.31e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3D9O_B        7 FNSELYSL*D*KPP-ISKAK*TQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQ---FGQEKD 82
Cdd:cd16984   3 FEATLKSLQALKPPgVSGSKIKKLTDIAVDNVQSESQIVSKLYRYFKKAPPTHKLGVLYVVDSVVRAWIDQakkNGQSID 82

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*....
3D9O_B       83 VFAP---------RFSNNIISTFQNLYR-CPGDDKSKIVRVLNLWQKNNVFKSEIIQPL 131
Cdd:cd16984  83 SSAPdgtfaagvyKITELIESLMNDAIQsAPEDQKEKIKKLVDIWEKGNTFPAEMLNSI 141
CID_Pcf11 cd16982
CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied ...
 6-117 7.35e-13

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: 61.04  E-value: 7.35e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3D9O_B        6 TFNSelysl*d*KPPIskak*TQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVrqsrhqfgqeKDV-- 83
Cdd:cd16982  12 TFNS--------KPII-----NNLTMLAEENIQAAQAIVEAIEERIRKVPPEQKLPALYLLDSIV----------KNVgg 68

                        90       100       110
                ....*....|....*....|....*....|....*.
3D9O_B       84 -FAPRFSNNIISTFQNLYR-CPGDDKSKIVRVLNLW 117
Cdd:cd16982  69 pYTSLFSPNLVDLFLDAYRlVDEKTRKKLEKLLNTW 104
CID_Rtt103 cd17003
CID (CTD-Interacting Domain) of yeast transcription termination factor Rtt103 and similar ...
 59-131 4.75e-09

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: 51.07  E-value: 4.75e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
3D9O_B       59 KVPGLYVIDSIVRQSRHQfgqEKDVFAPRFSNNIISTFQNLYR-CPGDDKSKIVRVLNLWQKNNVFKSEIIQPL 131
Cdd:cd17003  53 KLLLIYLANDVVQQAKAK---KKTEFIDAFSKVLPEVLEKIYPsLPSDIKKKIKRVVNVWKQRQIFSKDVIDDI 123
CID_RPRD_like cd16981
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; ...
 38-133 1.53e-06

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: 44.49  E-value: 1.53e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3D9O_B       38 KFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFGQEkdvFAPRFSNNIISTFQnLYRCPGDD--KSKIVRVLN 115
Cdd:cd16981  30 KHAKQIVKIWLKELKKAKPERKLTLLYLANDVLQNSRRKGAPE---FVEAFKKVLPEALA-LVRSEGDEsvRKKVLRVLN 105

                        90
                ....*....|....*...
3D9O_B      116 LWQKNNVFKSEIIQPLLD 133
Cdd:cd16981 106 IWEERNVFGSEFLAELRA 123
CID_RPRD1B cd17012
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1B; ...
 37-131 2.71e-06

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: 43.84  E-value: 2.71e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3D9O_B       37 IKFYKH---VVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQfGQEkdvFAPRFSNNIISTFQNLYRcPGDD--KSKIV 111
Cdd:cd17012  29 IHHRKHagpIVSVWHRELRKAKSSRKLTFLYLANDVIQNSKRK-GPE---FTREFESVLVDAFSHVAR-EADEgcKKPLE 103

                        90       100
                ....*....|....*....|
3D9O_B      112 RVLNLWQKNNVFKSEIIQPL 131
Cdd:cd17012 104 RLLNIWQERSVYGGDFIQQL 123
CID_RPRD1A cd17011
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A; ...
 38-131 5.40e-06

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: 43.11  E-value: 5.40e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3D9O_B       38 KFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQfGQEkdvFAPRFSNNIISTFQNLYRcPGDD--KSKIVRVLN 115
Cdd:cd17011  32 KHSRPIVTVWERELRKAKPNRKLTFLYLANDVIQNSKRK-GPE---FTKDFAPVIVEAFKHVSS-ETDEscKKHLGRVLS 106

                        90
                ....*....|....*.
3D9O_B      116 LWQKNNVFKSEIIQPL 131
Cdd:cd17011 107 IWEERSVYENDVLEQL 122
CID_RPRD1 cd17002
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1 and ...
 37-131 8.94e-03

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: 34.16  E-value: 8.94e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3D9O_B       37 IKFYKH---VVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQfGQEkdvFAPRFSNNIISTFQNLYRCPGDD-KSKIVR 112
Cdd:cd17002  28 IHHRKHaktIVRVWLKELRKEKPSKKLTLLYLANDVIQNSRKK-GPE---FTKEFAPVLEDAFKHVAKLTDSEvLKALER 103

                        90
                ....*....|....*....
3D9O_B      113 VLNLWQKNNVFKSEIIQPL 131
Cdd:cd17002 104 ILNIWKERQVYEKDFIEQL 122
 
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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