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Conserved domains on  [gi|17506321|ref|NP_491403|]
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CID domain-containing protein [Caenorhabditis elegans]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CID_SCAF8_like cd16983
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins; ...
 7-135 3.16e-62

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: 207.08  E-value: 3.16e-62
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17506321   7 KSFNNELSSLFDSK-NMSKNKIQDITKAAIKAKSQYKHVVFSVEKLINKCKPDQRLNVLYVIDSIVRASKHQL-KEKDTF 84
Cdd:cd16983   1 EEFNKELSSLLDSKpPVSKSKINAITKLAIKAIKFYKHVVQSVEKFIQKCKPEYKLPGLYVIDSIIRQSRHQYgKEKDVY 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 17506321  85 GPRFMKQFDKFLMPLLKCGQKEKMRTVRTLNLWMSNKVFKESEIQPLREMC 135
Cdd:cd16983  81 APRFAKNLSKTFLNLLKCPEKDKPKVKRVLNLWQKNGVFPKEIIQPLLDAA 131
RRM_SF super family cl17169
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 523-599 2.16e-10

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


The actual alignment was detected with superfamily member cd12227:

Pssm-ID: 473069 [Multi-domain]  Cd Length: 77  Bit Score: 57.83  E-value: 2.16e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17506321 523 ASRTLWLKKIPTNIVENDLKQAVESCGEASRVKVIGNRACAYITMENRRSANDVVSKMREVSVAKKMVKVYWARSPG 599
Cdd:cd12227   1 CSTTLWVGHLSKKVTQEELKNLFEEYGEIQSIDMIPPRGCAYVCMKTRQDAHRALQKLKNHKLRGKSIKIAWAPNKG 77
Extensin_2 super family cl25884
Extensin-like region;
740-787 1.20e-03

Extensin-like region;


The actual alignment was detected with superfamily member pfam04554:

Pssm-ID: 252669 [Multi-domain]  Cd Length: 57  Bit Score: 37.82  E-value: 1.20e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 17506321   740 NKPPPPMFQQGFnagaPPPPFgrgagPMSSFPPPPRGGMHHMPPPPSF 787
Cdd:pfam04554   3 YKSPPPPVKQYS----PPPPY-----YYKSPPPPVKSPVYKSPPPPVY 41
 
Name Accession Description Interval E-value
CID_SCAF8_like cd16983
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins; ...
 7-135 3.16e-62

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: 207.08  E-value: 3.16e-62
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17506321   7 KSFNNELSSLFDSK-NMSKNKIQDITKAAIKAKSQYKHVVFSVEKLINKCKPDQRLNVLYVIDSIVRASKHQL-KEKDTF 84
Cdd:cd16983   1 EEFNKELSSLLDSKpPVSKSKINAITKLAIKAIKFYKHVVQSVEKFIQKCKPEYKLPGLYVIDSIIRQSRHQYgKEKDVY 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 17506321  85 GPRFMKQFDKFLMPLLKCGQKEKMRTVRTLNLWMSNKVFKESEIQPLREMC 135
Cdd:cd16983  81 APRFAKNLSKTFLNLLKCPEKDKPKVKRVLNLWQKNGVFPKEIIQPLLDAA 131
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
8-136 8.68e-38

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 137.41  E-value: 8.68e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17506321      8 SFNNELSSLfdskNMSKNKIQDITKAAIKAKSQYKHVVFSVEKLINKCKPDQRLNVLYVIDSIVRASKHQ--LKEKDTFG 85
Cdd:smart00582   1 AFEQKLESL----NNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKRKygSEFGDELG 76

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 17506321     86 PRFMKQFDKFLMPLLkcgQKEKMRTVRTLNLWMSNKVFKESEIQPLREMCK 136
Cdd:smart00582  77 PVFQDALRRVLGAAP---EELKKKIRRLLNIWEERGIFPPEVLRPLREKLN 124
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 7-128 1.08e-26

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: 105.37  E-value: 1.08e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17506321     7 KSFNNELSSLfdskNMSKNKIQDITKAAIKAKSQYKHVVFSVEKLINKCKPDQRLNVLYVIDSIVRASKHQLKEKdtFGP 86
Cdd:pfam04818   1 EALEKKLSSL----NNSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSRKKGKSE--FAD 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 17506321    87 RFMKQFDKFLMPLLK-CGQKEKMRTVRTLNLWMSNKVFKESEI 128
Cdd:pfam04818  75 AFEPVLPEAFASAYKkCDEKLKKKLERLLNIWEERNVFSPEVI 117
RRM_SCAF4_SCAF8 cd12227
RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), ...
 523-599 2.16e-10

RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins; This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs.


Pssm-ID: 409674 [Multi-domain]  Cd Length: 77  Bit Score: 57.83  E-value: 2.16e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17506321 523 ASRTLWLKKIPTNIVENDLKQAVESCGEASRVKVIGNRACAYITMENRRSANDVVSKMREVSVAKKMVKVYWARSPG 599
Cdd:cd12227   1 CSTTLWVGHLSKKVTQEELKNLFEEYGEIQSIDMIPPRGCAYVCMKTRQDAHRALQKLKNHKLRGKSIKIAWAPNKG 77
RRM smart00360
RNA recognition motif;
526-592 1.44e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 52.21  E-value: 1.44e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17506321    526 TLWLKKIPTNIVENDLKQAVESCGEASRVKVI------GNRACAYITMENRRSANDVVSKMREVSVAKKMVKV 592
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVrdketgKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
Extensin_2 pfam04554
Extensin-like region;
740-787 1.20e-03

Extensin-like region;


Pssm-ID: 252669 [Multi-domain]  Cd Length: 57  Bit Score: 37.82  E-value: 1.20e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 17506321   740 NKPPPPMFQQGFnagaPPPPFgrgagPMSSFPPPPRGGMHHMPPPPSF 787
Cdd:pfam04554   3 YKSPPPPVKQYS----PPPPY-----YYKSPPPPVKSPVYKSPPPPVY 41
 
Name Accession Description Interval E-value
CID_SCAF8_like cd16983
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins; ...
 7-135 3.16e-62

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: 207.08  E-value: 3.16e-62
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17506321   7 KSFNNELSSLFDSK-NMSKNKIQDITKAAIKAKSQYKHVVFSVEKLINKCKPDQRLNVLYVIDSIVRASKHQL-KEKDTF 84
Cdd:cd16983   1 EEFNKELSSLLDSKpPVSKSKINAITKLAIKAIKFYKHVVQSVEKFIQKCKPEYKLPGLYVIDSIIRQSRHQYgKEKDVY 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 17506321  85 GPRFMKQFDKFLMPLLKCGQKEKMRTVRTLNLWMSNKVFKESEIQPLREMC 135
Cdd:cd16983  81 APRFAKNLSKTFLNLLKCPEKDKPKVKRVLNLWQKNGVFPKEIIQPLLDAA 131
CID_SCAF8 cd17004
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8; SR-related and ...
 7-134 2.56e-40

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: 145.17  E-value: 2.56e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17506321   7 KSFNNELSSLFDSKN-MSKNKIQDITKAAIKAKSQYKHVVFSVEKLINKCKPDQRLNVLYVIDSIVRASKHQL-KEKDTF 84
Cdd:cd17004   1 KTFNSELYSLNDYKPpISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQFgQEKDVF 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|
gi 17506321  85 GPRFMKQFDKFLMPLLKCGQKEKMRTVRTLNLWMSNKVFKESEIQPLREM 134
Cdd:cd17004  81 APRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKNNVFKSEIIQPLLDM 130
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
8-136 8.68e-38

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 137.41  E-value: 8.68e-38
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17506321      8 SFNNELSSLfdskNMSKNKIQDITKAAIKAKSQYKHVVFSVEKLINKCKPDQRLNVLYVIDSIVRASKHQ--LKEKDTFG 85
Cdd:smart00582   1 AFEQKLESL----NNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKRKygSEFGDELG 76

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 17506321     86 PRFMKQFDKFLMPLLkcgQKEKMRTVRTLNLWMSNKVFKESEIQPLREMCK 136
Cdd:smart00582  77 PVFQDALRRVLGAAP---EELKKKIRRLLNIWEERGIFPPEVLRPLREKLN 124
CID_SFRS15_SCAF4 cd17005
CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15; Splicing factor ...
 8-134 2.06e-37

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: 136.63  E-value: 2.06e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17506321   8 SFNNELSSLFDSKN-MSKNKIQDITKAAIKAKSQYKHVVFSVEKLINKCKPDQRLNVLYVIDSIVRASKHQL-KEKDTFG 85
Cdd:cd17005   2 AFNQELFSLMDMKPpISRAKMILITKAAIKAIKLYKHVVQIVEKFIKKCKPEYKVPGLYVIDSIVRQSRHQFgADKDVFG 81

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 17506321  86 PRFMKQFDKFLMPLLKCGQKEKMRTVRTLNLWMSNKVFKESEIQPLREM 134
Cdd:cd17005  82 PRFSKNITATFQYLYLCPSEDKSKIVRVLNLWQKNGVFKIEIIQPLLDM 130
CID cd03562
CID (CTD-Interacting Domain) family; The CTD-Interacting Domain (CID) is present in several ...
 7-134 5.23e-28

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: 109.53  E-value: 5.23e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17506321   7 KSFNNELSSLfdsKNMSKNKIQDITKAAIKAKSQYKHVVFSVEKLINKCKPDQRLNVLYVIDSIVRASKHQlkeKDTFGP 86
Cdd:cd03562   1 KAFNSKLEEL---SDLSQQSITTLTKWAIHHIKHSRPIVTVIEREIRKCKPNRKLTFLYLIDSIIRNSKRK---GPEFTK 74

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 17506321  87 RFMKQ-FDKFLMPLLKCGQKEKMRTVRTLNLWMSNKVFKESEIQPLREM 134
Cdd:cd03562  75 DFSPViVELFKHVYSETDEDCKKKLGRVLSIWEERNVFENSVLEQLKQA 123
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 7-128 1.08e-26

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: 105.37  E-value: 1.08e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17506321     7 KSFNNELSSLfdskNMSKNKIQDITKAAIKAKSQYKHVVFSVEKLINKCKPDQRLNVLYVIDSIVRASKHQLKEKdtFGP 86
Cdd:pfam04818   1 EALEKKLSSL----NNSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSRKKGKSE--FAD 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 17506321    87 RFMKQFDKFLMPLLK-CGQKEKMRTVRTLNLWMSNKVFKESEI 128
Cdd:pfam04818  75 AFEPVLPEAFASAYKkCDEKLKKKLERLLNIWEERNVFSPEVI 117
RRM_SCAF4_SCAF8 cd12227
RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), ...
 523-599 2.16e-10

RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins; This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs.


Pssm-ID: 409674 [Multi-domain]  Cd Length: 77  Bit Score: 57.83  E-value: 2.16e-10
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 17506321 523 ASRTLWLKKIPTNIVENDLKQAVESCGEASRVKVIGNRACAYITMENRRSANDVVSKMREVSVAKKMVKVYWARSPG 599
Cdd:cd12227   1 CSTTLWVGHLSKKVTQEELKNLFEEYGEIQSIDMIPPRGCAYVCMKTRQDAHRALQKLKNHKLRGKSIKIAWAPNKG 77
RRM smart00360
RNA recognition motif;
526-592 1.44e-08

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 52.21  E-value: 1.44e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17506321    526 TLWLKKIPTNIVENDLKQAVESCGEASRVKVI------GNRACAYITMENRRSANDVVSKMREVSVAKKMVKV 592
Cdd:smart00360   1 TLFVGNLPPDTTEEELRELFSKFGKVESVRLVrdketgKSKGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
RRM_SCAF8 cd12462
RNA recognition motif (RRM) found in SR-related and CTD-associated factor 8 (SCAF8) and ...
 524-599 8.62e-08

RNA recognition motif (RRM) found in SR-related and CTD-associated factor 8 (SCAF8) and similar proteins; This subgroup corresponds to the RRM of SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8), a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8, together with SCAF4, represents a new class of SCAFs (SR-like CTD-associated factors). They contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and serine/arginine-rich motifs.


Pssm-ID: 409895 [Multi-domain]  Cd Length: 79  Bit Score: 50.46  E-value: 8.62e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 17506321 524 SRTLWLKKIPTNIVENDLKQAVESCGEASRVKVIGNRACAYITMENRRSANDVVSKMREVS--VAKKMVKVYWARSPG 599
Cdd:cd12462   2 STTLWVGQVDKKATQQDLTNLFEEFGQIESINMIPPRGCAYVCMVHRQDAYRALQKLSTGSfkIGSKIIKIAWALNKG 79
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 527-592 1.56e-07

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 49.20  E-value: 1.56e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 17506321 527 LWLKKIPTNIVENDLKQAVESCGEASRVKVI-----GNRACAYITMENRRSANDVVSKMREVSVAKKMVKV 592
Cdd:cd00590   1 LFVGNLPPDTTEEDLRELFSKFGEVVSVRIVrdrdgKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKV 71
CID_Pcf11 cd16982
CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied ...
 9-72 3.98e-07

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: 49.87  E-value: 3.98e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 17506321   9 FNNELSSLfdsKNMSKNKIQDITKAAIKAKSQYKHVVFSVEKLINKCKPDQRLNVLYVIDSIVR 72
Cdd:cd16982   4 YRSALAEL---TFNSKPIINNLTMLAEENIQAAQAIVEAIEERIRKVPPEQKLPALYLLDSIVK 64
RRM_SCAF4 cd12461
RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4) and ...
 522-599 8.45e-07

RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins; The CD corresponds to the RRM of SCAF4 (also termed splicing factor, arginine/serine-rich 15 or SFR15, or CTD-binding SR-like protein RA4) that belongs to a new class of SCAFs (SR-like CTD-associated factors). Although its biological function remains unclear, SCAF4 shows high sequence similarity to SCAF8 that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II) and may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF4 and SCAF8 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and serine/arginine-rich motifs.


Pssm-ID: 409894 [Multi-domain]  Cd Length: 81  Bit Score: 47.73  E-value: 8.45e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17506321 522 IASRTLWLKKIPTNIVENDLKQAVESCGEASRVKVIGNRACAYITMENRRSANDVVSKMRE--VSVAKKMVKVYWARSPG 599
Cdd:cd12461   2 VCSTTLWVGQLDKRTTQQDVASLLEEFGQIESINMIPPRGCAYIVMVHRQDAYRALQKLSRgnYKVNQKSIKIAWALNKG 81
CID_Nrd1_like cd16984
CID (CTD-Interacting Domain) of Nrd1 and similar proteins; This subfamily includes ...
 9-79 2.13e-05

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: 45.29  E-value: 2.13e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17506321   9 FNNELSSLFDSKN--MSKNKIQDITKAA---IKAKSQYkhvvfsVEKLINKCK---PDQRLNVLYVIDSIVRASKHQLK 79
Cdd:cd16984   3 FEATLKSLQALKPpgVSGSKIKKLTDIAvdnVQSESQI------VSKLYRYFKkapPTHKLGVLYVVDSVVRAWIDQAK 75
RRM2_4_MRN1 cd12262
RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar ...
 523-596 1.94e-04

RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins; This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain).


Pssm-ID: 409706 [Multi-domain]  Cd Length: 78  Bit Score: 40.84  E-value: 1.94e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 17506321 523 ASRTLWLKKIPTNIVENDLKQAVESCGEASRVKVIGNRACAYITMENRRSANDVVSKMREVSVAKKMVKVYWAR 596
Cdd:cd12262   2 ASRNVYVGNLDDSLTEEEIRGILEKYGEIESIKILKEKNCAFVNYLNIANAIKAVQELPIKNPKFKKVRINYGK 75
CID_RPRD_like cd16981
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; ...
 27-135 2.70e-04

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: 41.80  E-value: 2.70e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17506321  27 IQDITKAAIKAKSQYKHVVFSVEKLINKCKPDQRLNVLYVIDSIVRASKHQlkekdtFGPRFMKQFDKFL---MPLLKCG 103
Cdd:cd16981  18 IQTLSLWCLFHKKHAKQIVKIWLKELKKAKPERKLTLLYLANDVLQNSRRK------GAPEFVEAFKKVLpeaLALVRSE 91

                        90       100       110
                ....*....|....*....|....*....|....
gi 17506321 104 QKEKMRTV--RTLNLWMSNKVFKESEIQPLREMC 135
Cdd:cd16981  92 GDESVRKKvlRVLNIWEERNVFGSEFLAELRAIL 125
CID_RPRD1A cd17011
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A; ...
 23-133 3.76e-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: 41.57  E-value: 3.76e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17506321  23 SKNKIQDITKAAIKAKSQYKHVVFSVEKLINKCKPDQRLNVLYVIDSIVRASKHQlkekdtfGPRFMKQFDKFLMPLLKC 102
Cdd:cd17011  16 SQQSVQTLSLWLIHHRKHSRPIVTVWERELRKAKPNRKLTFLYLANDVIQNSKRK-------GPEFTKDFAPVIVEAFKH 88

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 17506321 103 GQKE-----KMRTVRTLNLWMSNKVFKESEIQPLRE 133
Cdd:cd17011  89 VSSEtdescKKHLGRVLSIWEERSVYENDVLEQLKQ 124
Extensin_2 pfam04554
Extensin-like region;
740-787 1.20e-03

Extensin-like region;


Pssm-ID: 252669 [Multi-domain]  Cd Length: 57  Bit Score: 37.82  E-value: 1.20e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 17506321   740 NKPPPPMFQQGFnagaPPPPFgrgagPMSSFPPPPRGGMHHMPPPPSF 787
Cdd:pfam04554   3 YKSPPPPVKQYS----PPPPY-----YYKSPPPPVKSPVYKSPPPPVY 41
CID_RPRD1 cd17002
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1 and ...
 50-133 2.60e-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: 38.78  E-value: 2.60e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17506321  50 KLINKCKPDQRLNVLYVIDSIVRASKHQlkekdtfGPRFMKQFDKFLMPLLK-----CGQKEKMRTVRTLNLWMSNKVFK 124
Cdd:cd17002  43 KELRKEKPSKKLTLLYLANDVIQNSRKK-------GPEFTKEFAPVLEDAFKhvaklTDSEVLKALERILNIWKERQVYE 115


                ....*....
gi 17506321 125 ESEIQPLRE 133
Cdd:cd17002 116 KDFIEQLRA 124
 
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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