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Conserved domains on  [gi|56382023|gb|AAV85730|]
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At5g10060 [Arabidopsis thaliana]

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; ...
 8-130 8.75e-59

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; This family is composed of Regulation of nuclear pre-mRNA domain-containing proteins 1A (RPRD1A), 1B (RPRD1B), 2 (RPRD2), yeast Rtt103, and similar proteins. RPRD1A, RPRD1B, and RPRD2 are CID (CTD-Interacting Domain) containing proteins that co-purify with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. Yeast transcription termination factor Rtt103 is a CID containing protein that functions in DNA damage response. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


:

Pssm-ID: 340778  Cd Length: 125  Bit Score: 189.33  E-value: 8.75e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56382023   8 QILIDKLAKLNSSQQSIETLSHWCIFNRSKAELIVTTWEKQFHSTEMDQKVPLLYLANDILQNSKRQG-NEFVQEFWNVL 86
Cdd:cd16981   2 EALEKKLRSLNNTQQSIQTLSLWCLFHKKHAKQIVKIWLKELKKAKPERKLTLLYLANDVLQNSRRKGaPEFVEAFKKVL 81

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
gi 56382023  87 PKALKDIVSQGDDNGKSAVARVIKIWEERRVFGSRSKSLKDVML 130
Cdd:cd16981  82 PEALALVRSEGDESVRKKVLRVLNIWEERNVFGSEFLAELRAIL 125
PRK03918 super family cl35229
DNA double-strand break repair ATPase Rad50;
169-291 5.12e-03

DNA double-strand break repair ATPase Rad50;


The actual alignment was detected with superfamily member PRK03918:

Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 39.28  E-value: 5.12e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56382023  169 AEKIASAYHLVVAENSNEEAEMNKCKSAVKRIRKMEKDVEEACSTAKDNPKRKSLAKELeeeeyllrqciEKLKSvqgsr 248
Cdd:PRK03918 237 KEEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELEEKVKELKELKEKAEEY-----------IKLSE----- 300

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 56382023  249 ssLVNQLKDALREQESELDNLKAQIQVAKEQTEEAQNMQKRLN 291
Cdd:PRK03918 301 --FYEEYLDELREIEKRLSRLEEEINGIEERIKELEEKEERLE 341
 
Name Accession Description Interval E-value
CID_RPRD_like cd16981
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; ...
 8-130 8.75e-59

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; This family is composed of Regulation of nuclear pre-mRNA domain-containing proteins 1A (RPRD1A), 1B (RPRD1B), 2 (RPRD2), yeast Rtt103, and similar proteins. RPRD1A, RPRD1B, and RPRD2 are CID (CTD-Interacting Domain) containing proteins that co-purify with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. Yeast transcription termination factor Rtt103 is a CID containing protein that functions in DNA damage response. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340778  Cd Length: 125  Bit Score: 189.33  E-value: 8.75e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56382023   8 QILIDKLAKLNSSQQSIETLSHWCIFNRSKAELIVTTWEKQFHSTEMDQKVPLLYLANDILQNSKRQG-NEFVQEFWNVL 86
Cdd:cd16981   2 EALEKKLRSLNNTQQSIQTLSLWCLFHKKHAKQIVKIWLKELKKAKPERKLTLLYLANDVLQNSRRKGaPEFVEAFKKVL 81

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
gi 56382023  87 PKALKDIVSQGDDNGKSAVARVIKIWEERRVFGSRSKSLKDVML 130
Cdd:cd16981  82 PEALALVRSEGDESVRKKVLRVLNIWEERNVFGSEFLAELRAIL 125
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 8-120 1.11e-44

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: 151.98  E-value: 1.11e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56382023     8 QILIDKLAKLNSSQQSIETLSHWCIFNRSKAELIVTTWEKQFHSTEMDQKVPLLYLANDILQNSKRQG-NEFVQEFWNVL 86
Cdd:pfam04818   1 EALEKKLSSLNNSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSRKKGkSEFADAFEPVL 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 56382023    87 PKALKDIVSQGDDNGKSAVARVIKIWEERRVFGS 120
Cdd:pfam04818  81 PEAFASAYKKCDEKLKKKLERLLNIWEERNVFSP 114
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
10-130 1.25e-40

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 141.65  E-value: 1.25e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56382023     10 LIDKLAKLNSSQQSIETLSHWCIFNRSKAELIVTTWEKQFHSTEMDQKVPLLYLANDILQNSKRQ-GNEFVQEFWNVLPK 88
Cdd:smart00582   2 FEQKLESLNNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKRKyGSEFGDELGPVFQD 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 56382023     89 ALKDIVSQGDDNGKSAVARVIKIWEERRVFGSRSKSLKDVML 130
Cdd:smart00582  82 ALRRVLGAAPEELKKKIRRLLNIWEERGIFPPEVLRPLREKL 123
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
169-291 5.12e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 39.28  E-value: 5.12e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56382023  169 AEKIASAYHLVVAENSNEEAEMNKCKSAVKRIRKMEKDVEEACSTAKDNPKRKSLAKELeeeeyllrqciEKLKSvqgsr 248
Cdd:PRK03918 237 KEEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELEEKVKELKELKEKAEEY-----------IKLSE----- 300

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 56382023  249 ssLVNQLKDALREQESELDNLKAQIQVAKEQTEEAQNMQKRLN 291
Cdd:PRK03918 301 --FYEEYLDELREIEKRLSRLEEEINGIEERIKELEEKEERLE 341
 
Name Accession Description Interval E-value
CID_RPRD_like cd16981
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; ...
 8-130 8.75e-59

CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; This family is composed of Regulation of nuclear pre-mRNA domain-containing proteins 1A (RPRD1A), 1B (RPRD1B), 2 (RPRD2), yeast Rtt103, and similar proteins. RPRD1A, RPRD1B, and RPRD2 are CID (CTD-Interacting Domain) containing proteins that co-purify with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. Yeast transcription termination factor Rtt103 is a CID containing protein that functions in DNA damage response. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340778  Cd Length: 125  Bit Score: 189.33  E-value: 8.75e-59
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56382023   8 QILIDKLAKLNSSQQSIETLSHWCIFNRSKAELIVTTWEKQFHSTEMDQKVPLLYLANDILQNSKRQG-NEFVQEFWNVL 86
Cdd:cd16981   2 EALEKKLRSLNNTQQSIQTLSLWCLFHKKHAKQIVKIWLKELKKAKPERKLTLLYLANDVLQNSRRKGaPEFVEAFKKVL 81

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
gi 56382023  87 PKALKDIVSQGDDNGKSAVARVIKIWEERRVFGSRSKSLKDVML 130
Cdd:cd16981  82 PEALALVRSEGDESVRKKVLRVLNIWEERNVFGSEFLAELRAIL 125
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 8-120 1.11e-44

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: 151.98  E-value: 1.11e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56382023     8 QILIDKLAKLNSSQQSIETLSHWCIFNRSKAELIVTTWEKQFHSTEMDQKVPLLYLANDILQNSKRQG-NEFVQEFWNVL 86
Cdd:pfam04818   1 EALEKKLSSLNNSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSRKKGkSEFADAFEPVL 80

                          90       100       110
                  ....*....|....*....|....*....|....
gi 56382023    87 PKALKDIVSQGDDNGKSAVARVIKIWEERRVFGS 120
Cdd:pfam04818  81 PEAFASAYKKCDEKLKKKLERLLNIWEERNVFSP 114
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
10-130 1.25e-40

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 141.65  E-value: 1.25e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56382023     10 LIDKLAKLNSSQQSIETLSHWCIFNRSKAELIVTTWEKQFHSTEMDQKVPLLYLANDILQNSKRQ-GNEFVQEFWNVLPK 88
Cdd:smart00582   2 FEQKLESLNNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKRKyGSEFGDELGPVFQD 81

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 56382023     89 ALKDIVSQGDDNGKSAVARVIKIWEERRVFGSRSKSLKDVML 130
Cdd:smart00582  82 ALRRVLGAAPEELKKKIRRLLNIWEERGIFPPEVLRPLREKL 123
CID_RPRD1 cd17002
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1 and ...
 5-118 1.36e-39

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: 138.93  E-value: 1.36e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56382023   5 FSDQILIDKLAKLNSSQQSIETLSHWCIFNRSKAELIVTTWEKQFHSTEMDQKVPLLYLANDILQNSKRQGNEFVQEFWN 84
Cdd:cd17002   1 FSEAALEKKLAELSNSQQSIQTLSLWLIHHRKHAKTIVRVWLKELRKEKPSKKLTLLYLANDVIQNSRKKGPEFTKEFAP 80

                        90       100       110
                ....*....|....*....|....*....|....
gi 56382023  85 VLPKALKDIVSQGDDNGKSAVARVIKIWEERRVF 118
Cdd:cd17002  81 VLEDAFKHVAKLTDSEVLKALERILNIWKERQVY 114
CID_RPRD1A cd17011
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A; ...
 5-118 1.05e-32

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: 120.53  E-value: 1.05e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56382023   5 FSDQILIDKLAKLNSSQQSIETLSHWCIFNRSKAELIVTTWEKQFHSTEMDQKVPLLYLANDILQNSKRQGNEFVQEFWN 84
Cdd:cd17011   1 FSEAALEKKLSELSNSQQSVQTLSLWLIHHRKHSRPIVTVWERELRKAKPNRKLTFLYLANDVIQNSKRKGPEFTKDFAP 80

                        90       100       110
                ....*....|....*....|....*....|....
gi 56382023  85 VLPKALKDIVSQGDDNGKSAVARVIKIWEERRVF 118
Cdd:cd17011  81 VIVEAFKHVSSETDESCKKHLGRVLSIWEERSVY 114
CID_RPRD1B cd17012
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1B; ...
 5-120 4.10e-29

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: 110.87  E-value: 4.10e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56382023   5 FSDQILIDKLAKLNSSQQSIETLSHWCIFNRSKAELIVTTWEKQFHSTEMDQKVPLLYLANDILQNSKRQGNEFVQEFWN 84
Cdd:cd17012   2 FSESALEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSSRKLTFLYLANDVIQNSKRKGPEFTREFES 81

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 56382023  85 VLPKALKDIVSQGDDNGKSAVARVIKIWEERRVFGS 120
Cdd:cd17012  82 VLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGG 117
CID_Rtt103 cd17003
CID (CTD-Interacting Domain) of yeast transcription termination factor Rtt103 and similar ...
 8-118 7.84e-26

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: 101.92  E-value: 7.84e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56382023   8 QILIDKLAKLNSSQQSIETLSHWCIFNRSKAELIVTTWEKQFHSTEMD--QKVPLLYLANDILQNSKRQG-NEFVQEFWN 84
Cdd:cd17003   2 EQFISKLNALNETQESIVSISQWVLFHYRHADEIAEIWSDYLLKSSVNsrRKLLLIYLANDVVQQAKAKKkTEFIDAFSK 81

                        90       100       110
                ....*....|....*....|....*....|....
gi 56382023  85 VLPKALKDIVSQGDDNGKSAVARVIKIWEERRVF 118
Cdd:cd17003  82 VLPEVLEKIYPSLPSDIKKKIKRVVNVWKQRQIF 115
CID cd03562
CID (CTD-Interacting Domain) family; The CTD-Interacting Domain (CID) is present in several ...
 18-118 1.89e-19

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: 84.11  E-value: 1.89e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56382023  18 NSSQQSIETLSHWCIFNRSKAELIVTTWEKQFHSTEMDQKVPLLYLANDILQNSKRQGNEFVQEFWNVLPKALKDIVSQG 97
Cdd:cd03562  12 DLSQQSITTLTKWAIHHIKHSRPIVTVIEREIRKCKPNRKLTFLYLIDSIIRNSKRKGPEFTKDFSPVIVELFKHVYSET 91

                        90       100
                ....*....|....*....|.
gi 56382023  98 DDNGKSAVARVIKIWEERRVF 118
Cdd:cd03562  92 DEDCKKKLGRVLSIWEERNVF 112
CID_RPRD2 cd17001
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 2; ...
 13-118 1.30e-15

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: 73.03  E-value: 1.30e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56382023  13 KLAKLNSSQQSIETLSHWCIFNRSKAELIVTTWEKQFHSTEMDQKVPLLYLANDILQNSKRQGN-EFVQEFWNVLPKALK 91
Cdd:cd17001   9 KFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAiVFRESFAEVLPEAAA 88

                        90       100
                ....*....|....*....|....*..
gi 56382023  92 DIvsqGDDNGKSAVARVIKIWEERRVF 118
Cdd:cd17001  89 LV---KDASVSKSVERIFKIWEERNVY 112
CID_Pcf11 cd16982
CID (CTD-Interacting Domain) of Pcf11; Pcf11 is conserved across eukaryotes. The best studied ...
 12-116 1.80e-06

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: 46.79  E-value: 1.80e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56382023  12 DKLAKL-NSSQQSIETLSHWCIFNRSKAELIVTTWEKQFHSTEMDQKVPLLYLANDILQNSkrqGNEFVQEFWNVLPKAL 90
Cdd:cd16982   6 SALAELtFNSKPIINNLTMLAEENIQAAQAIVEAIEERIRKVPPEQKLPALYLLDSIVKNV---GGPYTSLFSPNLVDLF 82

                        90       100
                ....*....|....*....|....*.
gi 56382023  91 KDIVSQGDDNGKSAVARVIKIWEERR 116
Cdd:cd16982  83 LDAYRLVDEKTRKKLEKLLNTWKTVF 108
CID_SCAF8_like cd16983
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins; ...
 15-118 4.37e-06

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: 46.07  E-value: 4.37e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56382023  15 AKLNSSQQSIETLSHWCIFNRSKAELIVTTWEKQFHSTEMDQKVPLLYLANDILQNSKRQ----GNEFVQEFWNVLPKAL 90
Cdd:cd16983  13 SKPPVSKSKINAITKLAIKAIKFYKHVVQSVEKFIQKCKPEYKLPGLYVIDSIIRQSRHQygkeKDVYAPRFAKNLSKTF 92

                        90       100
                ....*....|....*....|....*...
gi 56382023  91 KDIVSQGDDNgKSAVARVIKIWEERRVF 118
Cdd:cd16983  93 LNLLKCPEKD-KPKVKRVLNLWQKNGVF 119
CTK3 pfam12243
CTD kinase subunit gamma CTK3; The C-terminal domain kinase (CTDK-1), is a three-subunit ...
 14-117 9.52e-05

CTD kinase subunit gamma CTK3; The C-terminal domain kinase (CTDK-1), is a three-subunit complex comprised of Ctk1, Ctk2, and Ctk3, that plays a key role in regulation of transcription and translation and in coordinating these two processes. Both Ctk2 and Ctk3 are regulated at the level of protein turnover, and are unstable proteins processed through a ubiquitin-proteasome pathway. Their physical interaction is required to protect both subunits from degradation, and both Ctk2 and Ctk3 are required for Ctk1 CTD kinase activation. The mammalian P-TEFb is mirrored by the combined complexes in yeast of the CTDK1 and the Bur1/2.


Pssm-ID: 403455  Cd Length: 123  Bit Score: 42.04  E-value: 9.52e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56382023    14 LAKLNSSQQSIETLSHWCIFNRSKAELIVTTWEKQFHSTEMDQKVPLLYLANDILQNSKRQGNEF---VQEFWNVLPKAL 90
Cdd:pfam12243  13 LRKLNASVQSLQKAAHFALKNRDLEEDLHSCILEQLERGDLNTRANIFYFIDTLCEESLKNGQSGkpyVRSLKRDIPRLV 92

                          90       100
                  ....*....|....*....|....*....
gi 56382023    91 KDIVSQGDDNGKSA--VARVIKIWEERRV 117
Cdd:pfam12243  93 DSVAPDDGSGAANVksVRKILQSLKLKSL 121
CID_SCAF8 cd17004
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8; SR-related and ...
 41-120 2.67e-03

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: 38.09  E-value: 2.67e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56382023  41 IVTTWEKQFHSTEMDQKVPLLYLANDILQNSKRQgneFVQEFWNVLPKALKDIVSQ--------GDDngKSAVARVIKIW 112
Cdd:cd17004  39 VVQSVEKFIQKCKPEYKVPGLYVIDSIVRQSRHQ---FGQEKDVFAPRFSNNIISTfqnlyrcpGDD--KSKIVRVLNLW 113


                ....*...
gi 56382023 113 EERRVFGS 120
Cdd:cd17004 114 QKNNVFKS 121
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
169-291 5.12e-03

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 39.28  E-value: 5.12e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56382023  169 AEKIASAYHLVVAENSNEEAEMNKCKSAVKRIRKMEKDVEEACSTAKDNPKRKSLAKELeeeeyllrqciEKLKSvqgsr 248
Cdd:PRK03918 237 KEEIEELEKELESLEGSKRKLEEKIRELEERIEELKKEIEELEEKVKELKELKEKAEEY-----------IKLSE----- 300

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 56382023  249 ssLVNQLKDALREQESELDNLKAQIQVAKEQTEEAQNMQKRLN 291
Cdd:PRK03918 301 --FYEEYLDELREIEKRLSRLEEEINGIEERIKELEEKEERLE 341
 
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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