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Conserved domains on  [gi|18204653|gb|AAH21294|]
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Calcium homeostasis endoplasmic reticulum protein [Homo sapiens]

Protein Classification

G patch domain-containing protein( domain architecture ID 10676401)

G patch domain-containing protein similar to Saccharomyces cerevisiae protein PXR1 that is involved in rRNA-processing at A0, A1 and A2 sites through its action in U18 and U24 snoRNA 3'-end final trimming, and pre-mRNA-splicing factor SPP382 that is involved in pre-mRNA splicing and spliceosome disassembly

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 128-246 7.11e-29

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: 111.53  E-value: 7.11e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18204653   128 LLQPIIDTC--TKDAISAGKNWMFSNAKSPPH-CELMAGHLRNritadgAHFELRLHLIYLINDVLHHCQRKQARELLAA 204
Cdd:pfam04818   2 ALEKKLSSLnnSQESIQTLSKWILFHRKHAKAiVEVWEKYLKK------AKPEKKLHLLYLANDVLQNSRKKGKSEFADA 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 18204653   205 LQKVVVPIYCTSFLAVEEDKQQKIARLLQLWEKNGYFDDSII 246
Cdd:pfam04818  76 FEPVLPEAFASAYKKCDEKLKKKLERLLNIWEERNVFSPEVI 117
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 810-855 9.01e-11

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


:

Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 57.52  E-value: 9.01e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 18204653   810 ENKGHQMLVKMGWSGSGGLGAKEQGIQDPIKGGDVRDKwdqyKGVG 855
Cdd:pfam01585   2 SNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDR----RGLG 43
PHA03377 super family cl31823
EBNA-3C; Provisional
 487-650 1.60e-06

EBNA-3C; Provisional


The actual alignment was detected with superfamily member PHA03377:

Pssm-ID: 177614 [Multi-domain]  Cd Length: 1000  Bit Score: 51.98  E-value: 1.60e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18204653   487 PPHFRGPFPPHQQhPQFNQPPHPHNFNRFPPR--FMQDDFPPRH-------PFERPPYPHRFDYPQGDFPaeMGPPHHHP 557
Cdd:PHA03377  741 PPSHQAPYSGHEE-PQAQQAPYPGYWEPRPPQapYLGYQEPQAQgvqvssyPGYAGPWGLRAQHPRYRHS--WAYWSQYP 817

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18204653   558 GHRMPHPGINEHPPWAGPQHPDFGPPPHGFNGQPPHMRRQ-GPPHINHddpSLVPNVPYFDLPAGLMAPLVkLEDHEYKP 636
Cdd:PHA03377  818 GHGHPQGPWAPRPPHLPPQWDGSAGHGQDQVSQFPHLQSEtGPPRLQL---SQVPQLPYSQTLVSSSAPSW-SSPQPRAP 893

                         170
                  ....*....|....
gi 18204653   637 LDPKDIRLPPPMPP 650
Cdd:PHA03377  894 IRPIPTRFPPPPMP 907
SWAP smart00648
Suppressor-of-White-APricot splicing regulator; domain present in regulators which are ...
 1-33 2.31e-05

Suppressor-of-White-APricot splicing regulator; domain present in regulators which are responsible for pre-mRNA splicing processes


:

Pssm-ID: 197818 [Multi-domain]  Cd Length: 54  Bit Score: 42.57  E-value: 2.31e-05
                           10        20        30
                   ....*....|....*....|....*....|....
gi 18204653      1 MTMEKQKDNPKFSFLF-GGEFYSYYKCKLALEQQ 33
Cdd:smart00648  21 KLMERERNNPQFDFLKpNDPYHAYYRKKLAEYRQ 54
 
Name Accession Description Interval E-value
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 128-246 7.11e-29

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: 111.53  E-value: 7.11e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18204653   128 LLQPIIDTC--TKDAISAGKNWMFSNAKSPPH-CELMAGHLRNritadgAHFELRLHLIYLINDVLHHCQRKQARELLAA 204
Cdd:pfam04818   2 ALEKKLSSLnnSQESIQTLSKWILFHRKHAKAiVEVWEKYLKK------AKPEKKLHLLYLANDVLQNSRKKGKSEFADA 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 18204653   205 LQKVVVPIYCTSFLAVEEDKQQKIARLLQLWEKNGYFDDSII 246
Cdd:pfam04818  76 FEPVLPEAFASAYKKCDEKLKKKLERLLNIWEERNVFSPEVI 117
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 810-855 9.01e-11

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 57.52  E-value: 9.01e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 18204653   810 ENKGHQMLVKMGWSGSGGLGAKEQGIQDPIKGGDVRDKwdqyKGVG 855
Cdd:pfam01585   2 SNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDR----RGLG 43
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 807-857 1.04e-10

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.


Pssm-ID: 197727 [Multi-domain]  Cd Length: 47  Bit Score: 57.55  E-value: 1.04e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 18204653    807 LGEENKGHQMLVKMGWSGSGGLGAKEQGIQDPIKGGDVRDKwdqyKGVGVA 857
Cdd:smart00443   1 ISTSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDR----KGLGAV 47
CID_Rtt103 cd17003
CID (CTD-Interacting Domain) of yeast transcription termination factor Rtt103 and similar ...
 108-251 2.60e-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: 56.08  E-value: 2.60e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18204653 108 EQQMQKL--LEETQldmnefdnllqpiidtctkDAISAGKNWMFSNAKsppHCELMAGHLRNRITADGAHFELRLHLIYL 185
Cdd:cd17003   2 EQFISKLnaLNETQ-------------------ESIVSISQWVLFHYR---HADEIAEIWSDYLLKSSVNSRRKLLLIYL 59

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18204653 186 INDVLHHCQRKQARELLAALQKVVVPIYCTSFLAVEEDKQQKIARLLQLWEKNGYFDDSIIQQLQS 251
Cdd:cd17003  60 ANDVVQQAKAKKKTEFIDAFSKVLPEVLEKIYPSLPSDIKKKIKRVVNVWKQRQIFSKDVIDDIEE 125
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
179-251 2.69e-09

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 55.75  E-value: 2.69e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 18204653    179 RLHLIYLINDVLHHCQRKQARELLAALQKVVVPIYCTSFLAVEEDKQQKIARLLQLWEKNGYFDDSIIQQLQS 251
Cdd:smart00582  49 KLPLLYLLDSIVQNSKRKYGSEFGDELGPVFQDALRRVLGAAPEELKKKIRRLLNIWEERGIFPPEVLRPLRE 121
PHA03377 PHA03377
EBNA-3C; Provisional
 487-650 1.60e-06

EBNA-3C; Provisional


Pssm-ID: 177614 [Multi-domain]  Cd Length: 1000  Bit Score: 51.98  E-value: 1.60e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18204653   487 PPHFRGPFPPHQQhPQFNQPPHPHNFNRFPPR--FMQDDFPPRH-------PFERPPYPHRFDYPQGDFPaeMGPPHHHP 557
Cdd:PHA03377  741 PPSHQAPYSGHEE-PQAQQAPYPGYWEPRPPQapYLGYQEPQAQgvqvssyPGYAGPWGLRAQHPRYRHS--WAYWSQYP 817

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18204653   558 GHRMPHPGINEHPPWAGPQHPDFGPPPHGFNGQPPHMRRQ-GPPHINHddpSLVPNVPYFDLPAGLMAPLVkLEDHEYKP 636
Cdd:PHA03377  818 GHGHPQGPWAPRPPHLPPQWDGSAGHGQDQVSQFPHLQSEtGPPRLQL---SQVPQLPYSQTLVSSSAPSW-SSPQPRAP 893

                         170
                  ....*....|....
gi 18204653   637 LDPKDIRLPPPMPP 650
Cdd:PHA03377  894 IRPIPTRFPPPPMP 907
SWAP smart00648
Suppressor-of-White-APricot splicing regulator; domain present in regulators which are ...
 1-33 2.31e-05

Suppressor-of-White-APricot splicing regulator; domain present in regulators which are responsible for pre-mRNA splicing processes


Pssm-ID: 197818 [Multi-domain]  Cd Length: 54  Bit Score: 42.57  E-value: 2.31e-05
                           10        20        30
                   ....*....|....*....|....*....|....
gi 18204653      1 MTMEKQKDNPKFSFLF-GGEFYSYYKCKLALEQQ 33
Cdd:smart00648  21 KLMERERNNPQFDFLKpNDPYHAYYRKKLAEYRQ 54
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 443-577 4.10e-04

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 44.26  E-value: 4.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18204653   443 QRDAPWNNQPDAAWNSQFEGPwnSQHEQPPWGGGQREPPFRMQRPPHFRGPFPPHQ-QHPQ--FNQP------PHPHNFN 513
Cdd:pfam09770 212 QQPAPAPAQPPAAPPAQQAQQ--QQQFPPQIQQQQQPQQQPQQPQQHPGQGHPVTIlQRPQspQPDPaqpsiqPQAQQFH 289

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18204653   514 RFPPRFMQDdfpPRHPFERP--PYPHRFDYPQGDFPAEmGPPHHHPGHRMPHPGINEHPPWAGPQH 577
Cdd:pfam09770 290 QQPPPVPVQ---PTQILQNPnrLSAARVGYPQNPQPGV-QPAPAHQAHRQQGSFGRQAPIITHPQQ 351
Surp pfam01805
Surp module; This domain is also known as the SWAP domain. SWAP stands for ...
 1-29 4.31e-04

Surp module; This domain is also known as the SWAP domain. SWAP stands for Suppressor-of-White-APricot. It has been suggested that these domains may be RNA binding.


Pssm-ID: 460339 [Multi-domain]  Cd Length: 52  Bit Score: 39.04  E-value: 4.31e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 18204653     1 MTMEKQKDNPKFSFLFGGE--FYSYYKCKLA 29
Cdd:pfam01805  20 LLMEREERNPQFDFLFDPDdpLHAYYRWKLE 50
 
Name Accession Description Interval E-value
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 128-246 7.11e-29

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: 111.53  E-value: 7.11e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18204653   128 LLQPIIDTC--TKDAISAGKNWMFSNAKSPPH-CELMAGHLRNritadgAHFELRLHLIYLINDVLHHCQRKQARELLAA 204
Cdd:pfam04818   2 ALEKKLSSLnnSQESIQTLSKWILFHRKHAKAiVEVWEKYLKK------AKPEKKLHLLYLANDVLQNSRKKGKSEFADA 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 18204653   205 LQKVVVPIYCTSFLAVEEDKQQKIARLLQLWEKNGYFDDSII 246
Cdd:pfam04818  76 FEPVLPEAFASAYKKCDEKLKKKLERLLNIWEERNVFSPEVI 117
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 810-855 9.01e-11

G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines.


Pssm-ID: 396249 [Multi-domain]  Cd Length: 45  Bit Score: 57.52  E-value: 9.01e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 18204653   810 ENKGHQMLVKMGWSGSGGLGAKEQGIQDPIKGGDVRDKwdqyKGVG 855
Cdd:pfam01585   2 SNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDR----RGLG 43
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 807-857 1.04e-10

glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins.


Pssm-ID: 197727 [Multi-domain]  Cd Length: 47  Bit Score: 57.55  E-value: 1.04e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 18204653    807 LGEENKGHQMLVKMGWSGSGGLGAKEQGIQDPIKGGDVRDKwdqyKGVGVA 857
Cdd:smart00443   1 ISTSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDR----KGLGAV 47
CID_Rtt103 cd17003
CID (CTD-Interacting Domain) of yeast transcription termination factor Rtt103 and similar ...
 108-251 2.60e-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: 56.08  E-value: 2.60e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18204653 108 EQQMQKL--LEETQldmnefdnllqpiidtctkDAISAGKNWMFSNAKsppHCELMAGHLRNRITADGAHFELRLHLIYL 185
Cdd:cd17003   2 EQFISKLnaLNETQ-------------------ESIVSISQWVLFHYR---HADEIAEIWSDYLLKSSVNSRRKLLLIYL 59

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18204653 186 INDVLHHCQRKQARELLAALQKVVVPIYCTSFLAVEEDKQQKIARLLQLWEKNGYFDDSIIQQLQS 251
Cdd:cd17003  60 ANDVVQQAKAKKKTEFIDAFSKVLPEVLEKIYPSLPSDIKKKIKRVVNVWKQRQIFSKDVIDDIEE 125
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
179-251 2.69e-09

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 55.75  E-value: 2.69e-09
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 18204653    179 RLHLIYLINDVLHHCQRKQARELLAALQKVVVPIYCTSFLAVEEDKQQKIARLLQLWEKNGYFDDSIIQQLQS 251
Cdd:smart00582  49 KLPLLYLLDSIVQNSKRKYGSEFGDELGPVFQDALRRVLGAAPEELKKKIRRLLNIWEERGIFPPEVLRPLRE 121
CID_RPRD_like cd16981
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; ...
 135-251 2.73e-08

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: 52.97  E-value: 2.73e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18204653 135 TCTKDAISAGKNWMFSNAKsppHCELMAGHLRNRI-TADGAHfelRLHLIYLINDVLHHCQRKQARELLAALQKvVVPIY 213
Cdd:cd16981  12 NNTQQSIQTLSLWCLFHKK---HAKQIVKIWLKELkKAKPER---KLTLLYLANDVLQNSRRKGAPEFVEAFKK-VLPEA 84

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 18204653 214 CTSFLAVEEDK-QQKIARLLQLWEKNGYFDDSIIQQLQS 251
Cdd:cd16981  85 LALVRSEGDESvRKKVLRVLNIWEERNVFGSEFLAELRA 123
PHA03377 PHA03377
EBNA-3C; Provisional
 487-650 1.60e-06

EBNA-3C; Provisional


Pssm-ID: 177614 [Multi-domain]  Cd Length: 1000  Bit Score: 51.98  E-value: 1.60e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18204653   487 PPHFRGPFPPHQQhPQFNQPPHPHNFNRFPPR--FMQDDFPPRH-------PFERPPYPHRFDYPQGDFPaeMGPPHHHP 557
Cdd:PHA03377  741 PPSHQAPYSGHEE-PQAQQAPYPGYWEPRPPQapYLGYQEPQAQgvqvssyPGYAGPWGLRAQHPRYRHS--WAYWSQYP 817

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18204653   558 GHRMPHPGINEHPPWAGPQHPDFGPPPHGFNGQPPHMRRQ-GPPHINHddpSLVPNVPYFDLPAGLMAPLVkLEDHEYKP 636
Cdd:PHA03377  818 GHGHPQGPWAPRPPHLPPQWDGSAGHGQDQVSQFPHLQSEtGPPRLQL---SQVPQLPYSQTLVSSSAPSW-SSPQPRAP 893

                         170
                  ....*....|....
gi 18204653   637 LDPKDIRLPPPMPP 650
Cdd:PHA03377  894 IRPIPTRFPPPPMP 907
CID cd03562
CID (CTD-Interacting Domain) family; The CTD-Interacting Domain (CID) is present in several ...
 122-251 2.30e-06

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: 47.51  E-value: 2.30e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18204653 122 MNEFDNLLQPIIDTCTKDAISAGK-------NWMFSNAKSPPhcelmaghlrnritadgahfELRLHLIYLINDVLHHCQ 194
Cdd:cd03562   7 LEELSDLSQQSITTLTKWAIHHIKhsrpivtVIEREIRKCKP--------------------NRKLTFLYLIDSIIRNSK 66

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 18204653 195 RKQArELLAALQKVVVPIYCTSFLAVEEDKQQKIARLLQLWEKNGYFDDSIIQQLQS 251
Cdd:cd03562  67 RKGP-EFTKDFSPVIVELFKHVYSETDEDCKKKLGRVLSIWEERNVFENSVLEQLKQ 122
SWAP smart00648
Suppressor-of-White-APricot splicing regulator; domain present in regulators which are ...
 1-33 2.31e-05

Suppressor-of-White-APricot splicing regulator; domain present in regulators which are responsible for pre-mRNA splicing processes


Pssm-ID: 197818 [Multi-domain]  Cd Length: 54  Bit Score: 42.57  E-value: 2.31e-05
                           10        20        30
                   ....*....|....*....|....*....|....
gi 18204653      1 MTMEKQKDNPKFSFLF-GGEFYSYYKCKLALEQQ 33
Cdd:smart00648  21 KLMERERNNPQFDFLKpNDPYHAYYRKKLAEYRQ 54
CID_SCAF8_like cd16983
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins; ...
 177-253 1.33e-04

CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins; This subfamily includes SR-related and CTD-associated factors 8 (SCAF8) and 4 (SCAF4), and similar proteins. SCAF4 is also called Splicing factor arginine serine rich 15 (SFRS15). Members may play roles in mRNA processing. Both SCAF4 and SCAF8 contains a CTD-interacting domain (CID) at the amino terminus and a Ser/Arg-rich domain followed by an RNA recognition motif. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340780  Cd Length: 131  Bit Score: 42.60  E-value: 1.33e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18204653 177 ELRLHLIYLINDVLHHCQRKQARE---LLAALQKVVVPIYcTSFLAVEEDKQQKIARLLQLWEKNGYFDDSIIQQLQSPA 253
Cdd:cd16983  53 EYKLPGLYVIDSIIRQSRHQYGKEkdvYAPRFAKNLSKTF-LNLLKCPEKDKPKVKRVLNLWQKNGVFPKEIIQPLLDAA 131
CID_RPRD1B cd17012
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1B; ...
 175-250 2.10e-04

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: 41.91  E-value: 2.10e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18204653 175 HFELR-------LHLIYLINDVLHHCQRKqARELLAALQKVVVPIYCTSFLAVEEDKQQKIARLLQLWEKNGYFDDSIIQ 247
Cdd:cd17012  43 HRELRkakssrkLTFLYLANDVIQNSKRK-GPEFTREFESVLVDAFSHVAREADEGCKKPLERLLNIWQERSVYGGDFIQ 121


                ...
gi 18204653 248 QLQ 250
Cdd:cd17012 122 QLK 124
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 443-577 4.10e-04

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 44.26  E-value: 4.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18204653   443 QRDAPWNNQPDAAWNSQFEGPwnSQHEQPPWGGGQREPPFRMQRPPHFRGPFPPHQ-QHPQ--FNQP------PHPHNFN 513
Cdd:pfam09770 212 QQPAPAPAQPPAAPPAQQAQQ--QQQFPPQIQQQQQPQQQPQQPQQHPGQGHPVTIlQRPQspQPDPaqpsiqPQAQQFH 289

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18204653   514 RFPPRFMQDdfpPRHPFERP--PYPHRFDYPQGDFPAEmGPPHHHPGHRMPHPGINEHPPWAGPQH 577
Cdd:pfam09770 290 QQPPPVPVQ---PTQILQNPnrLSAARVGYPQNPQPGV-QPAPAHQAHRQQGSFGRQAPIITHPQQ 351
Surp pfam01805
Surp module; This domain is also known as the SWAP domain. SWAP stands for ...
 1-29 4.31e-04

Surp module; This domain is also known as the SWAP domain. SWAP stands for Suppressor-of-White-APricot. It has been suggested that these domains may be RNA binding.


Pssm-ID: 460339 [Multi-domain]  Cd Length: 52  Bit Score: 39.04  E-value: 4.31e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 18204653     1 MTMEKQKDNPKFSFLFGGE--FYSYYKCKLA 29
Cdd:pfam01805  20 LLMEREERNPQFDFLFDPDdpLHAYYRWKLE 50
CID_RPRD2 cd17001
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 2; ...
 125-251 5.16e-04

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: 40.67  E-value: 5.16e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18204653 125 FDNLLQPIidTCTKDAISAGKNWMFSNAKSppHCELMAGHLRNRITADGAHfelRLHLIYLINDVLHHCQRKQA---REL 201
Cdd:cd17001   6 LDRKFQSV--TNTMESIQGLSSWCIENKKH--HSTIVYHWMKWLRRSAYPH---RLNLFYLANDVIQNCKRKNAivfRES 78

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 18204653 202 LAAlqkvVVPiycTSFLAVEEDKQQK-IARLLQLWEKNGYFDDSIIQQLQS 251
Cdd:cd17001  79 FAE----VLP---EAAALVKDASVSKsVERIFKIWEERNVYPEETIAALKE 122
CID_SFRS15_SCAF4 cd17005
CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15; Splicing factor ...
 177-249 7.87e-04

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: 40.34  E-value: 7.87e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18204653 177 ELRLHLIYLINDVLhhcqrKQARELLAALQKVVVPIYCTSFLAV-------EEDKQQKIARLLQLWEKNGYFDDSIIQQL 249
Cdd:cd17005  53 EYKVPGLYVIDSIV-----RQSRHQFGADKDVFGPRFSKNITATfqylylcPSEDKSKIVRVLNLWQKNGVFKIEIIQPL 127
CID_RPRD1A cd17011
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A; ...
 179-255 7.93e-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: 40.41  E-value: 7.93e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18204653 179 RLHLIYLINDVLHHCQRKqARELLAALQKVVVPIYCTSFLAVEEDKQQKIARLLQLWEKNGYFDDSIIQQLQSPALG 255
Cdd:cd17011  53 KLTFLYLANDVIQNSKRK-GPEFTKDFAPVIVEAFKHVSSETDESCKKHLGRVLSIWEERSVYENDVLEQLKQALYG 128
CID_SCAF8 cd17004
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8; SR-related and ...
 177-249 9.65e-04

CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8; SR-related and CTD-associated factor 8 (SCAF8) is also called CDC5L complex-associated protein 7 (CCAP7) or RNA-binding motif protein 16 (RBM16). It may play a role in mRNA processing. SCAF8 contains a CTD-interacting domain (CID) at the amino terminus and a Ser/Arg-rich domain followed by an RNA recognition motif. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.


Pssm-ID: 340801  Cd Length: 131  Bit Score: 40.02  E-value: 9.65e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18204653 177 ELRLHLIYLINDVLhhcqrKQARELLAALQKVVVPIYCTSFLAVEE-------DKQQKIARLLQLWEKNGYFDDSIIQQL 249
Cdd:cd17004  53 EYKVPGLYVIDSIV-----RQSRHQFGQEKDVFAPRFSNNIISTFQnlyrcpgDDKSKIVRVLNLWQKNNVFKSEIIQPL 127
Gag_spuma pfam03276
Spumavirus gag protein;
466-607 1.81e-03

Spumavirus gag protein;


Pssm-ID: 460872 [Multi-domain]  Cd Length: 614  Bit Score: 42.04  E-value: 1.81e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18204653   466 SQHEQPPWGGGQREPPFRMQRPPHFRGPFPPHQQHPqfnQPPHPHNFNRFPPRFMQDDFPPRHPFERPPYPhRFDYPQGD 545
Cdd:pfam03276 182 AQGGIPPGASFSGLPSLPAIGGIHLPAIPGIHARAP---PGNIARSLGDDIMPSLGDAGMPQPRFAFHPGN-PFAEAEGH 257

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 18204653   546 FPAEMGPPHHHPGHRMPH---------PGINEHPPWAGPQHPDFGPPPHG--FNGQPPHMRRQGPPHINHDDP 607
Cdd:pfam03276 258 PFAEAEGERPRDIPRAPRidapsapaiPAIQPIAPPMIPPIGAPIPIPHGasIPGEHIRNPREEPIRLGREAP 330
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 467-561 2.53e-03

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.


Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 41.56  E-value: 2.53e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18204653   467 QHEQPPWGGGQREPPFRMQRP------PHFRGPFPPHQQHPQFNQPPHPH------NFNRFPPRFMQddFPPRHPFERPP 534
Cdd:pfam09770 249 QPQQPQQHPGQGHPVTILQRPqspqpdPAQPSIQPQAQQFHQQPPPVPVQptqilqNPNRLSAARVG--YPQNPQPGVQP 326

                          90       100
                  ....*....|....*....|....*..
gi 18204653   535 YPHRFDYPQGDFPAEMGPPHHHPGHRM 561
Cdd:pfam09770 327 APAHQAHRQQGSFGRQAPIITHPQQLA 353
 
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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