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Conserved domains on  [gi|1314817971|ref|NP_001345953|]
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calcium homeostasis endoplasmic reticulum protein isoform 2 [Mus musculus]

Protein Classification

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 ...
 160-289 6.84e-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: 103.06  E-value: 6.84e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971 160 LLQPIIDTC--TKDAISAGKNWMFSNAKSPPH-CELMAGHLRNritadgAHFELRLHLIYLINDVLHHwaltrgrslphS 236
Cdd:pfam04818   2 ALEKKLSSLnnSQESIQTLSKWILFHRKHAKAiVEVWEKYLKK------AKPEKKLHLLYLANDVLQN-----------S 64

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1314817971 237 QRKQARELLAALQKVVVPIYCTSFLAVEEDKQQKIARLLQLWEKNGYFDDSII 289
Cdd:pfam04818  65 RKKGKSEFADAFEPVLPEAFASAYKKCDEKLKKKLERLLNIWEERNVFSPEVI 117
SWAP smart00648
Suppressor-of-White-APricot splicing regulator; domain present in regulators which are ...
 13-65 9.43e-19

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: 80.71  E-value: 9.43e-19
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1314817971   13 RNVIDKLAQFVARNGPEFEKMTMEKQKDNPKFSFLF-GGEFYSYYKCKLALEQQ 65
Cdd:smart00648   1 LDIIDKTAQFVARNGPEFEAKLMERERNNPQFDFLKpNDPYHAYYRKKLAEYRQ 54
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 861-911 8.71e-11

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: 8.71e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1314817971  861 LGEENKGHQMLVKMGWSGSGGLGAKEQGIQDPIKGGDVRDKwdqyKGVGVA 911
Cdd:smart00443   1 ISTSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDR----KGLGAV 47
PAT1 super family cl37801
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 519-659 3.85e-05

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


The actual alignment was detected with superfamily member pfam09770:

Pssm-ID: 401645 [Multi-domain]  Cd Length: 846  Bit Score: 47.72  E-value: 3.85e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971 519 QHEPPPWGGAQREPPFRMQRPPHFRGPFPPHQQHPQFNQPPHPHNfnrfpprfmQDDFPPRHPFERPPYPHRFDYPQGdf 598
Cdd:pfam09770 223 AAPPAQQAQQQQQFPPQIQQQQQPQQQPQQPQQHPGQGHPVTILQ---------RPQSPQPDPAQPSIQPQAQQFHQQ-- 291

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1314817971 599 padMGPPHHHPGHRMPHPgiNEHPPwagPQHPDFGPPPHGFNGQPPHMRRQGPPHINHDDP 659
Cdd:pfam09770 292 ---PPPVPVQPTQILQNP--NRLSA---ARVGYPQNPQPGVQPAPAHQAHRQQGSFGRQAP 344
PHA03377 super family cl31823
EBNA-3C; Provisional
 393-702 1.43e-04

EBNA-3C; Provisional


The actual alignment was detected with superfamily member PHA03377:

Pssm-ID: 177614 [Multi-domain]  Cd Length: 1000  Bit Score: 45.81  E-value: 1.43e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971  393 TTQPDDNKPPIQMPGSSEYDTSAGVQDPAAAGPRGPGPHEQIPPNKPPWFDQPHPVAPWGQQQPPEQPPyphhqGGPPHC 472
Cdd:PHA03377   575 TGPRVMATPSTGPRDMAPPSTGPRQQAKCKDGPPASGPHEKQPPSSAPRDMAPSVVRMFLRERLLEQST-----GPKPKS 649

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971  473 ppWNNSHEGMWGEQRGDPGWNGQRDAPWNNQPDPNW-NNQFEGPWNNQHEPPPWGGAQREP------------------- 532
Cdd:PHA03377   650 --FWEMRAGRDGSGIQQEPSSRRQPATQSTPPRPSWlPSVFVLPSVDAGRAQPSEESHLSSmsptqpisheeqpryedpd 727

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971  533 --------PFRMQRPPHfRGPFPPHQQhPQFNQPPHPHNFNRFPPR--FMQDDFPPRH-------PFERPPYPHRFDYPQ 595
Cdd:PHA03377   728 dpldlslhPDQAPPPSH-QAPYSGHEE-PQAQQAPYPGYWEPRPPQapYLGYQEPQAQgvqvssyPGYAGPWGLRAQHPR 805

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971  596 GDFPadMGPPHHHPGHRMPHPGINEHPPWAGPQHPDFGPPPHGFNGQPPHMRRQ-GPPHINHddpSLVPNVPYFDLPAGL 674
Cdd:PHA03377   806 YRHS--WAYWSQYPGHGHPQGPWAPRPPHLPPQWDGSAGHGQDQVSQFPHLQSEtGPPRLQL---SQVPQLPYSQTLVSS 880

                          330       340
                   ....*....|....*....|....*...
gi 1314817971  675 MAPLVkLEDHEYKPLDPKDIRLPPPMPP 702
Cdd:PHA03377   881 SAPSW-SSPQPRAPIRPIPTRFPPPPMP 907
 
Name Accession Description Interval E-value
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 160-289 6.84e-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: 103.06  E-value: 6.84e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971 160 LLQPIIDTC--TKDAISAGKNWMFSNAKSPPH-CELMAGHLRNritadgAHFELRLHLIYLINDVLHHwaltrgrslphS 236
Cdd:pfam04818   2 ALEKKLSSLnnSQESIQTLSKWILFHRKHAKAiVEVWEKYLKK------AKPEKKLHLLYLANDVLQN-----------S 64

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1314817971 237 QRKQARELLAALQKVVVPIYCTSFLAVEEDKQQKIARLLQLWEKNGYFDDSII 289
Cdd:pfam04818  65 RKKGKSEFADAFEPVLPEAFASAYKKCDEKLKKKLERLLNIWEERNVFSPEVI 117
SWAP smart00648
Suppressor-of-White-APricot splicing regulator; domain present in regulators which are ...
 13-65 9.43e-19

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: 80.71  E-value: 9.43e-19
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1314817971   13 RNVIDKLAQFVARNGPEFEKMTMEKQKDNPKFSFLF-GGEFYSYYKCKLALEQQ 65
Cdd:smart00648   1 LDIIDKTAQFVARNGPEFEAKLMERERNNPQFDFLKpNDPYHAYYRKKLAEYRQ 54
Surp pfam01805
Surp module; This domain is also known as the SWAP domain. SWAP stands for ...
 14-61 5.82e-18

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: 78.33  E-value: 5.82e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1314817971  14 NVIDKLAQFVARNGPEFEKMTMEKQKDNPKFSFLFGGE--FYSYYKCKLA 61
Cdd:pfam01805   1 DIIKKTAQFVARNGPEFEALLMEREERNPQFDFLFDPDdpLHAYYRWKLE 50
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 861-911 8.71e-11

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: 8.71e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1314817971  861 LGEENKGHQMLVKMGWSGSGGLGAKEQGIQDPIKGGDVRDKwdqyKGVGVA 911
Cdd:smart00443   1 ISTSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDR----KGLGAV 47
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 864-909 9.68e-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: 9.68e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1314817971 864 ENKGHQMLVKMGWSGSGGLGAKEQGIQDPIKGGDVRDKwdqyKGVG 909
Cdd:pfam01585   2 SNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDR----RGLG 43
CID_Rtt103 cd17003
CID (CTD-Interacting Domain) of yeast transcription termination factor Rtt103 and similar ...
 140-294 2.29e-07

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: 50.68  E-value: 2.29e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971 140 EQQMQKL--LEETQldmsefdnllqpiidtctkDAISAGKNWMFSNAKsppHCELMAGHLRNRITADGAHFELRLHLIYL 217
Cdd:cd17003     2 EQFISKLnaLNETQ-------------------ESIVSISQWVLFHYR---HADEIAEIWSDYLLKSSVNSRRKLLLIYL 59

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1314817971 218 INDVLHHwaltrgrslphSQRKQARELLAALQKVVVPIYCTSFLAVEEDKQQKIARLLQLWEKNGYFDDSIIQQLQS 294
Cdd:cd17003    60 ANDVVQQ-----------AKAKKKTEFIDAFSKVLPEVLEKIYPSLPSDIKKKIKRVVNVWKQRQIFSKDVIDDIEE 125
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
211-294 1.20e-06

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 48.43  E-value: 1.20e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971  211 RLHLIYLINDVLHHwaltrgrslphSQRKQARELLAALQKVVVPIYCTSFLAVEEDKQQKIARLLQLWEKNGYFDDSIIQ 290
Cdd:smart00582  49 KLPLLYLLDSIVQN-----------SKRKYGSEFGDELGPVFQDALRRVLGAAPEELKKKIRRLLNIWEERGIFPPEVLR 117


                   ....
gi 1314817971  291 QLQS 294
Cdd:smart00582 118 PLRE 121
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 519-659 3.85e-05

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: 47.72  E-value: 3.85e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971 519 QHEPPPWGGAQREPPFRMQRPPHFRGPFPPHQQHPQFNQPPHPHNfnrfpprfmQDDFPPRHPFERPPYPHRFDYPQGdf 598
Cdd:pfam09770 223 AAPPAQQAQQQQQFPPQIQQQQQPQQQPQQPQQHPGQGHPVTILQ---------RPQSPQPDPAQPSIQPQAQQFHQQ-- 291

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1314817971 599 padMGPPHHHPGHRMPHPgiNEHPPwagPQHPDFGPPPHGFNGQPPHMRRQGPPHINHDDP 659
Cdd:pfam09770 292 ---PPPVPVQPTQILQNP--NRLSA---ARVGYPQNPQPGVQPAPAHQAHRQQGSFGRQAP 344
PHA03377 PHA03377
EBNA-3C; Provisional
 393-702 1.43e-04

EBNA-3C; Provisional


Pssm-ID: 177614 [Multi-domain]  Cd Length: 1000  Bit Score: 45.81  E-value: 1.43e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971  393 TTQPDDNKPPIQMPGSSEYDTSAGVQDPAAAGPRGPGPHEQIPPNKPPWFDQPHPVAPWGQQQPPEQPPyphhqGGPPHC 472
Cdd:PHA03377   575 TGPRVMATPSTGPRDMAPPSTGPRQQAKCKDGPPASGPHEKQPPSSAPRDMAPSVVRMFLRERLLEQST-----GPKPKS 649

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971  473 ppWNNSHEGMWGEQRGDPGWNGQRDAPWNNQPDPNW-NNQFEGPWNNQHEPPPWGGAQREP------------------- 532
Cdd:PHA03377   650 --FWEMRAGRDGSGIQQEPSSRRQPATQSTPPRPSWlPSVFVLPSVDAGRAQPSEESHLSSmsptqpisheeqpryedpd 727

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971  533 --------PFRMQRPPHfRGPFPPHQQhPQFNQPPHPHNFNRFPPR--FMQDDFPPRH-------PFERPPYPHRFDYPQ 595
Cdd:PHA03377   728 dpldlslhPDQAPPPSH-QAPYSGHEE-PQAQQAPYPGYWEPRPPQapYLGYQEPQAQgvqvssyPGYAGPWGLRAQHPR 805

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971  596 GDFPadMGPPHHHPGHRMPHPGINEHPPWAGPQHPDFGPPPHGFNGQPPHMRRQ-GPPHINHddpSLVPNVPYFDLPAGL 674
Cdd:PHA03377   806 YRHS--WAYWSQYPGHGHPQGPWAPRPPHLPPQWDGSAGHGQDQVSQFPHLQSEtGPPRLQL---SQVPQLPYSQTLVSS 880

                          330       340
                   ....*....|....*....|....*...
gi 1314817971  675 MAPLVkLEDHEYKPLDPKDIRLPPPMPP 702
Cdd:PHA03377   881 SAPSW-SSPQPRAPIRPIPTRFPPPPMP 907
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 423-573 3.81e-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: 41.17  E-value: 3.81e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971 423 AGPRGPGPHEQIPPNKPPwFDQPHPVAPWGQQQPPEQPPYPHHQGGPPHCPPWNNSHEGMWGEQRgdpgwngqrdaPWNN 502
Cdd:pfam09770 205 AQAKKPAQQPAPAPAQPP-AAPPAQQAQQQQQFPPQIQQQQQPQQQPQQPQQHPGQGHPVTILQR-----------PQSP 272

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971 503 QPDPNWNNQFEGPWNNQHEPPPWGGA--------QREPPFRM---QRPPHFRGPFPPHQQHPQFNQPPHPHNFNRFPPRF 571
Cdd:pfam09770 273 QPDPAQPSIQPQAQQFHQQPPPVPVQptqilqnpNRLSAARVgypQNPQPGVQPAPAHQAHRQQGSFGRQAPIITHPQQL 352


                  ..
gi 1314817971 572 MQ 573
Cdd:pfam09770 353 AQ 354
 
Name Accession Description Interval E-value
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 160-289 6.84e-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: 103.06  E-value: 6.84e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971 160 LLQPIIDTC--TKDAISAGKNWMFSNAKSPPH-CELMAGHLRNritadgAHFELRLHLIYLINDVLHHwaltrgrslphS 236
Cdd:pfam04818   2 ALEKKLSSLnnSQESIQTLSKWILFHRKHAKAiVEVWEKYLKK------AKPEKKLHLLYLANDVLQN-----------S 64

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1314817971 237 QRKQARELLAALQKVVVPIYCTSFLAVEEDKQQKIARLLQLWEKNGYFDDSII 289
Cdd:pfam04818  65 RKKGKSEFADAFEPVLPEAFASAYKKCDEKLKKKLERLLNIWEERNVFSPEVI 117
SWAP smart00648
Suppressor-of-White-APricot splicing regulator; domain present in regulators which are ...
 13-65 9.43e-19

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: 80.71  E-value: 9.43e-19
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1314817971   13 RNVIDKLAQFVARNGPEFEKMTMEKQKDNPKFSFLF-GGEFYSYYKCKLALEQQ 65
Cdd:smart00648   1 LDIIDKTAQFVARNGPEFEAKLMERERNNPQFDFLKpNDPYHAYYRKKLAEYRQ 54
Surp pfam01805
Surp module; This domain is also known as the SWAP domain. SWAP stands for ...
 14-61 5.82e-18

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: 78.33  E-value: 5.82e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1314817971  14 NVIDKLAQFVARNGPEFEKMTMEKQKDNPKFSFLFGGE--FYSYYKCKLA 61
Cdd:pfam01805   1 DIIKKTAQFVARNGPEFEALLMEREERNPQFDFLFDPDdpLHAYYRWKLE 50
G_patch smart00443
glycine rich nucleic binding domain; A predicted glycine rich nucleic binding domain found in ...
 861-911 8.71e-11

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: 8.71e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1314817971  861 LGEENKGHQMLVKMGWSGSGGLGAKEQGIQDPIKGGDVRDKwdqyKGVGVA 911
Cdd:smart00443   1 ISTSNIGAKLLRKMGWKEGQGLGKNEQGIVEPISAEIKKDR----KGLGAV 47
G-patch pfam01585
G-patch domain; This domain is found in a number of RNA binding proteins, and is also found in ...
 864-909 9.68e-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: 9.68e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1314817971 864 ENKGHQMLVKMGWSGSGGLGAKEQGIQDPIKGGDVRDKwdqyKGVG 909
Cdd:pfam01585   2 SNIGFKLLQKMGWKEGQGLGKNEQGIAEPIEAKIKKDR----RGLG 43
CID_Rtt103 cd17003
CID (CTD-Interacting Domain) of yeast transcription termination factor Rtt103 and similar ...
 140-294 2.29e-07

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: 50.68  E-value: 2.29e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971 140 EQQMQKL--LEETQldmsefdnllqpiidtctkDAISAGKNWMFSNAKsppHCELMAGHLRNRITADGAHFELRLHLIYL 217
Cdd:cd17003     2 EQFISKLnaLNETQ-------------------ESIVSISQWVLFHYR---HADEIAEIWSDYLLKSSVNSRRKLLLIYL 59

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1314817971 218 INDVLHHwaltrgrslphSQRKQARELLAALQKVVVPIYCTSFLAVEEDKQQKIARLLQLWEKNGYFDDSIIQQLQS 294
Cdd:cd17003    60 ANDVVQQ-----------AKAKKKTEFIDAFSKVLPEVLEKIYPSLPSDIKKKIKRVVNVWKQRQIFSKDVIDDIEE 125
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
211-294 1.20e-06

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 48.43  E-value: 1.20e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971  211 RLHLIYLINDVLHHwaltrgrslphSQRKQARELLAALQKVVVPIYCTSFLAVEEDKQQKIARLLQLWEKNGYFDDSIIQ 290
Cdd:smart00582  49 KLPLLYLLDSIVQN-----------SKRKYGSEFGDELGPVFQDALRRVLGAAPEELKKKIRRLLNIWEERGIFPPEVLR 117


                   ....
gi 1314817971  291 QLQS 294
Cdd:smart00582 118 PLRE 121
CID_RPRD_like cd16981
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; ...
 167-294 2.76e-05

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


Pssm-ID: 340778  Cd Length: 125  Bit Score: 44.49  E-value: 2.76e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971 167 TCTKDAISAGKNWMFSNAKsppHCELMAGHLRNRI-TADGAHfelRLHLIYLINDVLHHwaltrgrslphSQRKQARELL 245
Cdd:cd16981    12 NNTQQSIQTLSLWCLFHKK---HAKQIVKIWLKELkKAKPER---KLTLLYLANDVLQN-----------SRRKGAPEFV 74

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1314817971 246 AALQKVVvPIYCTSFLAVEEDK-QQKIARLLQLWEKNGYFDDSIIQQLQS 294
Cdd:cd16981    75 EAFKKVL-PEALALVRSEGDESvRKKVLRVLNIWEERNVFGSEFLAELRA 123
CID cd03562
CID (CTD-Interacting Domain) family; The CTD-Interacting Domain (CID) is present in several ...
 154-294 2.81e-05

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: 44.43  E-value: 2.81e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971 154 MSEFDNLLQPIIDTCTKDAISAGK-------NWMFSNAKSPPhcelmaghlrnritadgahfELRLHLIYLINDVLHHWa 226
Cdd:cd03562     7 LEELSDLSQQSITTLTKWAIHHIKhsrpivtVIEREIRKCKP--------------------NRKLTFLYLIDSIIRNS- 65

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1314817971 227 ltrGRSLPHSQRKQARELLAALQKVvvpiyctsFLAVEEDKQQKIARLLQLWEKNGYFDDSIIQQLQS 294
Cdd:cd03562    66 ---KRKGPEFTKDFSPVIVELFKHV--------YSETDEDCKKKLGRVLSIWEERNVFENSVLEQLKQ 122
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 519-659 3.85e-05

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: 47.72  E-value: 3.85e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971 519 QHEPPPWGGAQREPPFRMQRPPHFRGPFPPHQQHPQFNQPPHPHNfnrfpprfmQDDFPPRHPFERPPYPHRFDYPQGdf 598
Cdd:pfam09770 223 AAPPAQQAQQQQQFPPQIQQQQQPQQQPQQPQQHPGQGHPVTILQ---------RPQSPQPDPAQPSIQPQAQQFHQQ-- 291

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1314817971 599 padMGPPHHHPGHRMPHPgiNEHPPwagPQHPDFGPPPHGFNGQPPHMRRQGPPHINHDDP 659
Cdd:pfam09770 292 ---PPPVPVQPTQILQNP--NRLSA---ARVGYPQNPQPGVQPAPAHQAHRQQGSFGRQAP 344
PHA03377 PHA03377
EBNA-3C; Provisional
 393-702 1.43e-04

EBNA-3C; Provisional


Pssm-ID: 177614 [Multi-domain]  Cd Length: 1000  Bit Score: 45.81  E-value: 1.43e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971  393 TTQPDDNKPPIQMPGSSEYDTSAGVQDPAAAGPRGPGPHEQIPPNKPPWFDQPHPVAPWGQQQPPEQPPyphhqGGPPHC 472
Cdd:PHA03377   575 TGPRVMATPSTGPRDMAPPSTGPRQQAKCKDGPPASGPHEKQPPSSAPRDMAPSVVRMFLRERLLEQST-----GPKPKS 649

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971  473 ppWNNSHEGMWGEQRGDPGWNGQRDAPWNNQPDPNW-NNQFEGPWNNQHEPPPWGGAQREP------------------- 532
Cdd:PHA03377   650 --FWEMRAGRDGSGIQQEPSSRRQPATQSTPPRPSWlPSVFVLPSVDAGRAQPSEESHLSSmsptqpisheeqpryedpd 727

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971  533 --------PFRMQRPPHfRGPFPPHQQhPQFNQPPHPHNFNRFPPR--FMQDDFPPRH-------PFERPPYPHRFDYPQ 595
Cdd:PHA03377   728 dpldlslhPDQAPPPSH-QAPYSGHEE-PQAQQAPYPGYWEPRPPQapYLGYQEPQAQgvqvssyPGYAGPWGLRAQHPR 805

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971  596 GDFPadMGPPHHHPGHRMPHPGINEHPPWAGPQHPDFGPPPHGFNGQPPHMRRQ-GPPHINHddpSLVPNVPYFDLPAGL 674
Cdd:PHA03377   806 YRHS--WAYWSQYPGHGHPQGPWAPRPPHLPPQWDGSAGHGQDQVSQFPHLQSEtGPPRLQL---SQVPQLPYSQTLVSS 880

                          330       340
                   ....*....|....*....|....*...
gi 1314817971  675 MAPLVkLEDHEYKPLDPKDIRLPPPMPP 702
Cdd:PHA03377   881 SAPSW-SSPQPRAPIRPIPTRFPPPPMP 907
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 519-629 1.65e-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: 45.41  E-value: 1.65e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971 519 QHEPPPWGGAQREPPFRMQRPPHFRGPFPPHQ-QHPQ--FNQP------PHPHNFNRFPPRFMQDdfpPRHPFERP--PY 587
Cdd:pfam09770 234 QQFPPQIQQQQQPQQQPQQPQQHPGQGHPVTIlQRPQspQPDPaqpsiqPQAQQFHQQPPPVPVQ---PTQILQNPnrLS 310

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1314817971 588 PHRFDYPQGDFPAdMGPPHHHPGHRMPHPGINEHPPWAGPQH 629
Cdd:pfam09770 311 AARVGYPQNPQPG-VQPAPAHQAHRQQGSFGRQAPIITHPQQ 351
CID_SCAF8_like cd16983
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins; ...
 209-296 4.92e-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: 41.06  E-value: 4.92e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971 209 ELRLHLIYLINdvlhhwALTRGrslPHSQRKQARELLAA-LQKVVVPIYcTSFLAVEEDKQQKIARLLQLWEKNGYFDDS 287
Cdd:cd16983    53 EYKLPGLYVID------SIIRQ---SRHQYGKEKDVYAPrFAKNLSKTF-LNLLKCPEKDKPKVKRVLNLWQKNGVFPKE 122


                  ....*....
gi 1314817971 288 IIQQLQSPA 296
Cdd:cd16983   123 IIQPLLDAA 131
PAT1 pfam09770
Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate ...
 423-573 3.81e-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: 41.17  E-value: 3.81e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971 423 AGPRGPGPHEQIPPNKPPwFDQPHPVAPWGQQQPPEQPPYPHHQGGPPHCPPWNNSHEGMWGEQRgdpgwngqrdaPWNN 502
Cdd:pfam09770 205 AQAKKPAQQPAPAPAQPP-AAPPAQQAQQQQQFPPQIQQQQQPQQQPQQPQQHPGQGHPVTILQR-----------PQSP 272

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314817971 503 QPDPNWNNQFEGPWNNQHEPPPWGGA--------QREPPFRM---QRPPHFRGPFPPHQQHPQFNQPPHPHNFNRFPPRF 571
Cdd:pfam09770 273 QPDPAQPSIQPQAQQFHQQPPPVPVQptqilqnpNRLSAARVgypQNPQPGVQPAPAHQAHRQQGSFGRQAPIITHPQQL 352


                  ..
gi 1314817971 572 MQ 573
Cdd:pfam09770 353 AQ 354
CID_SFRS15_SCAF4 cd17005
CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15; Splicing factor ...
 239-292 4.68e-03

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: 38.41  E-value: 4.68e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1314817971 239 KQARELLAALQKVVVPIYCTSFLAV-------EEDKQQKIARLLQLWEKNGYFDDSIIQQL 292
Cdd:cd17005    67 RQSRHQFGADKDVFGPRFSKNITATfqylylcPSEDKSKIVRVLNLWQKNGVFKIEIIQPL 127
 
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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