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Conserved domains on  [gi|183396804|ref|NP_056018|]
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regulation of nuclear pre-mRNA domain-containing protein 2 isoform 1 [Homo sapiens]

Protein Classification

CID_RPRD2 and PHA03307 domain-containing protein( domain architecture ID 13017324)

CID_RPRD2 and PHA03307 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CID_RPRD2 cd17001
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 2; ...
 27-146 7.25e-85

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: 272.56  E-value: 7.25e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804   27 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAIIFRESFADVLPE 106
Cdd:cd17001     6 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAIVFRESFAEVLPE 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 183396804  107 AAALVKDPSVSKSVERIFKIWEDRNVYPEEMIVALREALS 146
Cdd:cd17001    86 AAALVKDASVSKSVERIFKIWEERNVYPEETIAALKEALS 125
PHA03247 super family cl33720
large tegument protein UL36; Provisional
 314-587 7.32e-06

large tegument protein UL36; Provisional


The actual alignment was detected with superfamily member PHA03247:

Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 51.09  E-value: 7.32e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804  314 PDPEESPVPSPSMDAPSPTGSESPFQGMGGEESQSPTMESEKSATPEPVTDNRdvedmelsdveddgskiivedRKEKPA 393
Cdd:PHA03247 2612 APPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRP---------------------RRARRL 2670

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804  394 EKSAVSTSVPTKPTEnisKASSCTPVPVTMTATPPLPKPVNTSLSPSPALALPNLANVDLAKISSILssltsvmknTGVS 473
Cdd:PHA03247 2671 GRAAQASSPPQRPRR---RAARPTVGSLTSLADPPPPPPTPEPAPHALVSATPLPPGPAAARQASPA---------LPAA 2738

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804  474 PASRPSPGTPTSPSNLTSGLKTPAPATTTSHNPLANilskveitpesilSALSKTQTQSAPALQGLSSLLQSVTGNPVPA 553
Cdd:PHA03247 2739 PAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAA-------------PAAGPPRRLTRPAVASLSESRESLPSPWDPA 2805

                         250       260       270
                  ....*....|....*....|....*....|....
gi 183396804  554 SEAASQSTSASPANTTVSTIKGRNLPSSAQPFIP 587
Cdd:PHA03247 2806 DPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAP 2839
PRK03918 super family cl35229
DNA double-strand break repair ATPase Rad50;
142-318 3.62e-04

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: 45.05  E-value: 3.62e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804  142 REALSTTFKTQKQLKENLNKQpNKQWKKSQTStnpKAALKSKIVaEFRSQalIEELllyKRSEDQIELKEKQLSTMRVDV 221
Cdd:PRK03918  223 LEKLEKEVKELEELKEEIEEL-EKELESLEGS---KRKLEEKIR-ELEER--IEEL---KKEIEELEEKVKELKELKEKA 292

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804  222 CSTETLKCLKDKTggKKFSKEFEEASSKLEEFVNGLDKQVKNGPSLTEALENagifYEAQYKEVKVVANAYKTFA---NR 298
Cdd:PRK03918  293 EEYIKLSEFYEEY--LDELREIEKRLSRLEEEINGIEERIKELEEKEERLEE----LKKKLKELEKRLEELEERHelyEE 366

                         170       180
                  ....*....|....*....|..
gi 183396804  299 VNNLKKKLDQLKSTLPD--PEE 318
Cdd:PRK03918  367 AKAKKEELERLKKRLTGltPEK 388
 
Name Accession Description Interval E-value
CID_RPRD2 cd17001
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 2; ...
 27-146 7.25e-85

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: 272.56  E-value: 7.25e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804   27 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAIIFRESFADVLPE 106
Cdd:cd17001     6 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAIVFRESFAEVLPE 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 183396804  107 AAALVKDPSVSKSVERIFKIWEDRNVYPEEMIVALREALS 146
Cdd:cd17001    86 AAALVKDASVSKSVERIFKIWEERNVYPEETIAALKEALS 125
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 27-138 6.84e-42

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: 149.28  E-value: 6.84e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804    27 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAIIFRESFADVLPE 106
Cdd:pfam04818    3 LEKKLSSLNNSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSRKKGKSEFADAFEPVLPE 82

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 183396804   107 AAALV---KDPSVSKSVERIFKIWEDRNVYPEEMI 138
Cdd:pfam04818   83 AFASAykkCDEKLKKKLERLLNIWEERNVFSPEVI 117
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
27-145 5.23e-31

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 118.53  E-value: 5.23e-31
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804     27 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAIIFRESFADVLPE 106
Cdd:smart00582    2 FEQKLESLNNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKRKYGSEFGDELGPVFQD 81

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|..
gi 183396804    107 AAALVKDPSVS---KSVERIFKIWEDRNVYPEEMIVALREAL 145
Cdd:smart00582   82 ALRRVLGAAPEelkKKIRRLLNIWEERGIFPPEVLRPLREKL 123
PHA03247 PHA03247
large tegument protein UL36; Provisional
 314-587 7.32e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 51.09  E-value: 7.32e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804  314 PDPEESPVPSPSMDAPSPTGSESPFQGMGGEESQSPTMESEKSATPEPVTDNRdvedmelsdveddgskiivedRKEKPA 393
Cdd:PHA03247 2612 APPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRP---------------------RRARRL 2670

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804  394 EKSAVSTSVPTKPTEnisKASSCTPVPVTMTATPPLPKPVNTSLSPSPALALPNLANVDLAKISSILssltsvmknTGVS 473
Cdd:PHA03247 2671 GRAAQASSPPQRPRR---RAARPTVGSLTSLADPPPPPPTPEPAPHALVSATPLPPGPAAARQASPA---------LPAA 2738

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804  474 PASRPSPGTPTSPSNLTSGLKTPAPATTTSHNPLANilskveitpesilSALSKTQTQSAPALQGLSSLLQSVTGNPVPA 553
Cdd:PHA03247 2739 PAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAA-------------PAAGPPRRLTRPAVASLSESRESLPSPWDPA 2805

                         250       260       270
                  ....*....|....*....|....*....|....
gi 183396804  554 SEAASQSTSASPANTTVSTIKGRNLPSSAQPFIP 587
Cdd:PHA03247 2806 DPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAP 2839
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 319-575 1.69e-05

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 49.53  E-value: 1.69e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804   319 SPVPSPSMDAPSPTgSESPFQGMGGEESQSPTMESEKSATPEPVTDNRDVEDMELSDVEDDGSkiivedrkekPAEKSAV 398
Cdd:pfam05109  475 SPTPAGTTSGASPV-TPSPSPRDNGTESKAPDMTSPTSAVTTPTPNATSPTPAVTTPTPNATS----------PTLGKTS 543

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804   399 STSVPTKPTENiskasSCTPVPVTMTATPPLPKPVNTSLSPSPALALP--NLANVDLAKISSILSSLTSVMKNTGVSPAs 476
Cdd:pfam05109  544 PTSAVTTPTPN-----ATSPTPAVTTPTPNATIPTLGKTSPTSAVTTPtpNATSPTVGETSPQANTTNHTLGGTSSTPV- 617

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804   477 rpspgTPTSPSNLTSGLktpapaTTTSHNPLANILSKVEITPESILSALSKTQTQSAPALQGLSSLLQSVTGNPV----- 551
Cdd:pfam05109  618 -----VTSPPKNATSAV------TTGQHNITSSSTSSMSLRPSSISETLSPSTSDNSTSHMPLLTSAHPTGGENItqvtp 686

                          250       260       270
                   ....*....|....*....|....*....|....*.
gi 183396804   552 ------------PASEAASQSTSASPANTTVSTIKG 575
Cdd:pfam05109  687 aststhhvstssPAPRPGTTSQASGPGNSSTSTKPG 722
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
142-318 3.62e-04

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 45.05  E-value: 3.62e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804  142 REALSTTFKTQKQLKENLNKQpNKQWKKSQTStnpKAALKSKIVaEFRSQalIEELllyKRSEDQIELKEKQLSTMRVDV 221
Cdd:PRK03918  223 LEKLEKEVKELEELKEEIEEL-EKELESLEGS---KRKLEEKIR-ELEER--IEEL---KKEIEELEEKVKELKELKEKA 292

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804  222 CSTETLKCLKDKTggKKFSKEFEEASSKLEEFVNGLDKQVKNGPSLTEALENagifYEAQYKEVKVVANAYKTFA---NR 298
Cdd:PRK03918  293 EEYIKLSEFYEEY--LDELREIEKRLSRLEEEINGIEERIKELEEKEERLEE----LKKKLKELEKRLEELEERHelyEE 366

                         170       180
                  ....*....|....*....|..
gi 183396804  299 VNNLKKKLDQLKSTLPD--PEE 318
Cdd:PRK03918  367 AKAKKEELERLKKRLTGltPEK 388
 
Name Accession Description Interval E-value
CID_RPRD2 cd17001
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 2; ...
 27-146 7.25e-85

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: 272.56  E-value: 7.25e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804   27 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAIIFRESFADVLPE 106
Cdd:cd17001     6 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAIVFRESFAEVLPE 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 183396804  107 AAALVKDPSVSKSVERIFKIWEDRNVYPEEMIVALREALS 146
Cdd:cd17001    86 AAALVKDASVSKSVERIFKIWEERNVYPEETIAALKEALS 125
CID_RPRD_like cd16981
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins; ...
 27-145 7.61e-57

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: 192.41  E-value: 7.61e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804   27 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAIIFRESFADVLPE 106
Cdd:cd16981     4 LEKKLRSLNNTQQSIQTLSLWCLFHKKHAKQIVKIWLKELKKAKPERKLTLLYLANDVLQNSRRKGAPEFVEAFKKVLPE 83

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 183396804  107 AAALVK---DPSVSKSVERIFKIWEDRNVYPEEMIVALREAL 145
Cdd:cd16981    84 ALALVRsegDESVRKKVLRVLNIWEERNVFGSEFLAELRAIL 125
CID pfam04818
CID domain; This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase ...
 27-138 6.84e-42

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: 149.28  E-value: 6.84e-42
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804    27 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAIIFRESFADVLPE 106
Cdd:pfam04818    3 LEKKLSSLNNSQESIQTLSKWILFHRKHAKAIVEVWEKYLKKAKPEKKLHLLYLANDVLQNSRKKGKSEFADAFEPVLPE 82

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 183396804   107 AAALV---KDPSVSKSVERIFKIWEDRNVYPEEMI 138
Cdd:pfam04818   83 AFASAykkCDEKLKKKLERLLNIWEERNVFSPEVI 117
CID_RPRD1 cd17002
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1 and ...
 27-145 3.12e-35

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: 130.84  E-value: 3.12e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804   27 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAiIFRESFADVLPE 106
Cdd:cd17002     6 LEKKLAELSNSQQSIQTLSLWLIHHRKHAKTIVRVWLKELRKEKPSKKLTLLYLANDVIQNSRKKGP-EFTKEFAPVLED 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 183396804  107 AAALV---KDPSVSKSVERIFKIWEDRNVYPEEMIVALREAL 145
Cdd:cd17002    85 AFKHVaklTDSEVLKALERILNIWKERQVYEKDFIEQLRAAL 126
RPR smart00582
domain present in proteins, which are involved in regulation of nuclear pre-mRNA;
27-145 5.23e-31

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


Pssm-ID: 214731  Cd Length: 124  Bit Score: 118.53  E-value: 5.23e-31
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804     27 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAIIFRESFADVLPE 106
Cdd:smart00582    2 FEQKLESLNNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKRKYGSEFGDELGPVFQD 81

                            90       100       110       120
                    ....*....|....*....|....*....|....*....|..
gi 183396804    107 AAALVKDPSVS---KSVERIFKIWEDRNVYPEEMIVALREAL 145
Cdd:smart00582   82 ALRRVLGAAPEelkKKIRRLLNIWEERGIFPPEVLRPLREKL 123
CID_Rtt103 cd17003
CID (CTD-Interacting Domain) of yeast transcription termination factor Rtt103 and similar ...
 30-145 1.34e-25

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: 103.07  E-value: 1.34e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804   30 KFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAY--PHRLNLFYLANDVIQNCKRKNAIIFRESFADVLPEA 107
Cdd:cd17003     7 KLNALNETQESIVSISQWVLFHYRHADEIAEIWSDYLLKSSVnsRRKLLLIYLANDVVQQAKAKKKTEFIDAFSKVLPEV 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 183396804  108 AALVK---DPSVSKSVERIFKIWEDRNVYPEEMIVALREAL 145
Cdd:cd17003    87 LEKIYpslPSDIKKKIKRVVNVWKQRQIFSKDVIDDIEERL 127
CID_RPRD1A cd17011
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A; ...
 27-145 7.23e-25

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: 101.27  E-value: 7.23e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804   27 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAiIFRESFADVLPE 106
Cdd:cd17011     6 LEKKLSELSNSQQSVQTLSLWLIHHRKHSRPIVTVWERELRKAKPNRKLTFLYLANDVIQNSKRKGP-EFTKDFAPVIVE 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 183396804  107 AAALVK---DPSVSKSVERIFKIWEDRNVYPEEMIVALREAL 145
Cdd:cd17011    85 AFKHVSsetDESCKKHLGRVLSIWEERSVYENDVLEQLKQAL 126
CID_RPRD1B cd17012
CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1B; ...
 27-142 1.35e-23

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: 97.77  E-value: 1.35e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804   27 LDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAIIFREsFADVLPE 106
Cdd:cd17012     7 LEKKLSELSNSQQSVQTLSLWLIHHRKHAGPIVSVWHRELRKAKSSRKLTFLYLANDVIQNSKRKGPEFTRE-FESVLVD 85

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 183396804  107 AAALVK---DPSVSKSVERIFKIWEDRNVYPEEMIVALR 142
Cdd:cd17012    86 AFSHVAreaDEGCKKPLERLLNIWQERSVYGGDFIQQLK 124
CID cd03562
CID (CTD-Interacting Domain) family; The CTD-Interacting Domain (CID) is present in several ...
 36-144 1.80e-13

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: 68.31  E-value: 1.80e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804   36 NTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAiIFRESFADVLPEA---AALVK 112
Cdd:cd03562    13 LSQQSITTLTKWAIHHIKHSRPIVTVIEREIRKCKPNRKLTFLYLIDSIIRNSKRKGP-EFTKDFSPVIVELfkhVYSET 91

                          90       100       110
                  ....*....|....*....|....*....|..
gi 183396804  113 DPSVSKSVERIFKIWEDRNVYPEEMIVALREA 144
Cdd:cd03562    92 DEDCKKKLGRVLSIWEERNVFENSVLEQLKQA 123
CID_SCAF8_like cd16983
CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins; ...
 41-144 3.56e-08

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: 53.38  E-value: 3.56e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804   41 IQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAII---FRESFADVL-PEAAALVKDPSV 116
Cdd:cd16983    22 INAITKLAIKAIKFYKHVVQSVEKFIQKCKPEYKLPGLYVIDSIIRQSRHQYGKEkdvYAPRFAKNLsKTFLNLLKCPEK 101

                          90       100
                  ....*....|....*....|....*....
gi 183396804  117 SKS-VERIFKIWEDRNVYPEEMIVALREA 144
Cdd:cd16983   102 DKPkVKRVLNLWQKNGVFPKEIIQPLLDA 130
PHA03247 PHA03247
large tegument protein UL36; Provisional
 314-587 7.32e-06

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 51.09  E-value: 7.32e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804  314 PDPEESPVPSPSMDAPSPTGSESPFQGMGGEESQSPTMESEKSATPEPVTDNRdvedmelsdveddgskiivedRKEKPA 393
Cdd:PHA03247 2612 APPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRP---------------------RRARRL 2670

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804  394 EKSAVSTSVPTKPTEnisKASSCTPVPVTMTATPPLPKPVNTSLSPSPALALPNLANVDLAKISSILssltsvmknTGVS 473
Cdd:PHA03247 2671 GRAAQASSPPQRPRR---RAARPTVGSLTSLADPPPPPPTPEPAPHALVSATPLPPGPAAARQASPA---------LPAA 2738

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804  474 PASRPSPGTPTSPSNLTSGLKTPAPATTTSHNPLANilskveitpesilSALSKTQTQSAPALQGLSSLLQSVTGNPVPA 553
Cdd:PHA03247 2739 PAPPAVPAGPATPGGPARPARPPTTAGPPAPAPPAA-------------PAAGPPRRLTRPAVASLSESRESLPSPWDPA 2805

                         250       260       270
                  ....*....|....*....|....*....|....
gi 183396804  554 SEAASQSTSASPANTTVSTIKGRNLPSSAQPFIP 587
Cdd:PHA03247 2806 DPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAP 2839
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 319-575 1.69e-05

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 49.53  E-value: 1.69e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804   319 SPVPSPSMDAPSPTgSESPFQGMGGEESQSPTMESEKSATPEPVTDNRDVEDMELSDVEDDGSkiivedrkekPAEKSAV 398
Cdd:pfam05109  475 SPTPAGTTSGASPV-TPSPSPRDNGTESKAPDMTSPTSAVTTPTPNATSPTPAVTTPTPNATS----------PTLGKTS 543

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804   399 STSVPTKPTENiskasSCTPVPVTMTATPPLPKPVNTSLSPSPALALP--NLANVDLAKISSILSSLTSVMKNTGVSPAs 476
Cdd:pfam05109  544 PTSAVTTPTPN-----ATSPTPAVTTPTPNATIPTLGKTSPTSAVTTPtpNATSPTVGETSPQANTTNHTLGGTSSTPV- 617

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804   477 rpspgTPTSPSNLTSGLktpapaTTTSHNPLANILSKVEITPESILSALSKTQTQSAPALQGLSSLLQSVTGNPV----- 551
Cdd:pfam05109  618 -----VTSPPKNATSAV------TTGQHNITSSSTSSMSLRPSSISETLSPSTSDNSTSHMPLLTSAHPTGGENItqvtp 686

                          250       260       270
                   ....*....|....*....|....*....|....*.
gi 183396804   552 ------------PASEAASQSTSASPANTTVSTIKG 575
Cdd:pfam05109  687 aststhhvstssPAPRPGTTSQASGPGNSSTSTKPG 722
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
142-318 3.62e-04

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 45.05  E-value: 3.62e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804  142 REALSTTFKTQKQLKENLNKQpNKQWKKSQTStnpKAALKSKIVaEFRSQalIEELllyKRSEDQIELKEKQLSTMRVDV 221
Cdd:PRK03918  223 LEKLEKEVKELEELKEEIEEL-EKELESLEGS---KRKLEEKIR-ELEER--IEEL---KKEIEELEEKVKELKELKEKA 292

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804  222 CSTETLKCLKDKTggKKFSKEFEEASSKLEEFVNGLDKQVKNGPSLTEALENagifYEAQYKEVKVVANAYKTFA---NR 298
Cdd:PRK03918  293 EEYIKLSEFYEEY--LDELREIEKRLSRLEEEINGIEERIKELEEKEERLEE----LKKKLKELEKRLEELEERHelyEE 366

                         170       180
                  ....*....|....*....|..
gi 183396804  299 VNNLKKKLDQLKSTLPD--PEE 318
Cdd:PRK03918  367 AKAKKEELERLKKRLTGltPEK 388
Herpes_BLLF1 pfam05109
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ...
 392-703 2.46e-03

Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo.


Pssm-ID: 282904 [Multi-domain]  Cd Length: 886  Bit Score: 42.60  E-value: 2.46e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804   392 PAEKSAVSTSVPTKPTENISKASSCTPVPVTMTATPPLPKPVNTSLSPSPALALPNLANVDLAKissilssltsvmkntg 471
Cdd:pfam05109  478 PAGTTSGASPVTPSPSPRDNGTESKAPDMTSPTSAVTTPTPNATSPTPAVTTPTPNATSPTLGK---------------- 541

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804   472 VSPASRPSPGTPTSPSnltsglktPAPATTTShNPLANILSKVEITPESILSalSKTQTQSAPALQGLSSllQSVTGNPV 551
Cdd:pfam05109  542 TSPTSAVTTPTPNATS--------PTPAVTTP-TPNATIPTLGKTSPTSAVT--TPTPNATSPTVGETSP--QANTTNHT 608

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804   552 PASEAASQSTSASPANTTVSTIKGR-NLPSSAQPFI---PKSFNYSPNSSTSEVSSTSASKASIGQSPGLPSTTFKLPSN 627
Cdd:pfam05109  609 LGGTSSTPVVTSPPKNATSAVTTGQhNITSSSTSSMslrPSSISETLSPSTSDNSTSHMPLLTSAHPTGGENITQVTPAS 688

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804   628 slgfTATHNTSPAAPPTEVTicQSSEVSKPKLESESTSPSLEmkihNFLKGNP--------GFSGLNLNIPILSSLGSSA 699
Cdd:pfam05109  689 ----TSTHHVSTSSPAPRPG--TTSQASGPGNSSTSTKPGEV----NVTKGTPpknatspqAPSGQKTAVPTVTSTGGKA 758


                   ....
gi 183396804   700 PSES 703
Cdd:pfam05109  759 NSTT 762
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 314-589 4.96e-03

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 41.70  E-value: 4.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804  314 PDPEESPVPSPSMDAPSPTGSESPFQGMGGEESQSPTMES---EKSATPEPVTDNRDVEDMELSDVEDDGSKIIVEDRKE 390
Cdd:PHA03307  113 SPDPPPPTPPPASPPPSPAPDLSEMLRPVGSPGPPPAASPpaaGASPAAVASDAASSRQAALPLSSPEETARAPSSPPAE 192

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804  391 KPAEKSAVSTSVPTKPTENI--SKASSCTPVPVTMTATPPLPKPVNTSLSPSPALALPNLANVDLAKISSILSSLTSVMK 468
Cdd:PHA03307  193 PPPSTPPAAASPRPPRRSSPisASASSPAPAPGRSAADDAGASSSDSSSSESSGCGWGPENECPLPRPAPITLPTRIWEA 272

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 183396804  469 NTGVSPASRPSPGTPTSPSNLTSGLKTPAPATTTSHNPLANILSKVEITPESILSALSKTQTQSAPALQGLSSLLQSvtg 548
Cdd:PHA03307  273 SGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPSPSR--- 349

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 183396804  549 NPVPASEAASQSTSASPANTTVSTIKGRNLPSSAQPFIPKS 589
Cdd:PHA03307  350 SPSPSRPPPPADPSSPRKRPRPSRAPSSPAASAGRPTRRRA 390
 
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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