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Conserved domains on  [gi|767948361|ref|XP_011514742|]
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zinc finger protein 398 isoform X2 [Homo sapiens]

Protein Classification

KRAB domain-containing zinc finger protein( domain architecture ID 12204268)

KRAB (Kruppel-associated box) domain-containing zinc finger protein (KRAB-ZFP) plays important roles in cell differentiation and organ development, and in regulating viral replication and transcription

CATH:  3.30.160.60
Gene Ontology:  GO:0003700|GO:0046872
PubMed:  22803940
SCOP:  4003583

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
KRAB smart00349
krueppel associated box;
136-194 4.51e-18

krueppel associated box;


:

Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 78.40  E-value: 4.51e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 767948361   136 VAFDDVSIYFSTPEWEKLEEWQKELYKNIMKGNYESLISMDYAINQPDVLSQIQPEGEH 194
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEEP 59
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
337-581 3.49e-09

FOG: Zn-finger [General function prediction only];


:

Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 59.32  E-value: 3.49e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767948361 337 SCHHCGKNLSQDMLLTHQCSHATEHPLPCAQCPKHFTPQADL---SSTSQDHASETPPTCPHCARTFTHPSRLT---YHL 410
Cdd:COG5048  201 ENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSQLSPKSLLSqspSSLSSSDSSSSASESPRSSLPTASSQSSSpneSDS 280

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767948361 411 RVHNSTERPFPCPDCPKRFADQARLTSHRRA--HASE--RPFRC--AQCGRSFSLKISLLLHQRGHAQERPFSCP--QCG 482
Cdd:COG5048  281 SSEKGFSLPIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCpySLCGKLFSRNDALKRHILLHTSISPAKEKllNSS 360

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767948361 483 IDFNG-----HSALIRHQMIHTGERPYPCTD--CSKSFMRKEHLLNHRRLHTGERP--FSCPHCGKSFIRKHHLMKHQRI 553
Cdd:COG5048  361 SKFSPllnnePPQSLQQYKDLKNDKKSETLSnsCIRNFKRDSNLSLHIITHLSFRPynCKNPPCSKSFNRHYNLIPHKKI 440

                        250       260
                 ....*....|....*....|....*...
gi 767948361 554 HTGERPYPCSYCgRSFRYKQTLKDHLRS 581
Cdd:COG5048  441 HTNHAPLLCSIL-KSFRRDLDLSNHGKD 467
 
Name Accession Description Interval E-value
KRAB smart00349
krueppel associated box;
136-194 4.51e-18

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 78.40  E-value: 4.51e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 767948361   136 VAFDDVSIYFSTPEWEKLEEWQKELYKNIMKGNYESLISMDYAINQPDVLSQIQPEGEH 194
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEEP 59
KRAB_A-box cd07765
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 136-175 3.92e-17

KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression module, found in a subgroup of the zinc finger proteins (ZFPs) of the C2H2 family, KRAB-ZFPs. KRAB-ZFPs comprise the largest group of transcriptional regulators in mammals, and are only found in tetrapods. These proteins have been shown to play important roles in cell differentiation and organ development, and in regulating viral replication and transcription. A KRAB domain may consist of an A-box, or of an A-box plus either a B-box, a divergent B-box (b), or a C-box. Only the A-box is included in this model. The A-box is needed for repression, the B- and C- boxes are not. KRAB-ZFPs have one or two KRAB domains at their amino-terminal end, and multiple C2H2 zinc finger motifs at their C-termini. Some KRAB-ZFPs also contain a SCAN domain which mediates homo- and hetero-oligomerization. The KRAB domain is a protein-protein interaction module which represses transcription through recruiting corepressors. A key mechanism appears to be the following: KRAB-AFPs tethered to DNA recruit, via their KRAB domain, the repressor KAP1 (KRAB-associated protein-1, also known as transcription intermediary factor 1 beta , KRAB-A interacting protein , and tripartite motif protein 28). The KAP1/ KRAB-AFP complex in turn recruits the heterochromatin protein 1 (HP1) family, and other chromatin modulating proteins, leading to transcriptional repression through heterochromatin formation.


Pssm-ID: 143639  Cd Length: 40  Bit Score: 74.89  E-value: 3.92e-17
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 767948361 136 VAFDDVSIYFSTPEWEKLEEWQKELYKNIMKGNYESLISM 175
Cdd:cd07765    1 VTFEDVAVYFSQEEWELLDPAQRDLYRDVMLENYENLVSL 40
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 135-176 5.18e-14

KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.


Pssm-ID: 460171  Cd Length: 42  Bit Score: 66.34  E-value: 5.18e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 767948361  135 PVAFDDVSIYFSTPEWEKLEEWQKELYKNIMKGNYESLISMD 176
Cdd:pfam01352   1 SVTFEDVAVDFTQEEWALLDPAQRNLYRDVMLENYRNLVSLG 42
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
337-581 3.49e-09

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 59.32  E-value: 3.49e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767948361 337 SCHHCGKNLSQDMLLTHQCSHATEHPLPCAQCPKHFTPQADL---SSTSQDHASETPPTCPHCARTFTHPSRLT---YHL 410
Cdd:COG5048  201 ENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSQLSPKSLLSqspSSLSSSDSSSSASESPRSSLPTASSQSSSpneSDS 280

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767948361 411 RVHNSTERPFPCPDCPKRFADQARLTSHRRA--HASE--RPFRC--AQCGRSFSLKISLLLHQRGHAQERPFSCP--QCG 482
Cdd:COG5048  281 SSEKGFSLPIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCpySLCGKLFSRNDALKRHILLHTSISPAKEKllNSS 360

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767948361 483 IDFNG-----HSALIRHQMIHTGERPYPCTD--CSKSFMRKEHLLNHRRLHTGERP--FSCPHCGKSFIRKHHLMKHQRI 553
Cdd:COG5048  361 SKFSPllnnePPQSLQQYKDLKNDKKSETLSnsCIRNFKRDSNLSLHIITHLSFRPynCKNPPCSKSFNRHYNLIPHKKI 440

                        250       260
                 ....*....|....*....|....*...
gi 767948361 554 HTGERPYPCSYCgRSFRYKQTLKDHLRS 581
Cdd:COG5048  441 HTNHAPLLCSIL-KSFRRDLDLSNHGKD 467
zf-H2C2_2 pfam13465
Zinc-finger double domain;
546-571 4.75e-06

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 43.51  E-value: 4.75e-06
                          10        20
                  ....*....|....*....|....*.
gi 767948361  546 HLMKHQRIHTGERPYPCSYCGRSFRY 571
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
ZnF_C2H2 smart00355
zinc finger;
532-554 5.38e-03

zinc finger;


Pssm-ID: 197676  Cd Length: 23  Bit Score: 34.75  E-value: 5.38e-03
                           10        20
                   ....*....|....*....|...
gi 767948361   532 FSCPHCGKSFIRKHHLMKHQRIH 554
Cdd:smart00355   1 YRCPECGKVFKSKSALREHMRTH 23
 
Name Accession Description Interval E-value
KRAB smart00349
krueppel associated box;
136-194 4.51e-18

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 78.40  E-value: 4.51e-18
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 767948361   136 VAFDDVSIYFSTPEWEKLEEWQKELYKNIMKGNYESLISMDYAINQPDVLSQIQPEGEH 194
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEEP 59
KRAB_A-box cd07765
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 136-175 3.92e-17

KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression module, found in a subgroup of the zinc finger proteins (ZFPs) of the C2H2 family, KRAB-ZFPs. KRAB-ZFPs comprise the largest group of transcriptional regulators in mammals, and are only found in tetrapods. These proteins have been shown to play important roles in cell differentiation and organ development, and in regulating viral replication and transcription. A KRAB domain may consist of an A-box, or of an A-box plus either a B-box, a divergent B-box (b), or a C-box. Only the A-box is included in this model. The A-box is needed for repression, the B- and C- boxes are not. KRAB-ZFPs have one or two KRAB domains at their amino-terminal end, and multiple C2H2 zinc finger motifs at their C-termini. Some KRAB-ZFPs also contain a SCAN domain which mediates homo- and hetero-oligomerization. The KRAB domain is a protein-protein interaction module which represses transcription through recruiting corepressors. A key mechanism appears to be the following: KRAB-AFPs tethered to DNA recruit, via their KRAB domain, the repressor KAP1 (KRAB-associated protein-1, also known as transcription intermediary factor 1 beta , KRAB-A interacting protein , and tripartite motif protein 28). The KAP1/ KRAB-AFP complex in turn recruits the heterochromatin protein 1 (HP1) family, and other chromatin modulating proteins, leading to transcriptional repression through heterochromatin formation.


Pssm-ID: 143639  Cd Length: 40  Bit Score: 74.89  E-value: 3.92e-17
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 767948361 136 VAFDDVSIYFSTPEWEKLEEWQKELYKNIMKGNYESLISM 175
Cdd:cd07765    1 VTFEDVAVYFSQEEWELLDPAQRDLYRDVMLENYENLVSL 40
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 135-176 5.18e-14

KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation.


Pssm-ID: 460171  Cd Length: 42  Bit Score: 66.34  E-value: 5.18e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 767948361  135 PVAFDDVSIYFSTPEWEKLEEWQKELYKNIMKGNYESLISMD 176
Cdd:pfam01352   1 SVTFEDVAVDFTQEEWALLDPAQRNLYRDVMLENYRNLVSLG 42
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
337-581 3.49e-09

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 59.32  E-value: 3.49e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767948361 337 SCHHCGKNLSQDMLLTHQCSHATEHPLPCAQCPKHFTPQADL---SSTSQDHASETPPTCPHCARTFTHPSRLT---YHL 410
Cdd:COG5048  201 ENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSQLSPKSLLSqspSSLSSSDSSSSASESPRSSLPTASSQSSSpneSDS 280

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767948361 411 RVHNSTERPFPCPDCPKRFADQARLTSHRRA--HASE--RPFRC--AQCGRSFSLKISLLLHQRGHAQERPFSCP--QCG 482
Cdd:COG5048  281 SSEKGFSLPIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCpySLCGKLFSRNDALKRHILLHTSISPAKEKllNSS 360

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767948361 483 IDFNG-----HSALIRHQMIHTGERPYPCTD--CSKSFMRKEHLLNHRRLHTGERP--FSCPHCGKSFIRKHHLMKHQRI 553
Cdd:COG5048  361 SKFSPllnnePPQSLQQYKDLKNDKKSETLSnsCIRNFKRDSNLSLHIITHLSFRPynCKNPPCSKSFNRHYNLIPHKKI 440

                        250       260
                 ....*....|....*....|....*...
gi 767948361 554 HTGERPYPCSYCgRSFRYKQTLKDHLRS 581
Cdd:COG5048  441 HTNHAPLLCSIL-KSFRRDLDLSNHGKD 467
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
379-573 1.53e-06

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 51.24  E-value: 1.53e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767948361 379 SSTSQDHASETPPTCPHCARTFTHPSRL--TYHLRVHNSTERPFPCPDCPKRFADQARLTSHRRAHASERPFrCAQCGRS 456
Cdd:COG5048  157 SSVNTPQSNSLHPPLPANSLSKDPSSNLslLISSNVSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLP-LTTNSQL 235

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767948361 457 FSLKISLLLHQRGHAQERPFSCPQCGIDFNGHSALIRHQMIHTGER-------PYPCTDCSKSFMRKEHLLNHRR--LHT 527
Cdd:COG5048  236 SPKSLLSQSPSSLSSSDSSSSASESPRSSLPTASSQSSSPNESDSSsekgfslPIKSKQCNISFSRSSPLTRHLRsvNHS 315

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 767948361 528 GE--RPFSCPH--CGKSFIRKHHLMKHQRIHTGERPYPCSYCGRSFRYKQ 573
Cdd:COG5048  316 GEslKPFSCPYslCGKLFSRNDALKRHILLHTSISPAKEKLLNSSSKFSP 365
zf-H2C2_2 pfam13465
Zinc-finger double domain;
546-571 4.75e-06

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 43.51  E-value: 4.75e-06
                          10        20
                  ....*....|....*....|....*.
gi 767948361  546 HLMKHQRIHTGERPYPCSYCGRSFRY 571
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 532-554 5.73e-06

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 43.06  E-value: 5.73e-06
                          10        20
                  ....*....|....*....|...
gi 767948361  532 FSCPHCGKSFIRKHHLMKHQRIH 554
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-H2C2_2 pfam13465
Zinc-finger double domain;
518-543 4.19e-05

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 40.82  E-value: 4.19e-05
                          10        20
                  ....*....|....*....|....*.
gi 767948361  518 HLLNHRRLHTGERPFSCPHCGKSFIR 543
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
502-572 7.98e-05

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 45.46  E-value: 7.98e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767948361 502 RPYPCTDCSKSFMRKEHLLNHRRLHTGERPFSCPH--CGKSFIRKHHLMKHQRIHTGERPYPCSYCGRSFRYK 572
Cdd:COG5048   32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYsgCDKSFSRPLELSRHLRTHHNNPSDLNSKSLPLSNSK 104
zf-H2C2_2 pfam13465
Zinc-finger double domain;
490-513 1.01e-04

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 39.66  E-value: 1.01e-04
                          10        20
                  ....*....|....*....|....
gi 767948361  490 ALIRHQMIHTGERPYPCTDCSKSF 513
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSF 24
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 504-526 2.09e-03

Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.


Pssm-ID: 395048 [Multi-domain]  Cd Length: 23  Bit Score: 35.74  E-value: 2.09e-03
                          10        20
                  ....*....|....*....|...
gi 767948361  504 YPCTDCSKSFMRKEHLLNHRRLH 526
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
ZnF_C2H2 smart00355
zinc finger;
532-554 5.38e-03

zinc finger;


Pssm-ID: 197676  Cd Length: 23  Bit Score: 34.75  E-value: 5.38e-03
                           10        20
                   ....*....|....*....|...
gi 767948361   532 FSCPHCGKSFIRKHHLMKHQRIH 554
Cdd:smart00355   1 YRCPECGKVFKSKSALREHMRTH 23
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
446-512 5.62e-03

FOG: Zn-finger [General function prediction only];


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 39.68  E-value: 5.62e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767948361 446 RPFRCAQCGRSFSLKISLLLHQRGHAQERPFSCPQCGID--FNGHSALIRHQMIHTGERPYPCTDCSKS 512
Cdd:COG5048   32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCSYSGCDksFSRPLELSRHLRTHHNNPSDLNSKSLPL 100
 
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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