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Conserved domains on  [gi|83816962|ref|NP_035888|]
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zinc finger protein 39 [Mus musculus]

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;
59-118 4.95e-31

krueppel associated box;


:

Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 115.38  E-value: 4.95e-31
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 83816962     59 VSFEDVSVDFTWDEWQDLDDSQRKLYRDVMLETYSSLESLGHCITKPEVIFKLEQGAEPW 118
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEEPW 60
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
407-699 1.81e-11

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


:

Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 67.03  E-value: 1.81e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83816962 407 KPYGCNLCGKAFYRKSHLGRHQKIHTGEKPYGC--EECKKTFYHKSSLTIHQRTHTGEKPYECKKCR------------- 471
Cdd:COG5048  32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCsySGCDKSFSRPLELSRHLRTHHNNPSDLNSKSLplsnskassssls 111

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83816962 472 ------------------------------------------------------------------KTFYCKSDLNVHHR 485
Cdd:COG5048 112 ssssnsndnnllsshslppssrdpqlpdllsisnlrnnplpgnnsssvntpqsnslhpplpanslsKDPSSNLSLLISSN 191

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83816962 486 THTGEKPYECDECRKTFYSKSHLVIHQKVHTGDKPYECEECQ----------------------------------KAFS 531
Cdd:COG5048 192 VSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSqlspksllsqspsslsssdssssasesprsslptASSQ 271

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83816962 532 RKSNLTVHQKTHTG-EKPYECNVCGKTFHRQSHLNMHQGT--HTGQ--KPYQCEE--CGKAFYQKSSLRRHQRNHTGSRP 604
Cdd:COG5048 272 SSSPNESDSSSEKGfSLPIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCPYslCGKLFSRNDALKRHILLHTSISP 351

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83816962 605 YACEECRKTFLHKSSLT-------VHQRSHTGYKPYSCE--ECRKTFYSKSHLTVHQRTHTGEKPYECK--LCKKAFHQK 673
Cdd:COG5048 352 AKEKLLNSSSKFSPLLNneppqslQQYKDLKNDKKSETLsnSCIRNFKRDSNLSLHIITHLSFRPYNCKnpPCSKSFNRH 431

                       410       420
                ....*....|....*....|....*.
gi 83816962 674 SYLNRHQVTHGSEKRFECQECRKTFY 699
Cdd:COG5048 432 YNLIPHKKIHTNHAPLLCSILKSFRR 457
 
Name Accession Description Interval E-value
KRAB smart00349
krueppel associated box;
59-118 4.95e-31

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 115.38  E-value: 4.95e-31
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 83816962     59 VSFEDVSVDFTWDEWQDLDDSQRKLYRDVMLETYSSLESLGHCITKPEVIFKLEQGAEPW 118
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEEPW 60
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 58-99 2.11e-20

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: 84.44  E-value: 2.11e-20
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 83816962    58 LVSFEDVSVDFTWDEWQDLDDSQRKLYRDVMLETYSSLESLG 99
Cdd:pfam01352   1 SVTFEDVAVDFTQEEWALLDPAQRNLYRDVMLENYRNLVSLG 42
KRAB_A-box cd07765
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 59-98 4.38e-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: 4.38e-17
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 83816962  59 VSFEDVSVDFTWDEWQDLDDSQRKLYRDVMLETYSSLESL 98
Cdd:cd07765   1 VTFEDVAVYFSQEEWELLDPAQRDLYRDVMLENYENLVSL 40
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
407-699 1.81e-11

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 67.03  E-value: 1.81e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83816962 407 KPYGCNLCGKAFYRKSHLGRHQKIHTGEKPYGC--EECKKTFYHKSSLTIHQRTHTGEKPYECKKCR------------- 471
Cdd:COG5048  32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCsySGCDKSFSRPLELSRHLRTHHNNPSDLNSKSLplsnskassssls 111

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83816962 472 ------------------------------------------------------------------KTFYCKSDLNVHHR 485
Cdd:COG5048 112 ssssnsndnnllsshslppssrdpqlpdllsisnlrnnplpgnnsssvntpqsnslhpplpanslsKDPSSNLSLLISSN 191

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83816962 486 THTGEKPYECDECRKTFYSKSHLVIHQKVHTGDKPYECEECQ----------------------------------KAFS 531
Cdd:COG5048 192 VSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSqlspksllsqspsslsssdssssasesprsslptASSQ 271

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83816962 532 RKSNLTVHQKTHTG-EKPYECNVCGKTFHRQSHLNMHQGT--HTGQ--KPYQCEE--CGKAFYQKSSLRRHQRNHTGSRP 604
Cdd:COG5048 272 SSSPNESDSSSEKGfSLPIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCPYslCGKLFSRNDALKRHILLHTSISP 351

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83816962 605 YACEECRKTFLHKSSLT-------VHQRSHTGYKPYSCE--ECRKTFYSKSHLTVHQRTHTGEKPYECK--LCKKAFHQK 673
Cdd:COG5048 352 AKEKLLNSSSKFSPLLNneppqslQQYKDLKNDKKSETLsnSCIRNFKRDSNLSLHIITHLSFRPYNCKnpPCSKSFNRH 431

                       410       420
                ....*....|....*....|....*.
gi 83816962 674 SYLNRHQVTHGSEKRFECQECRKTFY 699
Cdd:COG5048 432 YNLIPHKKIHTNHAPLLCSILKSFRR 457
zf-H2C2_2 pfam13465
Zinc-finger double domain;
535-558 2.00e-03

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 36.20  E-value: 2.00e-03
                          10        20
                  ....*....|....*....|....
gi 83816962   535 NLTVHQKTHTGEKPYECNVCGKTF 558
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSF 24
SUF4-like cd20908
N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), ...
 659-718 6.08e-03

N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins; Oryza sativa SUPPRESSOR OF FRI 4 (OsSUF4) is a C2H2-type zinc finger transcription factor which interacts with the major H3K36 methyltransferase SDG725 to promote H3K36me3 (tri-methylation at H3K9) establishment. The transcription factor OsSUF4 recognizes a specific 7-bp DNA element (5'-CGGAAAT-3'), which is contained in the promoter regions of many genes throughout the rice genome. Through interaction with OsSUF4, SDG725 is recruited to the promoters of key florigen genes, RICE FLOWERING LOCUS T1 (RFT1) and Heading date 3a (Hd3a), for H3K36 deposition to promote gene activation and rice plant flowering. OsSUF4 target genes include a number of genes involved in many biological processes. Flowering plant Arabidopsis SUF4 binds to a 15bp DNA element (5'-CCAAATTTTAAGTTT-3') within the promoter of the floral repressor gene FLOWERING LOCUS C (FLC) and recruits the FRI-C transcription activator complex to the FLC promoter. Although the DNA-binding element and target genes of AtSUF4 are different from those of OsSUF4, AtSUF4 is known to interact with the Arabidopsis H3K36 methyltransferase SDG8 (also known as ASHH2/EFS/SET8), and the methylation deposition mechanism mediated by the SUF4 transcription factor and H3K36 methyltransferase may be conserved in Arabidopsis and rice. Proteins in this family have two conserved C2H2-type zinc finger motifs at the N-terminus (included in this model), and a large proline-rich domain at the C-terminus; for OsSUF4, it has been shown that the N-terminal zinc-finger domain is responsible for DNA binding, and that the C-terminal domain interacts with SDG725.


Pssm-ID: 411020 [Multi-domain]  Cd Length: 82  Bit Score: 36.38  E-value: 6.08e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 83816962 659 KPYeCKLCKKAFHQKSYLNRHQVthgsEKRFECQECRKTFYHKSSLTVH-QRIHLRELLCV 718
Cdd:cd20908   1 KPW-CYYCDREFDDEKILIQHQK----AKHFKCHICHKKLYTAGGLAVHcLQVHKETLTKV 56
 
Name Accession Description Interval E-value
KRAB smart00349
krueppel associated box;
59-118 4.95e-31

krueppel associated box;


Pssm-ID: 214630 [Multi-domain]  Cd Length: 61  Bit Score: 115.38  E-value: 4.95e-31
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 83816962     59 VSFEDVSVDFTWDEWQDLDDSQRKLYRDVMLETYSSLESLGHCITKPEVIFKLEQGAEPW 118
Cdd:smart00349   1 VTFEDVAVYFTQEEWEQLDPAQKNLYRDVMLENYSNLVSLGFQVPKPDLISQLEQGEEPW 60
KRAB pfam01352
KRAB box; The KRAB domain (or Kruppel-associated box) is present in about a third of zinc ...
 58-99 2.11e-20

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: 84.44  E-value: 2.11e-20
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 83816962    58 LVSFEDVSVDFTWDEWQDLDDSQRKLYRDVMLETYSSLESLG 99
Cdd:pfam01352   1 SVTFEDVAVDFTQEEWALLDPAQRNLYRDVMLENYRNLVSLG 42
KRAB_A-box cd07765
KRAB (Kruppel-associated box) domain -A box; The KRAB domain is a transcription repression ...
 59-98 4.38e-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: 4.38e-17
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 83816962  59 VSFEDVSVDFTWDEWQDLDDSQRKLYRDVMLETYSSLESL 98
Cdd:cd07765   1 VTFEDVAVYFSQEEWELLDPAQRDLYRDVMLENYENLVSL 40
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
407-699 1.81e-11

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 67.03  E-value: 1.81e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83816962 407 KPYGCNLCGKAFYRKSHLGRHQKIHTGEKPYGC--EECKKTFYHKSSLTIHQRTHTGEKPYECKKCR------------- 471
Cdd:COG5048  32 RPDSCPNCTDSFSRLEHLTRHIRSHTGEKPSQCsySGCDKSFSRPLELSRHLRTHHNNPSDLNSKSLplsnskassssls 111

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83816962 472 ------------------------------------------------------------------KTFYCKSDLNVHHR 485
Cdd:COG5048 112 ssssnsndnnllsshslppssrdpqlpdllsisnlrnnplpgnnsssvntpqsnslhpplpanslsKDPSSNLSLLISSN 191

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83816962 486 THTGEKPYECDECRKTFYSKSHLVIHQKVHTGDKPYECEECQ----------------------------------KAFS 531
Cdd:COG5048 192 VSTSIPSSSENSPLSSSYSIPSSSSDQNLENSSSSLPLTTNSqlspksllsqspsslsssdssssasesprsslptASSQ 271

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83816962 532 RKSNLTVHQKTHTG-EKPYECNVCGKTFHRQSHLNMHQGT--HTGQ--KPYQCEE--CGKAFYQKSSLRRHQRNHTGSRP 604
Cdd:COG5048 272 SSSPNESDSSSEKGfSLPIKSKQCNISFSRSSPLTRHLRSvnHSGEslKPFSCPYslCGKLFSRNDALKRHILLHTSISP 351

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83816962 605 YACEECRKTFLHKSSLT-------VHQRSHTGYKPYSCE--ECRKTFYSKSHLTVHQRTHTGEKPYECK--LCKKAFHQK 673
Cdd:COG5048 352 AKEKLLNSSSKFSPLLNneppqslQQYKDLKNDKKSETLsnSCIRNFKRDSNLSLHIITHLSFRPYNCKnpPCSKSFNRH 431

                       410       420
                ....*....|....*....|....*.
gi 83816962 674 SYLNRHQVTHGSEKRFECQECRKTFY 699
Cdd:COG5048 432 YNLIPHKKIHTNHAPLLCSILKSFRR 457
COG5048 COG5048
FOG: Zn-finger [General function prediction only];
402-567 9.07e-07

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


Pssm-ID: 227381 [Multi-domain]  Cd Length: 467  Bit Score: 52.01  E-value: 9.07e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83816962 402 TRAGYKPYGCNLCGKAFYRKSHLGRHQ--KIHTGE--KPYGCEE--CKKTFYHKSSLTIHQRTHTGEKPYECKKCR---- 471
Cdd:COG5048 283 EKGFSLPIKSKQCNISFSRSSPLTRHLrsVNHSGEslKPFSCPYslCGKLFSRNDALKRHILLHTSISPAKEKLLNsssk 362

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83816962 472 ---KTFYCKSDLNVHHRTHTGEKPYECD--ECRKTFYSKSHLVIHQKVHTGDKPYECE--ECQKAFSRKSNLTVHQKTHT 544
Cdd:COG5048 363 fspLLNNEPPQSLQQYKDLKNDKKSETLsnSCIRNFKRDSNLSLHIITHLSFRPYNCKnpPCSKSFNRHYNLIPHKKIHT 442

                       170       180
                ....*....|....*....|...
gi 83816962 545 GEKPYECNVCGKtFHRQSHLNMH 567
Cdd:COG5048 443 NHAPLLCSILKS-FRRDLDLSNH 464
zf-H2C2_2 pfam13465
Zinc-finger double domain;
535-558 2.00e-03

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 36.20  E-value: 2.00e-03
                          10        20
                  ....*....|....*....|....
gi 83816962   535 NLTVHQKTHTGEKPYECNVCGKTF 558
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSF 24
SFP1 COG5189
Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division ...
 517-600 2.09e-03

Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning];


Pssm-ID: 227516 [Multi-domain]  Cd Length: 423  Bit Score: 41.24  E-value: 2.09e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 83816962 517 GDKPYECE--ECQKAFSRKSNLTVHQKT-HtgekpyecnvCGKTFHRQSHLNMHQGTHTGQKPYQCEECGKAFYQKSSLR 593
Cdd:COG5189 346 DGKPYKCPveGCNKKYKNQNGLKYHMLHgH----------QNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRYKNLNGLK 415


                ....*..
gi 83816962 594 RHQRNHT 600
Cdd:COG5189 416 YHRKHSH 422
zf-H2C2_2 pfam13465
Zinc-finger double domain;
591-616 2.54e-03

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 35.81  E-value: 2.54e-03
                          10        20
                  ....*....|....*....|....*.
gi 83816962   591 SLRRHQRNHTGSRPYACEECRKTFLH 616
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 577-599 3.42e-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: 35.35  E-value: 3.42e-03
                          10        20
                  ....*....|....*....|...
gi 83816962   577 YQCEECGKAFYQKSSLRRHQRNH 599
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
zf-H2C2_2 pfam13465
Zinc-finger double domain;
563-588 3.68e-03

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 35.42  E-value: 3.68e-03
                          10        20
                  ....*....|....*....|....*.
gi 83816962   563 HLNMHQGTHTGQKPYQCEECGKAFYQ 588
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-H2C2_2 pfam13465
Zinc-finger double domain;
479-502 3.91e-03

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 35.42  E-value: 3.91e-03
                          10        20
                  ....*....|....*....|....
gi 83816962   479 DLNVHHRTHTGEKPYECDECRKTF 502
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSF 24
zf-H2C2_2 pfam13465
Zinc-finger double domain;
647-670 3.91e-03

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 35.42  E-value: 3.91e-03
                          10        20
                  ....*....|....*....|....
gi 83816962   647 HLTVHQRTHTGEKPYECKLCKKAF 670
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSF 24
zf-C2H2 pfam00096
Zinc finger, C2H2 type; The C2H2 zinc finger is the classical zinc finger domain. The two ...
 521-543 4.29e-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: 34.97  E-value: 4.29e-03
                          10        20
                  ....*....|....*....|...
gi 83816962   521 YECEECQKAFSRKSNLTVHQKTH 543
Cdd:pfam00096   1 YKCPDCGKSFSRKSNLKRHLRTH 23
SUF4-like cd20908
N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), ...
 659-718 6.08e-03

N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins; Oryza sativa SUPPRESSOR OF FRI 4 (OsSUF4) is a C2H2-type zinc finger transcription factor which interacts with the major H3K36 methyltransferase SDG725 to promote H3K36me3 (tri-methylation at H3K9) establishment. The transcription factor OsSUF4 recognizes a specific 7-bp DNA element (5'-CGGAAAT-3'), which is contained in the promoter regions of many genes throughout the rice genome. Through interaction with OsSUF4, SDG725 is recruited to the promoters of key florigen genes, RICE FLOWERING LOCUS T1 (RFT1) and Heading date 3a (Hd3a), for H3K36 deposition to promote gene activation and rice plant flowering. OsSUF4 target genes include a number of genes involved in many biological processes. Flowering plant Arabidopsis SUF4 binds to a 15bp DNA element (5'-CCAAATTTTAAGTTT-3') within the promoter of the floral repressor gene FLOWERING LOCUS C (FLC) and recruits the FRI-C transcription activator complex to the FLC promoter. Although the DNA-binding element and target genes of AtSUF4 are different from those of OsSUF4, AtSUF4 is known to interact with the Arabidopsis H3K36 methyltransferase SDG8 (also known as ASHH2/EFS/SET8), and the methylation deposition mechanism mediated by the SUF4 transcription factor and H3K36 methyltransferase may be conserved in Arabidopsis and rice. Proteins in this family have two conserved C2H2-type zinc finger motifs at the N-terminus (included in this model), and a large proline-rich domain at the C-terminus; for OsSUF4, it has been shown that the N-terminal zinc-finger domain is responsible for DNA binding, and that the C-terminal domain interacts with SDG725.


Pssm-ID: 411020 [Multi-domain]  Cd Length: 82  Bit Score: 36.38  E-value: 6.08e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 83816962 659 KPYeCKLCKKAFHQKSYLNRHQVthgsEKRFECQECRKTFYHKSSLTVH-QRIHLRELLCV 718
Cdd:cd20908   1 KPW-CYYCDREFDDEKILIQHQK----AKHFKCHICHKKLYTAGGLAVHcLQVHKETLTKV 56
SUF4-like cd20908
N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), ...
 603-651 6.38e-03

N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins; Oryza sativa SUPPRESSOR OF FRI 4 (OsSUF4) is a C2H2-type zinc finger transcription factor which interacts with the major H3K36 methyltransferase SDG725 to promote H3K36me3 (tri-methylation at H3K9) establishment. The transcription factor OsSUF4 recognizes a specific 7-bp DNA element (5'-CGGAAAT-3'), which is contained in the promoter regions of many genes throughout the rice genome. Through interaction with OsSUF4, SDG725 is recruited to the promoters of key florigen genes, RICE FLOWERING LOCUS T1 (RFT1) and Heading date 3a (Hd3a), for H3K36 deposition to promote gene activation and rice plant flowering. OsSUF4 target genes include a number of genes involved in many biological processes. Flowering plant Arabidopsis SUF4 binds to a 15bp DNA element (5'-CCAAATTTTAAGTTT-3') within the promoter of the floral repressor gene FLOWERING LOCUS C (FLC) and recruits the FRI-C transcription activator complex to the FLC promoter. Although the DNA-binding element and target genes of AtSUF4 are different from those of OsSUF4, AtSUF4 is known to interact with the Arabidopsis H3K36 methyltransferase SDG8 (also known as ASHH2/EFS/SET8), and the methylation deposition mechanism mediated by the SUF4 transcription factor and H3K36 methyltransferase may be conserved in Arabidopsis and rice. Proteins in this family have two conserved C2H2-type zinc finger motifs at the N-terminus (included in this model), and a large proline-rich domain at the C-terminus; for OsSUF4, it has been shown that the N-terminal zinc-finger domain is responsible for DNA binding, and that the C-terminal domain interacts with SDG725.


Pssm-ID: 411020 [Multi-domain]  Cd Length: 82  Bit Score: 36.38  E-value: 6.38e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 83816962 603 RPYaCEECRKTFLHKSSLTVHQRSHTgykpYSCEECRKTFYSKSHLTVH 651
Cdd:cd20908   1 KPW-CYYCDREFDDEKILIQHQKAKH----FKCHICHKKLYTAGGLAVH 44
zf-H2C2_2 pfam13465
Zinc-finger double domain;
451-476 6.78e-03

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 34.65  E-value: 6.78e-03
                          10        20
                  ....*....|....*....|....*.
gi 83816962   451 SLTIHQRTHTGEKPYECKKCRKTFYC 476
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
zf-H2C2_2 pfam13465
Zinc-finger double domain;
507-532 9.56e-03

Zinc-finger double domain;


Pssm-ID: 463886 [Multi-domain]  Cd Length: 26  Bit Score: 34.27  E-value: 9.56e-03
                          10        20
                  ....*....|....*....|....*.
gi 83816962   507 HLVIHQKVHTGDKPYECEECQKAFSR 532
Cdd:pfam13465   1 NLKRHMRTHTGEKPYKCPECGKSFKS 26
 
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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