PlantRegMap/PlantTFDB v5.0
Plant Transcription
Factor Database
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Transcription Factor Information
Basic Information? help Back to Top | |||||||||
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TF ID | GSVIVT01025166001 | ||||||||
Common Name | VIT_06s0004g03070 | ||||||||
Organism | |||||||||
Taxonomic ID | |||||||||
Taxonomic Lineage |
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; rosids incertae sedis; Vitales; Vitaceae; Vitis
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Family | C2H2 | ||||||||
Protein Properties | Length: 478aa MW: 52536 Da PI: 9.6539 | ||||||||
Description | C2H2 family protein | ||||||||
Gene Model |
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Signature Domain? help Back to Top | |||||||
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No. | Domain | Score | E-value | Start | End | HMM Start | HMM End |
1 | zf-C2H2 | 16.2 | 2.9e-05 | 62 | 84 | 1 | 23 |
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C++C+k F r nL+ H r H GSVIVT01025166001 62 FICEICNKGFQRDQNLQLHRRGH 84 89*******************88 PP | |||||||
2 | zf-C2H2 | 12 | 0.00067 | 138 | 160 | 1 | 23 |
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k + +s+ k H + + GSVIVT01025166001 138 WKCEKCSKKYAVQSDWKAHSKIC 160 58*****************9876 PP |
Protein Features ? help Back to Top | ||||||
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Database | Entry ID | E-value | Start | End | InterPro ID | Description |
Gene3D | G3DSA:3.30.160.60 | 1.3E-5 | 61 | 84 | IPR013087 | Zinc finger C2H2-type/integrase DNA-binding domain |
SuperFamily | SSF57667 | 4.82E-7 | 61 | 84 | No hit | No description |
PROSITE profile | PS50157 | 10.845 | 62 | 84 | IPR007087 | Zinc finger, C2H2 |
Pfam | PF12171 | 5.7E-5 | 62 | 84 | IPR022755 | Zinc finger, double-stranded RNA binding |
SMART | SM00355 | 0.022 | 62 | 84 | IPR015880 | Zinc finger, C2H2-like |
PROSITE pattern | PS00028 | 0 | 64 | 84 | IPR007087 | Zinc finger, C2H2 |
SMART | SM00355 | 91 | 103 | 133 | IPR015880 | Zinc finger, C2H2-like |
Gene3D | G3DSA:3.30.160.60 | 5.0E-5 | 126 | 159 | IPR013087 | Zinc finger C2H2-type/integrase DNA-binding domain |
SuperFamily | SSF57667 | 4.82E-7 | 133 | 158 | No hit | No description |
SMART | SM00355 | 140 | 138 | 158 | IPR015880 | Zinc finger, C2H2-like |
Gene Ontology ? help Back to Top | ||||||
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GO Term | GO Category | GO Description | ||||
GO:0003676 | Molecular Function | nucleic acid binding | ||||
GO:0046872 | Molecular Function | metal ion binding |
Sequence ? help Back to Top |
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Protein Sequence Length: 478 aa Download sequence Send to blast |
MAEDGLTLPS SIRGFVQEPN SNPNPNPSAN PVKKKRNLPG TPDPEAEVIA LSPKSLMATN 60 RFICEICNKG FQRDQNLQLH RRGHNLPWKL RQRTSKEVRK KVYICPEKSC VHHNPTRALG 120 DLTGIKKHYS RKHGEKKWKC EKCSKKYAVQ SDWKAHSKIC GTREYKCDCG TLFSRKDSFI 180 THRAFCDALA EESARLTSVS APNPIFRNEL MNGSISNPQA HIIPQFSSPR LPLWLDHANS 240 HLNNPIGVNT NGSFLAPTSA GLPEMVQTAP MSMYGSPASS QNQWLQRCSE ASFTSSTLPR 300 VLKEEEENKG NLSESITSLF SSNQNQQESS AHMSATALLQ KAAQMGSTKS NSAFFSTTGF 360 GSINSSLSNT TPFSSYPHGR SNNQVHKFLI RQSNQSDSMN QLINSTSPSS TMGDGLLMGD 420 MNSTPLFHAS SNEVERGLTR DFLGVGSDAS RPFLQQELAK FASMGSAMGM SQYSGNH* |
3D Structure ? help Back to Top | ||||||
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PDB ID | Evalue | Query Start | Query End | Hit Start | Hit End | Description |
5b3h_C | 2e-38 | 134 | 203 | 3 | 72 | Zinc finger protein JACKDAW |
5b3h_F | 2e-38 | 134 | 203 | 3 | 72 | Zinc finger protein JACKDAW |
Search in ModeBase |
Nucleic Localization Signal ? help Back to Top | |||
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No. | Start | End | Sequence |
1 | 88 | 100 | KLRQRTSKEVRKK |
Expression -- UniGene ? help Back to Top | ||||||
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UniGene ID | E-value | Expressed in | ||||
Vvi.3360 | 0.0 | bud| fruit |
Expression -- Description ? help Back to Top | ||||||
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Source | Description | |||||
Uniprot | DEVELOPMENTAL STAGE: Start to accumulate during the 16- to 32-cell stage of embryogenesis. {ECO:0000269|PubMed:17785527}. | |||||
Uniprot | TISSUE SPECIFICITY: Expressed in the quiescent center, the ground tissue stem cells and to a lesser extent in mature cortex and endodermis cells. {ECO:0000269|PubMed:17785527}. |
Functional Description ? help Back to Top | ||||||
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Source | Description | |||||
UniProt | Transcription factor that, together with BIB, regulates tissue boundaries and asymmetric cell division by a rapid up-regulation of 'SCARECROW' (SCR), thus controlling the nuclear localization of 'SHORT-ROOT' (SHR) and restricting its action (PubMed:17785527, PubMed:25829440). Binds DNA via its zinc fingers (PubMed:28211915, PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Confines CYCD6 expression to the cortex-endodermis initial/daughter (CEI/CEID) tissues (PubMed:25829440). Required for radial patterning and stem cell maintenance (PubMed:17785527). Counteracted by 'MAGPIE' (MGP) (PubMed:17785527). Binds to the SCR and MGP promoter sequences (PubMed:21935722). Controls position-dependent signals that regulate epidermal-cell-type patterning (PubMed:20356954). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:20356954, ECO:0000269|PubMed:21935722, ECO:0000269|PubMed:24821766, ECO:0000269|PubMed:25829440, ECO:0000269|PubMed:28211915}. |
Regulation -- Description ? help Back to Top | ||||||
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Source | Description | |||||
UniProt | INDUCTION: Not regulated by SCR and SHR. {ECO:0000269|PubMed:21935722}. |
Regulation -- PlantRegMap ? help Back to Top | ||||||
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Source | Upstream Regulator | Target Gene | ||||
PlantRegMap | Retrieve | - |
Annotation -- Nucleotide ? help Back to Top | ||||||
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Source | Hit ID | E-value | Description | |||
GenBank | AM451995 | 0.0 | AM451995.1 Vitis vinifera, whole genome shotgun sequence, contig VV78X227225.4, clone ENTAV 115. |
Annotation -- Protein ? help Back to Top | |||||||
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Source | Hit ID | E-value | Description | ||||
Refseq | XP_002282251.2 | 0.0 | PREDICTED: protein indeterminate-domain 9 | ||||
Swissprot | Q700D2 | 1e-124 | IDD10_ARATH; Zinc finger protein JACKDAW | ||||
TrEMBL | F6GTZ5 | 0.0 | F6GTZ5_VITVI; Uncharacterized protein | ||||
STRING | VIT_06s0004g03070.t01 | 0.0 | (Vitis vinifera) |
Orthologous Group ? help Back to Top | |||
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Lineage | Orthologous Group ID | Taxa Number | Gene Number |
Representative plant | OGRP95 | 16 | 242 |
Best hit in Arabidopsis thaliana ? help Back to Top | ||||||
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Hit ID | E-value | Description | ||||
AT5G03150.1 | 1e-113 | C2H2-like zinc finger protein |
Link Out ? help Back to Top | |
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Phytozome | GSVIVT01025166001 |
Publications ? help Back to Top | |||
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