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PlantRegMap/PlantTFDB v5.0
Plant Transcription
Factor Database
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Home TFext BLAST Prediction Download Help About Links PlantRegMap |
Transcription Factor Information
Basic Information? help Back to Top | |||||||||
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TF ID | Sopen09g002420.1 | ||||||||
Organism | |||||||||
Taxonomic ID | |||||||||
Taxonomic Lineage |
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon
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Family | C2H2 | ||||||||
Protein Properties | Length: 458aa MW: 51267.5 Da PI: 9.7749 | ||||||||
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 | 16.3 | 2.7e-05 | 61 | 83 | 1 | 23 |
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C++C+k F r nL+ H r H Sopen09g002420.1 61 FICEICNKGFQRDQNLQLHRRGH 83 89*******************88 PP | |||||||
2 | zf-C2H2 | 14.1 | 0.00014 | 138 | 160 | 1 | 23 |
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k + +s+ k H +t+ Sopen09g002420.1 138 WKCEKCSKKYAVQSDWKAHTKTC 160 58*******************98 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 | 1.2E-5 | 60 | 83 | IPR013087 | Zinc finger C2H2-type/integrase DNA-binding domain |
SuperFamily | SSF57667 | 2.7E-7 | 60 | 83 | No hit | No description |
SMART | SM00355 | 0.022 | 61 | 83 | IPR015880 | Zinc finger, C2H2-like |
PROSITE profile | PS50157 | 10.845 | 61 | 83 | IPR007087 | Zinc finger, C2H2 |
Pfam | PF12171 | 5.4E-5 | 61 | 83 | IPR022755 | Zinc finger, double-stranded RNA binding |
PROSITE pattern | PS00028 | 0 | 63 | 83 | IPR007087 | Zinc finger, C2H2 |
SMART | SM00355 | 110 | 103 | 133 | IPR015880 | Zinc finger, C2H2-like |
Gene3D | G3DSA:3.30.160.60 | 1.3E-4 | 126 | 159 | IPR013087 | Zinc finger C2H2-type/integrase DNA-binding domain |
SuperFamily | SSF57667 | 2.7E-7 | 133 | 158 | No hit | No description |
SMART | SM00355 | 130 | 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: 458 aa Download sequence Send to blast |
MMSGDLFSIH QQQHQQVLVE QNPNPKANSS SKKRRNLPGT PDPDAEVIAI SPKTLMATNR 60 FICEICNKGF QRDQNLQLHR RGHNLPWKLK QRNKQEIVKK KVYICPEKSC VHHDPSRALG 120 DLTGIKKHFS RKHGEKKWKC EKCSKKYAVQ SDWKAHTKTC GTREYKCDCG TLFSRKDSFI 180 THRAFCDALA EESARITTTN NLNFNQQQQQ QPVGVSQIGT SFAQDFTSMT TVNPLHQHQQ 240 KPRLSLWLNQ ANNNMSSQSS NLFGLPDHHM VQIPSHNMFA TNQILNPTPT TNTNTNTNTN 300 TPATPNPPIP MSATALLQKA AQMGSTKSTP NYFSNTFGVM HSSSSPSSNN TTQIFNNNEI 360 HQAFAKQTED YNQTENILIN GCPNMNSSVN SKAINLDQAL LQTGGMHNQN VHFNLHNSLT 420 RDFLGMGNEG GQPFLPQELA KFASINSAMG LSHYSTGH |
3D Structure ? help Back to Top | ||||||
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PDB ID | Evalue | Query Start | Query End | Hit Start | Hit End | Description |
5b3h_C | 6e-38 | 134 | 203 | 3 | 72 | Zinc finger protein JACKDAW |
5b3h_F | 6e-38 | 134 | 203 | 3 | 72 | Zinc finger protein JACKDAW |
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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 | HG975448 | 0.0 | HG975448.1 Solanum pennellii chromosome ch09, complete genome. |
Annotation -- Protein ? help Back to Top | |||||||
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Source | Hit ID | E-value | Description | ||||
Refseq | XP_015086419.1 | 0.0 | zinc finger protein JACKDAW-like isoform X1 | ||||
Swissprot | Q700D2 | 1e-129 | IDD10_ARATH; Zinc finger protein JACKDAW | ||||
TrEMBL | A0A3Q7HWE3 | 0.0 | A0A3Q7HWE3_SOLLC; Uncharacterized protein | ||||
STRING | Solyc09g007550.2.1 | 0.0 | (Solanum lycopersicum) |
Orthologous Group ? help Back to Top | |||
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Lineage | Orthologous Group ID | Taxa Number | Gene Number |
Asterids | OGEA103 | 24 | 350 |
Best hit in Arabidopsis thaliana ? help Back to Top | ||||||
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Hit ID | E-value | Description | ||||
AT5G03150.1 | 1e-103 | C2H2-like zinc finger protein |
Publications ? help Back to Top | |||
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