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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 | Rsa1.0_48209.1_g00001.1 | ||||||||
Organism | |||||||||
Taxonomic ID | |||||||||
Taxonomic Lineage |
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
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Family | C2H2 | ||||||||
Protein Properties | Length: 126aa MW: 14842.3 Da PI: 10.3005 | ||||||||
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 | 19.8 | 2.1e-06 | 9 | 31 | 1 | 23 |
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ++C++C+k F r nL+ H r H Rsa1.0_48209.1_g00001.1 9 FVCEICNKGFQRDQNLQLHRRGH 31 89*******************88 PP | |||||||
2 | zf-C2H2 | 18.3 | 6.4e-06 | 86 | 108 | 1 | 23 |
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ykC++C+k + +s+ k H +t+ Rsa1.0_48209.1_g00001.1 86 YKCEKCSKKYAVQSDWKAHAKTC 108 9*******************998 PP |
Protein Features ? help Back to Top | ||||||
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Database | Entry ID | E-value | Start | End | InterPro ID | Description |
SuperFamily | SSF57667 | 5.74E-9 | 8 | 31 | No hit | No description |
Gene3D | G3DSA:3.30.160.60 | 2.5E-6 | 8 | 31 | IPR013087 | Zinc finger C2H2-type/integrase DNA-binding domain |
PROSITE profile | PS50157 | 10.949 | 9 | 31 | IPR007087 | Zinc finger, C2H2 |
SMART | SM00355 | 0.017 | 9 | 31 | IPR015880 | Zinc finger, C2H2-like |
Pfam | PF12171 | 1.2E-5 | 9 | 31 | IPR022755 | Zinc finger, double-stranded RNA binding |
PROSITE pattern | PS00028 | 0 | 11 | 31 | IPR007087 | Zinc finger, C2H2 |
SMART | SM00355 | 73 | 51 | 81 | IPR015880 | Zinc finger, C2H2-like |
Gene3D | G3DSA:3.30.160.60 | 1.2E-6 | 74 | 107 | IPR013087 | Zinc finger C2H2-type/integrase DNA-binding domain |
SuperFamily | SSF57667 | 5.74E-9 | 81 | 106 | No hit | No description |
SMART | SM00355 | 74 | 86 | 106 | 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: 126 aa Download sequence Send to blast |
TTLMATNRFV CEICNKGFQR DQNLQLHRRG HNLPWKLKQR SNKEVIKKKV YICPIKTCVH 60 HDSSRALGDL TGIKKHYSRK HGEKKYKCEK CSKKYAVQSD WKAHAKTCGT REYKCDCGTL 120 FSRYYI |
3D Structure ? help Back to Top | ||||||
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PDB ID | Evalue | Query Start | Query End | Hit Start | Hit End | Description |
5b3h_C | 5e-23 | 82 | 123 | 3 | 44 | Zinc finger protein JACKDAW |
5b3h_F | 5e-23 | 82 | 123 | 3 | 44 | Zinc finger protein JACKDAW |
Search in ModeBase |
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}. |
Cis-element ? help Back to Top | |
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Source | Link |
PlantRegMap | Rsa1.0_48209.1_g00001.1 |
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 | AB005240 | 1e-138 | AB005240.1 Arabidopsis thaliana genomic DNA, chromosome 5, P1 clone:MOK16. | |||
GenBank | AL163002 | 1e-138 | AL163002.1 Arabidopsis thaliana DNA chromosome 5, BAC clone F15A17 (ESSA project). | |||
GenBank | CP002688 | 1e-138 | CP002688.1 Arabidopsis thaliana chromosome 5 sequence. |
Annotation -- Protein ? help Back to Top | |||||||
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Source | Hit ID | E-value | Description | ||||
Refseq | XP_018473110.1 | 3e-88 | PREDICTED: zinc finger protein JACKDAW-like | ||||
Swissprot | Q700D2 | 3e-85 | IDD10_ARATH; Zinc finger protein JACKDAW | ||||
TrEMBL | A0A0D3AZI4 | 1e-89 | A0A0D3AZI4_BRAOL; Uncharacterized protein | ||||
TrEMBL | A0A3N6QF84 | 1e-89 | A0A3N6QF84_BRACR; Uncharacterized protein | ||||
STRING | Bra005741.1-P | 8e-87 | (Brassica rapa) | ||||
STRING | Bo3g002190.1 | 2e-90 | (Brassica oleracea) |
Orthologous Group ? help Back to Top | |||
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Lineage | Orthologous Group ID | Taxa Number | Gene Number |
Malvids | OGEM155 | 28 | 306 |
Best hit in Arabidopsis thaliana ? help Back to Top | ||||||
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Hit ID | E-value | Description | ||||
AT5G03150.1 | 1e-75 | C2H2-like zinc finger protein |
Publications ? help Back to Top | |||
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