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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 | GSBRNA2T00136485001 | ||||||||
Common Name | GSBRNA2T00136485001 | ||||||||
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; Brassica
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Family | C2H2 | ||||||||
Protein Properties | Length: 515aa MW: 56710.5 Da PI: 10.2448 | ||||||||
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 | 17.2 | 1.5e-05 | 82 | 104 | 1 | 23 |
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ++C++C+k F r nL+ H r H GSBRNA2T00136485001 82 FVCEICNKGFQRDQNLQLHRRGH 104 89*******************88 PP | |||||||
2 | zf-C2H2 | 15 | 7.2e-05 | 167 | 189 | 1 | 23 |
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k + +s+ k H +t+ GSBRNA2T00136485001 167 FKCEKCSKKYAVQSDWKAHAKTC 189 89******************998 PP |
Protein Features ? help Back to Top | ||||||
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Database | Entry ID | E-value | Start | End | InterPro ID | Description |
SuperFamily | SSF57667 | 5.76E-8 | 81 | 104 | No hit | No description |
Gene3D | G3DSA:3.30.160.60 | 1.7E-5 | 81 | 104 | IPR013087 | Zinc finger C2H2-type/integrase DNA-binding domain |
SMART | SM00355 | 0.017 | 82 | 104 | IPR015880 | Zinc finger, C2H2-like |
PROSITE profile | PS50157 | 10.949 | 82 | 104 | IPR007087 | Zinc finger, C2H2 |
Pfam | PF12171 | 8.2E-5 | 82 | 104 | IPR022755 | Zinc finger, double-stranded RNA binding |
PROSITE pattern | PS00028 | 0 | 84 | 104 | IPR007087 | Zinc finger, C2H2 |
SMART | SM00355 | 73 | 132 | 162 | IPR015880 | Zinc finger, C2H2-like |
Gene3D | G3DSA:3.30.160.60 | 1.3E-5 | 155 | 188 | IPR013087 | Zinc finger C2H2-type/integrase DNA-binding domain |
SuperFamily | SSF57667 | 5.76E-8 | 162 | 187 | No hit | No description |
SMART | SM00355 | 92 | 167 | 187 | 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: 515 aa Download sequence Send to blast |
MQMIPGDPFS ISSSMGGFVH QEQHLHHLQQ HIQDINPNSN PNPNAKPNSS SAKKKRNQPG 60 TPDPDADVIA LSPTTLMATN RFVCEICNKG FQRDQNLQLH RRGHNLPWKL KQRSNKELKQ 120 RSNKEVIKKK VYICPIKTCV HHDSSRALGD LTGIKKHYSR KHGEKKFKCE KCSKKYAVQS 180 DWKAHAKTCG TREYKCDCGT LFSRKDSFIT HRAFCDALTE EGARMSSLSN NSAISTTTMT 240 TNLNFGNDSH VMNNSNLPHG FVHRGVHHPD INAAISQFGL GFGHDLTGMH PQGLSEMVQM 300 TSSGNHHLFP LSSSSVLPDF SGHHHNQQFQ IPTTSTTSQQ TSASLPSLQQ QHQTLKDSSF 360 SPLFSSSSET KQNKPLSPMS ATALLQKAAQ MGSTRSNSTT APSIFAGPTM TSSSSAASPP 420 PRSSSPMMIQ QQLNNNFNTN VPREIHNLAP PSSGVTTNNV DNNHRFQSNR SGITPVQQMG 480 LTRDFLGVSN EHHPHQTGHR PFLPQELARF APSG* |
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-42 | 163 | 232 | 3 | 72 | Zinc finger protein JACKDAW |
5b3h_F | 6e-42 | 163 | 232 | 3 | 72 | Zinc finger protein JACKDAW |
Search in ModeBase |
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}. |
Cis-element ? help Back to Top | |
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Source | Link |
PlantRegMap | GSBRNA2T00136485001 |
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 | AJ621494 | 0.0 | AJ621494.1 Arabidopsis thaliana mRNA for ID1-like zinc finger protein 3 (idz3 gene). | |||
GenBank | AJ630493 | 0.0 | AJ630493.1 Arabidopsis thaliana mRNA for hypothetical protein, clone At5g03150. | |||
GenBank | AK228895 | 0.0 | AK228895.1 Arabidopsis thaliana mRNA for hypothetical protein, partial cds, clone: RAFL16-21-B02. |
Annotation -- Protein ? help Back to Top | |||||||
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Source | Hit ID | E-value | Description | ||||
Refseq | XP_013686539.1 | 0.0 | zinc finger protein JACKDAW isoform X1 | ||||
Swissprot | Q700D2 | 0.0 | IDD10_ARATH; Zinc finger protein JACKDAW | ||||
TrEMBL | A0A397XP91 | 0.0 | A0A397XP91_BRACM; Uncharacterized protein | ||||
STRING | Bra009549.1-P | 0.0 | (Brassica rapa) |
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 | 0.0 | C2H2-like zinc finger protein |