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 | XP_013623652.1 | ||||||||
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; Brassica
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Family | C2H2 | ||||||||
Protein Properties | Length: 505aa MW: 55397 Da PI: 9.8746 | ||||||||
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 | 1.4e-05 | 82 | 104 | 1 | 23 |
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ++C++C+k F r nL+ H r H XP_013623652.1 82 FVCEICNKGFQRDQNLQLHRRGH 104 89*******************88 PP | |||||||
2 | zf-C2H2 | 15.7 | 4.3e-05 | 159 | 181 | 1 | 23 |
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 ykC++C+k + +s+ k H +t+ XP_013623652.1 159 YKCEKCSKKYAVQSDWKAHAKTC 181 9*******************998 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 | 1.7E-5 | 81 | 104 | IPR013087 | Zinc finger C2H2-type/integrase DNA-binding domain |
SuperFamily | SSF57667 | 9.17E-8 | 81 | 104 | No hit | No description |
SMART | SM00355 | 0.017 | 82 | 104 | IPR015880 | Zinc finger, C2H2-like |
PROSITE profile | PS50157 | 10.949 | 82 | 104 | IPR007087 | Zinc finger, C2H2 |
Pfam | PF12171 | 8.1E-5 | 82 | 104 | IPR022755 | Zinc finger, double-stranded RNA binding |
PROSITE pattern | PS00028 | 0 | 84 | 104 | IPR007087 | Zinc finger, C2H2 |
SMART | SM00355 | 73 | 124 | 154 | IPR015880 | Zinc finger, C2H2-like |
Gene3D | G3DSA:3.30.160.60 | 7.6E-6 | 147 | 180 | IPR013087 | Zinc finger C2H2-type/integrase DNA-binding domain |
SuperFamily | SSF57667 | 9.17E-8 | 154 | 179 | No hit | No description |
SMART | SM00355 | 74 | 159 | 179 | 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: 505 aa Download sequence Send to blast |
MQMIPGDPFS ISSSMGGFVH QEQHIHHLQQ HIPELNPNSN PNPSAKPNSS SAKKKRNQPG 60 TPDPDADVIA LSPTTLMATN RFVCEICNKG FQRDQNLQLH RRGHNLPWKL KQRSNKEVIK 120 KKVYICPIKT CVHHDSSRAL GDLTGIKKHY SRKHGEKKYK CEKCSKKYAV QSDWKAHAKT 180 CGTREYKCDC GTLFSRKDSF ITHRAFCDAL TEEGARMSSL SNNPAISTTT SLNFANDSHV 240 INNPNLPHGF VHRGVHHPDI NAAISQFGLG FGHDLSAMHT QGSSEMVQMA STGNHHLFPL 300 SSSSFLSDFS DHHYNQQFEI PTTSTNPNLT LSSSSTSQQT SASLPSLHQQ HQTLKGSSFS 360 PLFSSSSDKK QNKPLSPMSA TALLQKAAQM GSTRSNSTTV PPLFAGPTMT SSSSAASPPP 420 RSSSPLMIQQ ELNNFNHNLA PPTSGVTTSS VDNNNPFQSN RSGLNPAQQM GLTRDFLGVS 480 NENHPHQMGR HPFLPQELAR FAPLG |
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-42 | 155 | 223 | 3 | 71 | Zinc finger protein JACKDAW |
5b3h_F | 2e-42 | 155 | 223 | 3 | 71 | 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 | XP_013623652.1 |
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 | 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. |
Annotation -- Protein ? help Back to Top | |||||||
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Source | Hit ID | E-value | Description | ||||
Refseq | XP_013623652.1 | 0.0 | PREDICTED: zinc finger protein JACKDAW | ||||
Swissprot | Q700D2 | 0.0 | IDD10_ARATH; Zinc finger protein JACKDAW | ||||
TrEMBL | A0A3P6ACK3 | 0.0 | A0A3P6ACK3_BRAOL; Uncharacterized protein | ||||
STRING | Bra005741.1-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 |
Publications ? help Back to Top | |||
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