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 | Potri.016G088500.1 | ||||||||
Organism | |||||||||
Taxonomic ID | |||||||||
Taxonomic Lineage |
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus
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Family | C2H2 | ||||||||
Protein Properties | Length: 509aa MW: 55541.4 Da PI: 9.5681 | ||||||||
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 | 16.1 | 3.1e-05 | 63 | 85 | 1 | 23 |
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 + C++C+k F r nL+ H r H Potri.016G088500.1 63 FICEICNKGFQRDQNLQLHRRGH 85 89*******************88 PP | |||||||
2 | zf-C2H2 | 12.7 | 0.00038 | 139 | 161 | 1 | 23 |
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k + +s+ k H +t+ Potri.016G088500.1 139 WKCEKCSKKYAVQSDWKAHSKTC 161 58*****************9998 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 | 62 | 85 | IPR013087 | Zinc finger C2H2-type/integrase DNA-binding domain |
SuperFamily | SSF57667 | 6.28E-7 | 62 | 85 | No hit | No description |
Pfam | PF12171 | 6.1E-5 | 63 | 85 | IPR022755 | Zinc finger, double-stranded RNA binding |
PROSITE profile | PS50157 | 10.845 | 63 | 85 | IPR007087 | Zinc finger, C2H2 |
SMART | SM00355 | 0.022 | 63 | 85 | IPR015880 | Zinc finger, C2H2-like |
PROSITE pattern | PS00028 | 0 | 65 | 85 | IPR007087 | Zinc finger, C2H2 |
SMART | SM00355 | 110 | 104 | 134 | IPR015880 | Zinc finger, C2H2-like |
Gene3D | G3DSA:3.30.160.60 | 1.3E-4 | 127 | 160 | IPR013087 | Zinc finger C2H2-type/integrase DNA-binding domain |
SuperFamily | SSF57667 | 6.28E-7 | 134 | 159 | No hit | No description |
SMART | SM00355 | 140 | 139 | 159 | 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: 509 aa Download sequence Send to blast |
MMSGDAFSLP SLIAGFAQDQ NNANPKPNPN PVAKRKRNLP GTPDPDAEVI ALSPKTLMAT 60 NRFICEICNK GFQRDQNLQL HRRGHNLPWK LKQRTNKEVR KKVYICPEKT CVHHDSSRAL 120 GDLTGIKKHF SRKHGEKKWK CEKCSKKYAV QSDWKAHSKT CGTREYKCDC GTLFSRKDSF 180 ITHRAFCDAL ADESARITSV QDTDLNFRND TVNLPHGFSN RPGVPDIAGI SQFSAGFRPD 240 FSGMSSPGNS LGADQQKTGL SLWINQANSH ITPNSNLYVP PISTGLPEMV QMVANLYSSS 300 SSANIHGNLT LSGLSHELKE EGINKANMGD TSASLYSDRI QNKQLKLAAV PMSATALLQK 360 AAQMGSTRSN QPFFGNSYGL MSSSSSSSPT TNPISLNQNP NELYHVFQNV KQPASESLTA 420 TYNSVAMSDA VMGTSSNLDQ LVMQTSGNLQ NDPTQLKLQR GSNSTESGLT RDFLGMSSES 480 GRLFLPHDLA KFASISSAMS SNHFTANH* |
3D Structure ? help Back to Top | ||||||
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PDB ID | Evalue | Query Start | Query End | Hit Start | Hit End | Description |
5b3h_C | 9e-38 | 135 | 200 | 3 | 68 | Zinc finger protein JACKDAW |
5b3h_F | 9e-38 | 135 | 200 | 3 | 68 | Zinc finger protein JACKDAW |
Search in ModeBase |
Nucleic Localization Signal ? help Back to Top | |||
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No. | Start | End | Sequence |
1 | 89 | 101 | KLKQRTNKEVRKK |
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 | Potri.016G088500.1 |
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 -- Protein ? help Back to Top | |||||||
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Source | Hit ID | E-value | Description | ||||
Refseq | XP_024442854.1 | 0.0 | zinc finger protein JACKDAW | ||||
Swissprot | Q700D2 | 1e-135 | IDD10_ARATH; Zinc finger protein JACKDAW | ||||
TrEMBL | A0A2K1XCY6 | 0.0 | A0A2K1XCY6_POPTR; Uncharacterized protein | ||||
STRING | POPTR_0006s13130.1 | 0.0 | (Populus trichocarpa) |
Orthologous Group ? help Back to Top | |||
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Lineage | Orthologous Group ID | Taxa Number | Gene Number |
Fabids | OGEF181 | 34 | 275 | 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-118 | C2H2-like zinc finger protein |
Link Out ? help Back to Top | |
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Phytozome | Potri.016G088500.1 |
Publications ? help Back to Top | |||
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