PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID XP_009101285.1
Organism
Brassica rapa
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
Family C2H2
Protein Properties Length: 444aa    MW: 49876.2 Da    PI: 9.0808
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009101285.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H217.51.1e-0580102123
                     EEETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                     y C++C++ F r  nL+ H r+H
  XP_009101285.1  80 YICEICNQGFQRDQNLQMHRRRH 102
                     89********************9 PP
2zf-C2H216.13.3e-05158180123
                     EEETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                     ++C++C+k +  +s++k H++t+
  XP_009101285.1 158 WVCEKCSKGYAVQSDYKAHLKTC 180
                     58*******************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576675.88E-577103No hitNo description
Gene3DG3DSA:3.30.160.601.3E-579102IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.006580102IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.86680102IPR007087Zinc finger, C2H2
PROSITE patternPS00028082102IPR007087Zinc finger, C2H2
SMARTSM00355170122152IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.604.6E-4149179IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM0035560158185IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 444 aa     Download sequence    Send to blast
MKTDQGAVVM LDDAASKKNT ANTRCVVFSS SDPLLSSSEN GVTTTKTSIQ KRKRRPAGTP  60
DPDAEVVSLS PRTLLESDRY ICEICNQGFQ RDQNLQMHRR RHKVPWKLLK RDNNIEVKKR  120
VYVCPEPSCL HHDPCHALGD LVGIKKHFRR KHSNHKQWVC EKCSKGYAVQ SDYKAHLKTC  180
GTRGHSCDCG RVFSRVESFI EHQDNCSVRN VHHEPPPPPQ TAVIVTACSS RTASTASTPS  240
SETNYGGAVT VATPLPLEGR PIHIRSSSLT PLLLTNSSNL NLELQLLPST PNLNPNQENQ  300
QHKVKEPSLH HHHHHHNHDT TNLNLSIAPS SSSYHHYNNF DRIKELMASE EIMKEKAYAE  360
EAKREAKRQR EIAENEFANA KKIRQQAQTE LKRAKLLKEQ SMKKISSTLM QVTCQTCKGQ  420
FQATEETSLV VSYMSSANTD GEGS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C6e-18154208357Zinc finger protein JACKDAW
5b3h_F6e-18154208357Zinc finger protein JACKDAW
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expression levels gradually decrease with aging in both the shoot and root vasculature. {ECO:0000269|PubMed:16813575}.
UniprotTISSUE SPECIFICITY: Mainly expressed in the endodermis, the gravity-sensing tissue in inflorescence stems. Mostly present in stems and flowers, and, to a lower extent, in seedlings, hypocotyls, roots and the shoot apical meristem (SAM). {ECO:0000269|PubMed:16813575}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor involved in inflorescence stems gravitropism, probably by regulating starch accumulation in amyloplasts of graviperceptive cells. Required for stem circumnutation movements. Regulates lateral organ morphogenesis and gravitropic responses (PubMed:24039602). Acts cooperatively with IDD16 to control silique and branche orientation (PubMed:24039602). Involved in the establishment of auxin gradients through the regulation of auxin biosynthesis and transport (PubMed:24039602). {ECO:0000269|PubMed:16813575, ECO:0000269|PubMed:18259878, ECO:0000269|PubMed:24039602, ECO:0000269|PubMed:9210330}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009101285.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Not regulated by auxin. {ECO:0000269|PubMed:24039602}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK2267030.0AK226703.1 Arabidopsis thaliana mRNA for putative C2H2-type zinc finger protein, complete cds, clone: RAFL07-61-I21.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009101285.10.0PREDICTED: protein SHOOT GRAVITROPISM 5-like
SwissprotF4IPE30.0IDD15_ARATH; Zinc finger protein SHOOT GRAVITROPISM 5
TrEMBLA0A078FSX30.0A0A078FSX3_BRANA; BnaA06g34390D protein
TrEMBLA0A397Z3J60.0A0A397Z3J6_BRACM; Uncharacterized protein
TrEMBLM4E7T50.0M4E7T5_BRARP; Uncharacterized protein
STRINGBra024841.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM69328131
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G01940.10.0C2H2-like zinc finger protein
Publications ? help Back to Top
  1. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  2. Kim JY,Ryu JY,Baek K,Park CM
    High temperature attenuates the gravitropism of inflorescence stems by inducing SHOOT GRAVITROPISM 5 alternative splicing in Arabidopsis.
    New Phytol., 2016. 209(1): p. 265-79
    [PMID:26256266]
  3. Ryu JY,Kim JY,Park CM
    Adaptive thermal control of stem gravitropism through alternative RNA splicing in Arabidopsis.
    Plant Signal Behav, 2015. 10(11): p. e1093715
    [PMID:26452406]
  4. Qu Y, et al.
    Peroxisomal CuAOζ and its product H2O2 regulate the distribution of auxin and IBA-dependent lateral root development in Arabidopsis.
    J. Exp. Bot., 2017. 68(17): p. 4851-4867
    [PMID:28992128]
  5. Shi H, et al.
    Zinc finger of Arabidopsis thaliana 6 is involved in melatonin-mediated auxin signaling through interacting INDETERMINATE DOMAIN15 and INDOLE-3-ACETIC ACID 17.
    J. Pineal Res., 2018. 65(2): p. e12494
    [PMID:29607541]