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_013594176.1
Organism
Brassica oleracea
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: 442aa    MW: 49628 Da    PI: 9.073
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_013594176.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H212.50.0004480102123
                     EEETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                     y C++C++   r  nL+ H r+H
  XP_013594176.1  80 YICEICNQGVQRDQNLQMHRRRH 102
                     89********************9 PP
2zf-C2H216.13.3e-05158180123
                     EEETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                     ++C++C+k +  +s++k H++t+
  XP_013594176.1 158 WVCEKCSKGYAVQSDYKAHLKTC 180
                     58*******************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS501579.36980102IPR007087Zinc finger, C2H2
SMARTSM003550.1980102IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028082102IPR007087Zinc finger, C2H2
SMARTSM00355160122152IPR015880Zinc 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: 442 aa     Download sequence    Send to blast
MKTDQGAVVM LDDAASKKNT TNTRCVVFSS SDILLPSSEN GVTTTKTSTQ KRKRRPAGTP  60
DPDAEVVSLS PRTLLESDRY ICEICNQGVQ RDQNLQMHRR RHKVPWKLLR RDNNIEVKKR  120
VYVCPEPTCL HHDPCHALGD LVGIKKHFRR KHSNHKQWVC EKCSKGYAVQ SDYKAHLKTC  180
GTRGHSCDCG RVFSRVESFI EHQDNCSVRN VHHEPPPPPQ TAAIITACSS RTASTASTPS  240
SETNYGGAVT AATPLPLEGR PIHIRSSSLT PLVLNNSSNL NLELQLLPLT PNLNPNQEYQ  300
QHKVKEPSLH HHHHNHDTTN LNLSIAPSSS SYHHYNNFDR IKELMASEQI MKEKAYAEEA  360
KREAKIQREI AENEFANAKK IRQQAQTELK RAKLLKEQSM KKISSTIMQV TCQTCKGQFQ  420
ATEETSLVVS YMSSANTDGE GS
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_013594176.1
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_013594176.10.0PREDICTED: protein SHOOT GRAVITROPISM 5
SwissprotF4IPE30.0IDD15_ARATH; Zinc finger protein SHOOT GRAVITROPISM 5
TrEMBLA0A0D3DAA00.0A0A0D3DAA0_BRAOL; Uncharacterized protein
STRINGBo7g080080.10.0(Brassica oleracea)
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]