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_009112327.1
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: 492aa    MW: 52078.4 Da    PI: 7.6719
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009112327.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H216.72.1e-056183123
                    EEETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                    ++C++C+k F r  nL+ H r H
  XP_009112327.1 61 FVCEICSKGFQRDQNLQLHRRGH 83
                    89*******************88 PP
2zf-C2H2157.2e-05137159123
                     EEETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                     +kC++C+ks+  +s+ k H + +
  XP_009112327.1 137 FKCEKCSKSYAVQSDWKAHSKIC 159
                     89*****************9876 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576673.33E-76083No hitNo description
Gene3DG3DSA:3.30.160.605.8E-56083IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.0366183IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.8876183IPR007087Zinc finger, C2H2
PROSITE patternPS0002806383IPR007087Zinc finger, C2H2
SMARTSM0035581102132IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.0E-4125158IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.33E-7132157No hitNo description
SMARTSM0035580137157IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009937Biological Processregulation of gibberellic acid mediated signaling pathway
GO:0010029Biological Processregulation of seed germination
GO:0010431Biological Processseed maturation
GO:0005634Cellular Componentnucleus
GO:0044212Molecular Functiontranscription regulatory region DNA binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 492 aa     Download sequence    Send to blast
MPVDLDDSST VSGDASVSST GNQNPPPQSA AKKKRNLPGM PDPDSEVIAL SPKTLMATNR  60
FVCEICSKGF QRDQNLQLHR RGHNLPWKLR QRSSKEVRKK VYVCPVSGCV HHDPSRALGD  120
LTGIKKHFCR KHGEKKFKCE KCSKSYAVQS DWKAHSKICG SKEYRCDCGT LFSRRDSFIT  180
HRAFCDVLAE ESAKNHTQSK ELYPETVVRN NLPEPEQKSP AAVDSPPSVA LVPAPAVSVE  240
TETEPQPANI VSSSVLPIRD SSDEPENNTL EVIMEEAPRT IGLNGSNDHS SNNSKSVYAG  300
LFASSSSSTS LYAASSTPSP SLFPPSSSME PISLCLSTTG PSLFGATIQD PPQPHFLTPL  360
PHPPQPAISA TALLQKAAQM GSTGSGGSLL RGLGIVSTTS SPMELSSHDP GFGLGLGLPC  420
SSGSGLKELM MGNSSVFDPK QTTLDFLGLG RAVGNNNPGG GGLSSALWGG GGGMDVFGSG  480
ELSDKDTGRR SS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C3e-31133199369Zinc finger protein JACKDAW
5b3h_F3e-31133199369Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
18799KLRQRSSKEVRKK
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.61670.0flower
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Strongly up-regulated during seed development. {ECO:0000269|PubMed:21571950}.
UniprotTISSUE SPECIFICITY: At 3 days post anthesis (DPA), expressed in the chalazal endosperm region. By 6 DPA, expressed in the endosperm and embryo. In fully germinated seed, strongest expression in the root tip and not detected in the cotyledons. In 4-days old seedlings, restricted to the vasculature of the cotyledons, the shoot apical meristem region, and the root tip. By 8 days, restricted to newly emerged leaves. {ECO:0000269|PubMed:21571950}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor promoting the transition to germination by regulating light and hormonal signaling during seed maturation (PubMed:21571950). Acts as a positive regulator of phytochrome and/or gibberellin action (PubMed:21571950, PubMed:25035403). {ECO:0000269|PubMed:21571950, ECO:0000269|PubMed:25035403}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00592DAPTransfer from AT5G66730Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009112327.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC1892250.0AC189225.2 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrB011P07, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009112327.10.0PREDICTED: protein indeterminate-domain 1-like
SwissprotQ9LVQ70.0IDD1_ARATH; Zinc finger protein ENHYDROUS
TrEMBLM4F7U00.0M4F7U0_BRARP; Uncharacterized protein
STRINGBra037151.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM15528306
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G66730.10.0C2H2-like zinc finger protein
Publications ? help Back to Top
  1. Fukazawa J, et al.
    DELLAs function as coactivators of GAI-ASSOCIATED FACTOR1 in regulation of gibberellin homeostasis and signaling in Arabidopsis.
    Plant Cell, 2014. 26(7): p. 2920-38
    [PMID:25035403]
  2. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]