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_009101276.1
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: 583aa    MW: 62136.2 Da    PI: 9.8677
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009101276.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H216.23e-0585107123
                     EEETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                     + C+ C+k F r  nL+ H r H
  XP_009101276.1  85 FICEVCNKGFQREQNLQLHRRGH 107
                     89*******************88 PP
2zf-C2H213.10.00028161183123
                     EEETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                     +kC++C+k++  +s+ k H +t+
  XP_009101276.1 161 WKCEKCSKRYAVQSDWKAHSKTC 183
                     58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.606.5E-684107IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576675.05E-784107No hitNo description
PfamPF121712.9E-585107IPR022755Zinc finger, double-stranded RNA binding
PROSITE profilePS5015710.9985107IPR007087Zinc finger, C2H2
SMARTSM003550.005285107IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028087107IPR007087Zinc finger, C2H2
SMARTSM00355110126156IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.602.7E-5149182IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576675.05E-7156181No hitNo description
SMARTSM00355130161181IPR015880Zinc 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: 583 aa     Download sequence    Send to blast
MAASSSSAAS FFGVRQDEQS HLLPPNSSAA VPPPPPPPPH HQPPQPQQPL EAPPQKKKRN  60
QPRTPNSDAE VIALSPKTLM ATNRFICEVC NKGFQREQNL QLHRRGHNLP WKLKQKSTKE  120
VKRKVYLCPE PSCVHHDPSR ALGDLTGIKK HYYRKHGEKK WKCEKCSKRY AVQSDWKAHS  180
KTCGTKEYRC DCGTLFSRRD SFITHRAFCD ALAQESARHP TSLTSLPSHH FPYGQTTNNS  240
NNNTPSMILG LPHIGNPQNL DHQSGDVLRL GSGGGGGGGA SRSSSDLIAA NASGYFMQEQ  300
NPSFHXGFLA ASNNIKPSPM NFQQSLMQFS NDNHNSPSSN LFNLSFLSGN NGIASGTSNP  360
NAAAVPSANH MLSNHFGGEN AVGGSGGGST GLFPNNLMSS AGRINSGAVP SLFSSSMQNP  420
NSASHMSATA LLQKAAQMGS STSSSNNNNT NNASSILRSF GSGMYGENES NLHDLMNSFS  480
NPGATGNSAN GVDSQFGTYG GVNKGLSADK QNMTRDFLGV GQIVRSMSGS AGFQQQQQQQ  540
HGNGGRERVG SSSDSADRNS MNVNPGGGGS TSSPPYGIHH ASF
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C4e-34157218364Zinc finger protein JACKDAW
5b3h_F4e-34157218364Zinc finger protein JACKDAW
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.310841e-137silique
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Highly expressed in leaf tissues. {ECO:0000305|PubMed:22898356}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor acting as a positive regulator of the starch synthase SS4. Controls chloroplast development and starch granule formation (PubMed:22898356). Binds DNA via its zinc fingers (PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). {ECO:0000269|PubMed:22898356, ECO:0000269|PubMed:24821766}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009101276.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAJ6214950.0AJ621495.1 Arabidopsis thaliana mRNA for ID1-like zinc finger protein 2 (idz2 gene).
GenBankAY0561740.0AY056174.1 Arabidopsis thaliana putative C2H2-type zinc finger protein (At2g02070) mRNA, complete cds.
GenBankAY0813140.0AY081314.1 Arabidopsis thaliana putative C2H2-type zinc finger protein (At2g02070) mRNA, complete cds.
GenBankBT0012150.0BT001215.1 Arabidopsis thaliana putative C2H2-type zinc finger protein (At2g02070) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009101276.10.0PREDICTED: LOW QUALITY PROTEIN: protein indeterminate-domain 5, chloroplastic
SwissprotQ9ZUL30.0IDD5_ARATH; Protein indeterminate-domain 5, chloroplastic
TrEMBLA0A397ZA720.0A0A397ZA72_BRACM; Uncharacterized protein
STRINGBra024834.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM43732654
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G02070.10.0indeterminate(ID)-domain 5
Publications ? help Back to Top
  1. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]