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_009129175.1
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: 590aa    MW: 63622.7 Da    PI: 9.2046
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009129175.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H216.23e-0581103123
                     EEETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                     + C+ C+k F r  nL+ H r H
  XP_009129175.1  81 FICEVCNKGFQREQNLQLHRRGH 103
                     89*******************88 PP
2zf-C2H213.10.00028157179123
                     EEETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                     +kC++C+k++  +s+ k H +t+
  XP_009129175.1 157 WKCEKCSKRYAVQSDWKAHSKTC 179
                     58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.606.6E-680103IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.15E-780103No hitNo description
SMARTSM003550.005281103IPR015880Zinc finger, C2H2-like
PfamPF121712.9E-581103IPR022755Zinc finger, double-stranded RNA binding
PROSITE profilePS5015710.9981103IPR007087Zinc finger, C2H2
PROSITE patternPS00028083103IPR007087Zinc finger, C2H2
SMARTSM00355110122152IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.602.7E-5145178IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.15E-7152177No hitNo description
SMARTSM00355130157177IPR015880Zinc 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: 590 aa     Download sequence    Send to blast
MAASSSSNAS FFGVREEDQT HLLPPNPSAA VAPPPHHQPP QSQQPLEAPP QKKKRNQPRT  60
PNSDAEVIAL SPKTLMATNR FICEVCNKGF QREQNLQLHR RGHNLPWKLK QKSTKEVKRK  120
VYLCPEPTCV HHDPSRALGD LTGIKKHYYR KHGEKKWKCE KCSKRYAVQS DWKAHSKTCG  180
TKEYRCDCGT LFSRRDSFIT HRAFCDALAQ ESARHPTSLT SLPSHHFPYG QNTNSNNNSS  240
SMMLGLSHTG PPQNLDHHSG DVLRLGSGEG VGEGAASRSS SDLIAANSSG YFMQDQNHSF  300
HDQQQGFLAA SNNIKPSPMN FQQSLMQFSH DSHNSPSSNL FNLSFLSGNN GVASATSNHN  360
AAAVSSGNLM ISNHFDGENA IGGGGGGEGS TGLFPNNMIN STDRTSSGAV PSLFSSSMQN  420
PISTPQMSAT ALLQKAAQMG STSSNNNNNN NNNGSSNNNN NNASSILRNF GSGMYGENES  480
NLYDLMNSFS NPDPTGNNSN GVNSPFGSYR GVNKGLNADK QSLTRDFLGV GQIVRSMSGS  540
GGVQQQQQQH GNSRERVGSS SDSVDRNSNT FNPGGGPATS PPYGIHHASF
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C1e-33153214364Zinc finger protein JACKDAW
5b3h_F1e-33153214364Zinc finger protein JACKDAW
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.310841e-52silique
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_009129175.1
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.
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_009129175.10.0PREDICTED: protein indeterminate-domain 5, chloroplastic-like
SwissprotQ9ZUL30.0IDD5_ARATH; Protein indeterminate-domain 5, chloroplastic
TrEMBLM4ECV70.0M4ECV7_BRARP; Uncharacterized protein
STRINGBra026617.1-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]