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_009123129.1
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: 585aa    MW: 62905.1 Da    PI: 9.3656
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009123129.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H216.23e-0582104123
                     EEETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                     + C+ C+k F r  nL+ H r H
  XP_009123129.1  82 FICEVCNKGFQREQNLQLHRRGH 104
                     89*******************88 PP
2zf-C2H213.10.00028158180123
                     EEETTTTEEESSHHHHHHHHHHT CS
         zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                     +kC++C+k++  +s+ k H +t+
  XP_009123129.1 158 WKCEKCSKRYAVQSDWKAHSKTC 180
                     58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576674.31E-781104No hitNo description
Gene3DG3DSA:3.30.160.606.5E-681104IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.9982104IPR007087Zinc finger, C2H2
PfamPF121712.9E-582104IPR022755Zinc finger, double-stranded RNA binding
SMARTSM003550.005282104IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028084104IPR007087Zinc finger, C2H2
SMARTSM00355110123153IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.602.7E-5146179IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576674.31E-7153178No hitNo description
SMARTSM00355130158178IPR015880Zinc 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: 585 aa     Download sequence    Send to blast
MAASSSSAAS FFGVQQDDQS HILPPNSSAT APPLLTHHQP PQSQQPLDAP PQKKKRNQPR  60
TPNSDAEVIA LSPKTLMATN RFICEVCNKG FQREQNLQLH RRGHNLPWKL KQKSTKEVKR  120
KVYLCPEPTC VHHDPSRALG DLTGIKKHYY RKHGEKKWKC EKCSKRYAVQ SDWKAHSKTC  180
GTKEYRCDCG TLFSRRDSFI THRAFCDALA QESARHPTSL TSLPSHHFPY GQNTNNSNNT  240
SSMILGLSHM GPSQNLDHQS GDRLRLGSSG GGGAGAASRS SSDLIAANAS GYFMQEQNPS  300
FHDQQDHHHQ GFLAASNNIK PSPMNFQQSL MQFSHDNHNC PSSNVFNLSF LSGRNGVASA  360
TSNPNAAAVS SGNLMISNNF DGENAVRGGG GEGEGSTGLF PNNLMTSADR ISTGAVPSLF  420
SSSMQNPNST THMSATALLQ KAAQIGSSSS NNNNSNNASS ILRSFGSGMY GESESSLNDL  480
MNSFSNPGAT GNNVNRVDSP FGSYGGVNKG LNADKQSMTR DFLGVGQIVR SMSESGGFQQ  540
QQQQHGNSTE RVGSSSDSAD RNSINVNPGG GPASSPPYGI HRASF
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C2e-33154215364Zinc finger protein JACKDAW
5b3h_F2e-33154215364Zinc finger protein JACKDAW
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.310842e-57silique
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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00255DAPTransfer from AT2G02070Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009123129.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
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_009123129.10.0PREDICTED: protein indeterminate-domain 5, chloroplastic-like
SwissprotQ9ZUL30.0IDD5_ARATH; Protein indeterminate-domain 5, chloroplastic
TrEMBLM4FIP50.0M4FIP5_BRARP; Uncharacterized protein
STRINGBra040974.1-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]