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 RrC8624_p1
Organism
Raphanus raphanistrum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family C2H2
Protein Properties Length: 589aa    MW: 63042.3 Da    PI: 9.6819
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC8624_p1genomeMSUView 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
  RrC8624_p1  81 FICEVCNKGFQREQNLQLHRRGH 103
                 89*******************88 PP
2zf-C2H213.10.00028157179123
                 EEETTTTEEESSHHHHHHHHHHT CS
     zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                 +kC++C+k++  +s+ k H +t+
  RrC8624_p1 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
SuperFamilySSF576674.84E-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
SuperFamilySSF576674.84E-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: 589 aa     Download sequence    Send to blast
MAASSSSAAS FFGVRQDEQS HLLPLNSSAA VPAPPHHQPP QPQQPLEAPP QKKKRNQPRT  60
PNSDAEVIAL SPKTLMATNR FICEVCNKGF QREQNLQLHR RGHNLPWKLK QKSTKEVKRK  120
VYLCPEPSCV HHDPSRALGD LTGIKKHYYR KHGEKKWKCE KCSKRYAVQS DWKAHSKTCG  180
TKEYRCDCGT LFSRRDSFIT HRAFCDALAQ ESARHPTSLT SLPSHHFPYG QNTNNSNNNT  240
SSMILGLPHM GAPQNLDHQS GDVLRLGSGG GGGGGASRSS SDLIAANASG YFMQEQNPSF  300
HDQQDHHQHQ QQGFLAANSN IKPSTMNFQQ SLMQFSNDNH NSPSSNLFNL SFLSGNNGVA  360
SATSNPNAAA VSSGNHMISN HFGGENAVGG SGGGSTGLFP NNLMSSAGRI NSGAVPSLFS  420
SSMQNPNSAP HMSATALLQK AAQMGSTSSS SNNNNTNNAS SILRSFGSGM YGENESNLHD  480
LMNSFSNPGA TGNNLNAVDS QFGTYGGVNK GLSADKQNMT RDFLGVGQIV RSMSGSAGFQ  540
QQQQQQHGNG GKERVGSSSD SADRNSMNVN PGGGGSTSSP SYGIHHASF
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
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
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.
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_018484448.10.0PREDICTED: protein indeterminate-domain 5, chloroplastic
SwissprotQ9ZUL30.0IDD5_ARATH; Protein indeterminate-domain 5, chloroplastic
TrEMBLA0A397ZA720.0A0A397ZA72_BRACM; Uncharacterized protein
STRINGBo7g080180.10.0(Brassica oleracea)
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]