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 Gorai.008G169000.1
Common NameB456_008G169000, LOC105764385
Organism
Gossypium raimondii
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium
Family C2H2
Protein Properties Length: 588aa    MW: 63556 Da    PI: 9.2468
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gorai.008G169000.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H216.23e-057597123
                        EEETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                        + C+ C+k F r  nL+ H r H
  Gorai.008G169000.1 75 FICEVCNKGFQREQNLQLHRRGH 97
                        89*******************88 PP
2zf-C2H213.10.00028151173123
                         EEETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                         +kC++C+k++  +s+ k H +t+
  Gorai.008G169000.1 151 WKCEKCSKRYAVQSDWKAHSKTC 173
                         58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576672.07E-77497No hitNo description
Gene3DG3DSA:3.30.160.606.6E-67497IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.00527597IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.997597IPR007087Zinc finger, C2H2
PfamPF121712.9E-57597IPR022755Zinc finger, double-stranded RNA binding
PROSITE patternPS0002807797IPR007087Zinc finger, C2H2
SMARTSM00355130116146IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.602.1E-5139172IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576672.07E-7146171No hitNo description
SMARTSM00355130151171IPR015880Zinc 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: 588 aa     Download sequence    Send to blast
MATASSSSGP FFGIREENQS QTKQQQQQQH TPTSSTGPVD PSPPPKKKRN QPGTPNPDAE  60
VVALSPKTLM ATNRFICEVC NKGFQREQNL QLHRRGHNLP WKLKQKTTKE VKKKVYLCPE  120
PTCVHHDPSR ALGDLTGIKK HYSRKHGEKK WKCEKCSKRY AVQSDWKAHS KTCGTREYRC  180
DCGTLFSRRD SFITHRAFCD ALAQETARHP PPLNSIGTHL YGTSNYMGLG LSQVGTQISS  240
IQDPNNNQTA ADILKLGGGG ASRSSQFDHL LPPSMGCSSS SSFRPQQQAM GFVMEESNQI  300
FNQEHQSQHG LLGNSKPFQG LMQFPPDDNN NNNNNNASNA SSAANLFNLS FLSNSGNNGG  360
AGDYNLTSSG LLMSDNFNNE NGGNGGTNNA ANLFSNNLMS DQMTSNIPSL FSSSVQNNDM  420
VPQMSATALL QKAAQMGSTS SNKNTNDDSL LRTFANSSST GTKTSNFGAI FGDTAGNNLH  480
ELMNSIASGN SPIFGSGYDA VHGQESPYTN RSSMGQEQPP QSMNVSGGGS DRLTRDFLGV  540
GQIVRNMRGG AAQQRQGIGI SRLSSERNSN ITAPTSQQSF GERGNFQ*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C6e-34147208364Zinc finger protein JACKDAW
5b3h_F6e-34147208364Zinc finger protein JACKDAW
Search in ModeBase
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}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJX6146061e-154JX614606.1 Gossypium hirsutum clone NBRI_GE58125 microsatellite sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_012438385.10.0PREDICTED: protein indeterminate-domain 5, chloroplastic-like
SwissprotQ9ZUL31e-145IDD5_ARATH; Protein indeterminate-domain 5, chloroplastic
TrEMBLA0A0D2T7B80.0A0A0D2T7B8_GOSRA; Uncharacterized protein
STRINGGorai.008G169000.10.0(Gossypium raimondii)
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
AT2G02080.11e-110indeterminate(ID)-domain 4
Publications ? help Back to Top
  1. Paterson AH, et al.
    Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres.
    Nature, 2012. 492(7429): p. 423-7
    [PMID:23257886]
  2. Moreno-Risueno MA, et al.
    Transcriptional control of tissue formation throughout root development.
    Science, 2015. 350(6259): p. 426-30
    [PMID:26494755]