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.006G120000.2
Common NameB456_006G120000, LOC105799304
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: 507aa    MW: 55676.5 Da    PI: 9.8517
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gorai.006G120000.2genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H214.10.000146787323
                        ETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2  3 CpdCgksFsrksnLkrHirtH 23
                        C++C+k F r  nL+ H r H
  Gorai.006G120000.2 67 CEICNKGFQRDQNLQLHRRGH 87
                        *******************88 PP
2zf-C2H211.90.00072141163123
                         EEETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                         +kC++C+k +  +s+ k H + +
  Gorai.006G120000.2 141 WKCEKCSKKYAVQSDWKAHSKIC 163
                         58*****************9876 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.602.3E-56487IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.96E-76487No hitNo description
SMARTSM003550.116587IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.8246587IPR007087Zinc finger, C2H2
PROSITE patternPS0002806787IPR007087Zinc finger, C2H2
SMARTSM00355100106136IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.6E-4129162IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576673.96E-7136161No hitNo description
SMARTSM00355140141161IPR015880Zinc finger, C2H2-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0005634Cellular Componentnucleus
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 507 aa     Download sequence    Send to blast
MMSHDGISNS IPSTIRGLTQ QPNPNPNPTL SVNPSKKKRN LPGTPDPDAE VIALSPKSLM  60
ATNRFLCEIC NKGFQRDQNL QLHRRGHNLP WKLKQRTNKE VRKKVYICPE KTCVHHDPSR  120
ALGDLTGIKK HFSRKHGEKK WKCEKCSKKY AVQSDWKAHS KICGTREYRC DCGTLFSRKD  180
SFITHRAFCD ALAEESGRFT SVSTTTMNPS AFTNDLTHIG GADNYETGFR PEFAAGSELV  240
DSGLQKPRLQ LWLDQANSQL NPIGIQSNAN AFLAPKSTSL PELGIAAAPM NMFGSLSQSQ  300
QWLSQYPQAS FPGANLSMSS VLQRGPKQEE NKGDLSESIT SLYSNNTRNS LRQNHTHMSA  360
TALLQKAAQT GSTRSNPAIT NSGLFGLMSS PASTIPSPIN DHNKNETYYK LFKQANQSEN  420
INEVVSSLPS TQAAIIKDGS FVNNASMKAN ERQGGQAVAS KLNTNANEVE ASLTRDFLGV  480
GSESSRPFFQ QEFAKFASMG SVQPWS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C9e-37137203369Zinc finger protein JACKDAW
5b3h_F9e-37137203369Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
191103KLKQRTNKEVRKK
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in roots, especially in vascular initials, cortex, endodermis, and quiescent center (QC). {ECO:0000269|PubMed:25829440}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that, together with JKD, regulates tissue boundaries and asymmetric cell division in roots by a rapid up-regulation of 'SCARECROW' (SCR), thus controlling the nuclear localization of 'SHORT-ROOT' (SHR) and restricting its action (PubMed:25829440). Confines CYCD6 expression to the cortex-endodermis initial/daughter (CEI/CEID) tissues (PubMed:25829440). 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:24821766, ECO:0000269|PubMed:25829440}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJX5775691e-100JX577569.1 Gossypium hirsutum clone NBRI_GE9421 microsatellite sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_012485236.10.0PREDICTED: protein indeterminate-domain 9
SwissprotQ944L31e-120IDD9_ARATH; Zinc finger protein BALDIBIS
TrEMBLA0A0D2RUM30.0A0A0D2RUM3_GOSRA; Uncharacterized protein
STRINGGorai.006G120000.10.0(Gossypium raimondii)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G45260.11e-109C2H2-like zinc finger protein
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]