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.001G131000.1
Common NameB456_001G131000, LOC105793540
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: 509aa    MW: 56014.9 Da    PI: 9.8219
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gorai.001G131000.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H2140.000146383323
                        ETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2  3 CpdCgksFsrksnLkrHirtH 23
                        C++C+k F r  nL+ H r H
  Gorai.001G131000.1 63 CEICNKGFQRDQNLQLHRRGH 83
                        *******************88 PP
2zf-C2H211.80.00072137159123
                         EEETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                         +kC++C+k +  +s+ k H + +
  Gorai.001G131000.1 137 WKCEKCSKKYAVQSDWKAHSKIC 159
                         58*****************9876 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576676.25E-76083No hitNo description
Gene3DG3DSA:3.30.160.602.4E-56083IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015710.8246183IPR007087Zinc finger, C2H2
SMARTSM003550.116183IPR015880Zinc finger, C2H2-like
PROSITE patternPS0002806383IPR007087Zinc finger, C2H2
SMARTSM00355100102132IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.6E-4125158IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576676.25E-7132157No hitNo description
SMARTSM00355140137157IPR015880Zinc 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: 509 aa     Download sequence    Send to blast
MMSQDGLSIP STVKGLAQAQ QPNPNPNPNP VKKKRNFPGT PDPDAEVIAL SPKSLMATNR  60
FLCEICNKGF QRDQNLQLHR RGHNLPWKLK QRTNKEVRKK VYICPEKTCV HHDPSRALGD  120
LTGIKKHFSR KHGEKKWKCE KCSKKYAVQS DWKAHSKICG TREYRCDCGT LFSRKDSFIT  180
HRAFCDALAE ESARFTSVST NVNPAAASFR NDLIHGANNN GMHQFSSGFR PEFGGLELVD  240
NLNSNGQKPR LQLWLDEANS QVNPFGIPSN ANAFLAPKST SFPDLGMAPM NMFGSLTTQW  300
LGKYPEDASF AGANLNMSAL RHGPKQEEEN KGDLSESITS LYSNNSLQQQ QQQNYTHMSA  360
TALLQKAAQM GSTRNNPAIN NSGFGLMSSN TYDQNKNHVY KLFKQANDQS DNINELVSSL  420
SSNQATIVKD GSALDDLKSS SFVRNASSKG KQGGQAVVLA SKLNNTNSNE VELSLTRDFL  480
GVGGESSRPL LQQGLAKFAS MGSIHPWS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C9e-38133201371Zinc finger protein JACKDAW
5b3h_F9e-38133201371Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
18799KLKQRTNKEVRKK
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
GenBankHQ5271851e-121HQ527185.1 Gossypium herbaceum clone NBRI_E_EYT27PB03GHRJ2 simple sequence repeat marker, mRNA sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_012477895.10.0PREDICTED: protein indeterminate-domain 9-like
SwissprotQ944L31e-117IDD9_ARATH; Zinc finger protein BALDIBIS
TrEMBLA0A0D2PY830.0A0A0D2PY83_GOSRA; Uncharacterized protein
STRINGGorai.001G131000.10.0(Gossypium raimondii)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM15528306
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G66730.11e-102C2H2-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]