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.009G336900.1
Common NameB456_009G336900, LOC105766002
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 HB-other
Protein Properties Length: 314aa    MW: 35622.3 Da    PI: 4.4682
Description HB-other family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gorai.009G336900.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox26.79.3e-092582922155
                         HSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHH CS
            Homeobox  21 knrypsaeereeLAkklgLterqVkvWFqNrRake 55 
                         k +yp++ ++  LA+ +gL+ +q+ +WF N+R ++
  Gorai.009G336900.1 258 KWPYPTEGDKMALAETTGLDPKQINNWFINQRKRH 292
                         579*****************************885 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM012551.2E-2074118IPR005540KNOX1
PfamPF037904.2E-2176115IPR005540KNOX1
SMARTSM012561.8E-24124175IPR005541KNOX2
PfamPF037911.7E-24128174IPR005541KNOX2
PROSITE profilePS5007112.584232295IPR001356Homeobox domain
SuperFamilySSF466898.55E-19233302IPR009057Homeodomain-like
SMARTSM003891.3E-12234299IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.601.2E-27237296IPR009057Homeodomain-like
CDDcd000862.22E-12244296No hitNo description
PfamPF059201.3E-16252291IPR008422Homeobox KN domain
PROSITE patternPS000270270293IPR017970Homeobox, conserved site
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 314 aa     Download sequence    Send to blast
MDEIYGFYSM GDQYVDNALM SPENMIFPSD YQPRLCSSDR VPAFGSDELI SVASAISEAA  60
YVTPQIQGEV DISNVIKAKI ASHPYYPRLL EAYIDCQKVG APPEIARILD EILMETDVNK  120
RDILPTCLGA DPELDEFMET YCDMLVKYKS DISRPFDEAT TFLNKIEMQL RNLCTGASIT  180
GLSDEGGESS EGDVSVGEDD VEELQPRSKD IGLKDLLLHR FGNHITTLKL EFSKKKKKGK  240
LPKEARQILL EWWNVHSKWP YPTEGDKMAL AETTGLDPKQ INNWFINQRK RHWKPSETFQ  300
MDELSGRFFI DQE*
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: First detected in torpedo stage embryos at the boundaries between the presumptive SAM and the cotyledons. Later expressed between the cotyledons and the meristem, and between the cotyledons. In seedlings, localised in stipules and at the boundaries between the SAM and the emerging primordia. Expressed at the site of lateral roots. {ECO:0000269|PubMed:16798887}.
UniprotTISSUE SPECIFICITY: Expressed predominantly in shoot apices of seedlings, and, to a lower extent, in rosette leaves. {ECO:0000269|PubMed:11311158}.
Functional Description ? help Back to Top
Source Description
UniProtPlays a role in meristem function. Contributes to the shoot apical meristem (SAM) maintenance and organ separation by controlling boundary establishment in embryo in a CUC1, CUC2 and STM-dependent manner. Involved in maintaining cells in an undifferentiated, meristematic state. Probably binds to the DNA sequence 5'-TGAC-3'. {ECO:0000269|PubMed:16798887}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Seems to be repressed by AS2 and AS1 but induced by STM, CUC1 and CUC2. {ECO:0000269|PubMed:11311158, ECO:0000269|PubMed:16798887}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJX5890394e-67JX589039.1 Gossypium hirsutum clone NBRI_GE23646 microsatellite sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_012440755.10.0PREDICTED: homeobox protein knotted-1-like 6
SwissprotQ84JS61e-134KNAT6_ARATH; Homeobox protein knotted-1-like 6
TrEMBLA0A0D2UXZ40.0A0A0D2UXZ4_GOSRA; Uncharacterized protein
STRINGGorai.009G336900.10.0(Gossypium raimondii)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM8352785
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G23380.11e-120KNOTTED1-like homeobox gene 6
Publications ? help Back to Top
  1. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]
  2. 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]
  3. Khan M, et al.
    Repression of Lateral Organ Boundary Genes by PENNYWISE and POUND-FOOLISH Is Essential for Meristem Maintenance and Flowering in Arabidopsis.
    Plant Physiol., 2015. 169(3): p. 2166-86
    [PMID:26417006]