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.006G167600.1
Common NameB456_006G167600, LOC105799794
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: 453aa    MW: 48935.1 Da    PI: 10.0427
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gorai.006G167600.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H215.55.1e-056486123
                        EEETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                        + C++C+k F r  nL+ H r H
  Gorai.006G167600.1 64 FICEICKKGFQRDQNLQLHRRGH 86
                        89*******************88 PP
2zf-C2H212.90.00033140162123
                         EEETTTTEEESSHHHHHHHHHHT CS
             zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                         +kC++C+k +  +s+ k H +t+
  Gorai.006G167600.1 140 WKCEKCSKKYAVQSDWKAHSKTC 162
                         58*****************9998 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.160.606.9E-56386IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576679.99E-76386No hitNo description
PROSITE profilePS5015710.5336486IPR007087Zinc finger, C2H2
SMARTSM003550.056486IPR015880Zinc finger, C2H2-like
PROSITE patternPS0002806686IPR007087Zinc finger, C2H2
SMARTSM00355100105135IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.1E-4128161IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576679.99E-7135160No hitNo description
SMARTSM00355140140160IPR015880Zinc 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: 453 aa     Download sequence    Send to blast
MSGEAFSLPA ASIGGFIQDP SNANPNPKPN ANPAKKKRNL PGTPDPDAEV IALSPKTLMA  60
TNRFICEICK KGFQRDQNLQ LHRRGHNLPW KLRQRTNKEV RKKVYICPEK TCVHHDPSRA  120
LGDLTGIKKH FSRKHGEKKW KCEKCSKKYA VQSDWKAHSK TCGTREYKCD CGTLFSRKDS  180
FITHRAFCDA LAEESARLTS VAATSLNFRN DTVNLPHGFA GRGVQDVAGI PQFGSGFPQD  240
FSGMPAPGLP EMVQMAPANV FGSSSHFPGF ENGGATSSNS NNLSLSQLPQ GLKEEGRNEG  300
NLMESLSSLY SDNQNKQSKA NASPMSATAL LQKAAQMGST RSNSSFFGNS FGVMSSSSSH  360
TAPTFMASSS ASMSATSNKL DKLMLQTGGK PSEPTLLSMH HPGSNSFAQS LTRDFLGMSN  420
DQSPRPFLPQ ELAKYAAIGS TMGLSQFTSS NH*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C1e-38136202369Zinc finger protein JACKDAW
5b3h_F1e-38136202369Zinc finger protein JACKDAW
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
190102KLRQRTNKEVRKK
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Start to accumulate during the 16- to 32-cell stage of embryogenesis. {ECO:0000269|PubMed:17785527}.
UniprotTISSUE SPECIFICITY: Expressed in the quiescent center, the ground tissue stem cells and to a lesser extent in mature cortex and endodermis cells. {ECO:0000269|PubMed:17785527}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that, together with BIB, regulates tissue boundaries and asymmetric cell division by a rapid up-regulation of 'SCARECROW' (SCR), thus controlling the nuclear localization of 'SHORT-ROOT' (SHR) and restricting its action (PubMed:17785527, PubMed:25829440). Binds DNA via its zinc fingers (PubMed:28211915, PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Confines CYCD6 expression to the cortex-endodermis initial/daughter (CEI/CEID) tissues (PubMed:25829440). Required for radial patterning and stem cell maintenance (PubMed:17785527). Counteracted by 'MAGPIE' (MGP) (PubMed:17785527). Binds to the SCR and MGP promoter sequences (PubMed:21935722). Controls position-dependent signals that regulate epidermal-cell-type patterning (PubMed:20356954). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:20356954, ECO:0000269|PubMed:21935722, ECO:0000269|PubMed:24821766, ECO:0000269|PubMed:25829440, ECO:0000269|PubMed:28211915}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Not regulated by SCR and SHR. {ECO:0000269|PubMed:21935722}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_012485978.10.0PREDICTED: zinc finger protein JACKDAW-like
SwissprotQ700D21e-146IDD10_ARATH; Zinc finger protein JACKDAW
TrEMBLA0A0D2SZ970.0A0A0D2SZ97_GOSRA; Uncharacterized protein
STRINGGorai.006G167600.10.0(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
AT5G03150.11e-122C2H2-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]
  3. Hirano Y, et al.
    Structure of the SHR-SCR heterodimer bound to the BIRD/IDD transcriptional factor JKD.
    Nat Plants, 2017. 3: p. 17010
    [PMID:28211915]
  4. Kobayashi A,Miura S,Kozaki A
    INDETERMINATE DOMAIN PROTEIN binding sequences in the 5'-untranslated region and promoter of the SCARECROW gene play crucial and distinct roles in regulating SCARECROW expression in roots and leaves.
    Plant Mol. Biol., 2017. 94(1-2): p. 1-13
    [PMID:28324206]
  5. Long Y, et al.
    In vivo FRET-FLIM reveals cell-type-specific protein interactions in Arabidopsis roots.
    Nature, 2017. 548(7665): p. 97-102
    [PMID:28746306]
  6. Bustillo-Avendaño E, et al.
    Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis.
    Plant Physiol., 2018. 176(2): p. 1709-1727
    [PMID:29233938]