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 Gh_Sca004794G01
Organism
Gossypium hirsutum
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: 412aa    MW: 45699.4 Da    PI: 8.7451
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gh_Sca004794G01genomeNAU-NBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H218.74.7e-065981123
                     EEETTTTEEESSHHHHHHHHHHT CS
          zf-C2H2  1 ykCpdCgksFsrksnLkrHirtH 23
                     y+C++C++ F r  nL+ H r+H
  Gh_Sca004794G01 59 YVCEICNQGFQRDQNLQMHRRRH 81
                     9*********************9 PP
2zf-C2H216.23e-05136158123
                      EEETTTTEEESSHHHHHHHHHHT CS
          zf-C2H2   1 ykCpdCgksFsrksnLkrHirtH 23 
                      ++C++C+k +  +s++k H++t+
  Gh_Sca004794G01 136 WVCEKCSKGYAVQSDYKAHLKTC 158
                      58*******************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF576671.8E-55881No hitNo description
Gene3DG3DSA:3.30.160.601.6E-55881IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.00525981IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015710.975981IPR007087Zinc finger, C2H2
PROSITE patternPS0002806181IPR007087Zinc finger, C2H2
PROSITE patternPS01359061141IPR019786Zinc finger, PHD-type, conserved site
SMARTSM00355190100130IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.609.0E-5127157IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SuperFamilySSF576671.8E-5131156No hitNo description
SMARTSM0035560136163IPR015880Zinc 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: 412 aa     Download sequence    Send to blast
MLDNSSISAA PLPSSSSDPL TPLENGATHK RKRKPAGTPD PNAEVVSLSP KTLLESDRYV  60
CEICNQGFQR DQNLQMHRRR HKVPWKLLKR ESQEVKKRVF VCPEPTCLHH DPCHALGDLV  120
GIKKHFRRKH SNQKQWVCEK CSKGYAVQSD YKAHLKTCGT RGHSCDCGRV FSRVESFIEH  180
QDACTTRRVQ PELQAQLQPA AACSSRTASS TSPSSDANFS IAPLHGLPIT KSTEPVFLYK  240
RVSGSDHQRQ HLQHNLELQL LPSSTANSRD SDEEYATHLK LSIGSNDGGE KNASKTTLEA  300
SRLKEFASGQ LKLAMAEKAY AEKARQEAKR QIEMAELEFA SAKRIRQQAQ GELEKAQALK  360
DQATKKISAT IMQITCQTCK HQFQTSTAAG PDDETSLAMS YMSSATTEGE GE
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5b3h_C3e-18133184455Zinc finger protein JACKDAW
5b3h_F3e-18133184455Zinc finger protein JACKDAW
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Ghi.165990.0boll| ovule| root| stem
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expression levels gradually decrease with aging in both the shoot and root vasculature. {ECO:0000269|PubMed:16813575}.
UniprotTISSUE SPECIFICITY: Mainly expressed in the endodermis, the gravity-sensing tissue in inflorescence stems. Mostly present in stems and flowers, and, to a lower extent, in seedlings, hypocotyls, roots and the shoot apical meristem (SAM). {ECO:0000269|PubMed:16813575}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor involved in inflorescence stems gravitropism, probably by regulating starch accumulation in amyloplasts of graviperceptive cells. Required for stem circumnutation movements. Regulates lateral organ morphogenesis and gravitropic responses (PubMed:24039602). Acts cooperatively with IDD16 to control silique and branche orientation (PubMed:24039602). Involved in the establishment of auxin gradients through the regulation of auxin biosynthesis and transport (PubMed:24039602). {ECO:0000269|PubMed:16813575, ECO:0000269|PubMed:18259878, ECO:0000269|PubMed:24039602, ECO:0000269|PubMed:9210330}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Not regulated by auxin. {ECO:0000269|PubMed:24039602}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_016731477.10.0PREDICTED: protein SHOOT GRAVITROPISM 5-like
SwissprotF4IPE31e-164IDD15_ARATH; Zinc finger protein SHOOT GRAVITROPISM 5
TrEMBLA0A1U8MXB50.0A0A1U8MXB5_GOSHI; protein SHOOT GRAVITROPISM 5-like
STRINGGorai.002G171100.10.0(Gossypium raimondii)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM69328131
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G68130.11e-147indeterminate(ID)-domain 14
Publications ? help Back to Top
  1. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  2. Kim JY,Ryu JY,Baek K,Park CM
    High temperature attenuates the gravitropism of inflorescence stems by inducing SHOOT GRAVITROPISM 5 alternative splicing in Arabidopsis.
    New Phytol., 2016. 209(1): p. 265-79
    [PMID:26256266]
  3. Ryu JY,Kim JY,Park CM
    Adaptive thermal control of stem gravitropism through alternative RNA splicing in Arabidopsis.
    Plant Signal Behav, 2015. 10(11): p. e1093715
    [PMID:26452406]
  4. Qu Y, et al.
    Peroxisomal CuAOζ and its product H2O2 regulate the distribution of auxin and IBA-dependent lateral root development in Arabidopsis.
    J. Exp. Bot., 2017. 68(17): p. 4851-4867
    [PMID:28992128]
  5. Shi H, et al.
    Zinc finger of Arabidopsis thaliana 6 is involved in melatonin-mediated auxin signaling through interacting INDETERMINATE DOMAIN15 and INDOLE-3-ACETIC ACID 17.
    J. Pineal Res., 2018. 65(2): p. e12494
    [PMID:29607541]