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 orange1.1g001121m
Organism
Citrus sinensis
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus
Family C2H2
Protein Properties Length: 1151aa    MW: 127965 Da    PI: 6.1215
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
orange1.1g001121mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H211.90.0006710591082223
                         EET..TTTEEESSHHHHHHHHHHT CS
            zf-C2H2    2 kCp..dCgksFsrksnLkrHirtH 23  
                         +Cp   Cgk+Fs++ +   H+r+H
  orange1.1g001121m 1059 RCPheGCGKRFSSHKYAIIHQRVH 1082
                         69999*****************99 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM003551810351057IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.44510581087IPR007087Zinc finger, C2H2
SuperFamilySSF576671.16E-610581095No hitNo description
SMARTSM003550.04610581082IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.0E-610591086IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028010601082IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.6E-1010871112IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.94610881117IPR007087Zinc finger, C2H2
SMARTSM003550.001610881112IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028010901112IPR007087Zinc finger, C2H2
SuperFamilySSF576671.93E-1010981141No hitNo description
Gene3DG3DSA:3.30.160.608.1E-1211131141IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS501579.49411181144IPR007087Zinc finger, C2H2
SMARTSM003550.7411181144IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028011201144IPR007087Zinc finger, C2H2
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009741Biological Processresponse to brassinosteroid
GO:0009826Biological Processunidimensional cell growth
GO:0033169Biological Processhistone H3-K9 demethylation
GO:0048577Biological Processnegative regulation of short-day photoperiodism, flowering
GO:0048579Biological Processnegative regulation of long-day photoperiodism, flowering
GO:0005634Cellular Componentnucleus
GO:0003676Molecular Functionnucleic acid binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 1151 aa     Download sequence    Send to blast
MTPQMAIGFN CGEAANFGTP QWLMVAKEAA VRRAAMNYLP MLSHQQLLYL LTMSFISRVP  60
RSLLPGARSS RLRDRQKEER ELLVKKAFVE DILKENNILS VLLGRQSTFN AVLWNADLLP  120
CQSKESQMPS ANETVSTTPG ETVPNNPYEK HNDHNNLLDE MNVYMEALND PYMGDDDISR  180
DFHIDSGALA CVACGILGFP FMSVVQLSER ASIELLADLV KEGPGVSELK NTHHHTNLDG  240
SVKSSVSDDL CLVPDISLLQ KDLSVPSITK SSRIWNTSNK YLRPRIFCLE HAAQIEEILQ  300
SKGGAEILVI CHSDYQKIKA HAAAVAEEIG SPFNYIDVPL DAASEEDLHL IDLAIDDGEL  360
DECREDWTSK LGINLRHCVK VRKNSPSMRV QHALSLGDLF SEKSLSSDFS KIKWQFRRSR  420
SKIKLYGRAH SKPCQNIEIK KDEVTGRKLD GATVKKEEKL IQYSRRKFKQ KPDLSTGACG  480
DQVHPRELLP EVSAATCDHL DGHNRSDFEI NPDGTGNSGS ISAGSIHSPI GMSEGLHDIP  540
VREATSNLSL NYSPSRVADS LATATLVVDS IVQNDTESMK ELNIEGDIFH MATCKSAEMQ  600
QNSGTDVTSE KTEISHHTVA SNEGSIIMRS DQITESMTIK NEKCNLASEG HCRKIEDLAP  660
DNSCMISEAC DHMISDNEVR QNVQSTNGGN DVEPISCDHK LIDEPPASTG ESCEDMREIS  720
TAESLQDNLQ HERNIGNGSN EELVSSSVTM MIQPTSAPME ISEVPSKECA AADLLNVGTK  780
QKLISSCVSR MEVDQPSPLK VGGCSEVPIE ICTKEDSGAD MTLDPRTQLQ NHTTAEAIMD  840
ELVCNSSAQL EENERIPASV AACSEESNGI FAEEKMDFDM TIGTQTKNAT SEEPKPTSLI  900
PIDQPIPAVI RKYSRTRRES YSAEKFCNGN EAYSSKDNKE RECNESNLED PSFSAGKGRK  960
RNRELERLTE NKFNGSGFIR SPCEGLRSRA GKDAANTSEV DIRKIAEKRA TKTMRNRESV  1020
PAPCQDKKKI LKGHHRCDLD GCRMSFETKR ELSLHKRNRC PHEGCGKRFS SHKYAIIHQR  1080
VHDDERPLKC PWKGCSMSFK WAWARTEHIR VHTGERPYKC KFEGCGLSFR FVSDISRHRR  1140
KTGHYENLSA *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A2e-521035114423132Lysine-specific demethylase REF6
6a58_A2e-521035114423132Lysine-specific demethylase REF6
6a59_A2e-521035114423132Lysine-specific demethylase REF6
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Csi.4600.0fruit
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed at low levels in cotyledons and leaves. Detected in inflorescences, stems, roots and siliques but not in shoot apical meristems or root tips. {ECO:0000269|PubMed:15377760, ECO:0000269|PubMed:18713399}.
Functional Description ? help Back to Top
Source Description
UniProtActs probably as a histone 'Lys-4' (H3K4me) demethylase. Involved in transcriptional gene regulation. Acts as a repressor of the photoperiodic flowering pathway and of FT. Binds around the transcription start site of the FT locus. {ECO:0000269|PubMed:15377760, ECO:0000269|PubMed:18467490, ECO:0000269|PubMed:19946624}.
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_006436450.10.0probable lysine-specific demethylase ELF6
RefseqXP_006485645.10.0probable lysine-specific demethylase ELF6
SwissprotQ6BDA01e-145ELF6_ARATH; Probable lysine-specific demethylase ELF6
TrEMBLA0A2H5PYG00.0A0A2H5PYG0_CITUN; Uncharacterized protein
STRINGXP_006485645.10.0(Citrus sinensis)
STRINGXP_006436450.10.0(Citrus clementina)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G04240.11e-147C2H2 family protein
Publications ? help Back to Top
  1. Heidari B,Nemie-Feyissa D,Kangasjärvi S,Lillo C
    Antagonistic regulation of flowering time through distinct regulatory subunits of protein phosphatase 2A.
    PLoS ONE, 2013. 8(7): p. e67987
    [PMID:23976921]
  2. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  3. Crevillén P, et al.
    Epigenetic reprogramming that prevents transgenerational inheritance of the vernalized state.
    Nature, 2014. 515(7528): p. 587-90
    [PMID:25219852]
  4. Yang H,Howard M,Dean C
    Physical coupling of activation and derepression activities to maintain an active transcriptional state at FLC.
    Proc. Natl. Acad. Sci. U.S.A., 2016. 113(33): p. 9369-74
    [PMID:27482092]