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 orange1.1g001193m
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: 1128aa    MW: 125498 Da    PI: 6.1669
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
orange1.1g001193mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H2120.0006610361059223
                         EET..TTTEEESSHHHHHHHHHHT CS
            zf-C2H2    2 kCp..dCgksFsrksnLkrHirtH 23  
                         +Cp   Cgk+Fs++ +   H+r+H
  orange1.1g001193m 1036 RCPheGCGKRFSSHKYAIIHQRVH 1059
                         69999*****************99 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM003551810121034IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.44510351064IPR007087Zinc finger, C2H2
SuperFamilySSF576671.12E-610351072No hitNo description
SMARTSM003550.04610351059IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.609.9E-710361063IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028010371059IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.5E-1010641089IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.94610651094IPR007087Zinc finger, C2H2
SMARTSM003550.001610651089IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028010671089IPR007087Zinc finger, C2H2
SuperFamilySSF576671.93E-1010751118No hitNo description
Gene3DG3DSA:3.30.160.607.9E-1210901118IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS501579.49410951121IPR007087Zinc finger, C2H2
SMARTSM003550.7410951121IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028010971121IPR007087Zinc 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: 1128 aa     Download sequence    Send to blast
MVAKEAAVRR AAMNYLPMLS HQQLLYLLTM SFISRVPRSL LPGARSSRLR DRQKEERELL  60
VKKAFVEDIL KENNILSVLL GRQSTFNAVL WNADLLPCQS KESQMPSANE TVSTTPGETV  120
PNNPYEKHND HNNLLDEMNV YMEALNDPYM GDDDISRDFH IDSGALACVA CGILGFPFMS  180
VVQLSERASI ELLADLVKEG PGVSELKNTH HHTNLDGSVK SSVSDDLCLV PDISLLQKDL  240
SVPSITKSSR IWNTSNKYLR PRIFCLEHAA QIEEILQSKG GAEILVICHS DYQKIKAHAA  300
AVAEEIGSPF NYIDVPLDAA SEEDLHLIDL AIDDGELDEC REDWTSKLGI NLRHCVKVRK  360
NSPSMRVQHA LSLGDLFSEK SLSSDFSKIK WQFRRSRSKI KLYGRAHSKP CQNIEIKKDE  420
VTGRKLDGAT VKKEEKLIQY SRRKFKQKPD LSTGACGDQV HPRELLPEVS AATCDHLDGH  480
NRSDFEINPD GTGNSGSISA GSIHSPIGMS EGLHDIPVRE ATSNLSLNYS PSRVADSLAT  540
ATLVVDSIVQ NDTESMKELN IEGDIFHMAT CKSAEMQQNS GTDVTSEKTE ISHHTVASNE  600
GSIIMRSDQI TESMTIKNEK CNLASEGHCR KIEDLAPDNS CMISEACDHM ISDNEVRQNV  660
QSTNGGNDVE PISCDHKLID EPPASTGESC EDMREISTAE SLQDNLQHER NIGNGSNEEL  720
VSSSVTMMIQ PTSAPMEISE VPSKECAAAD LLNVGTKQKL ISSCVSRMEV DQPSPLKVGG  780
CSEVPIEICT KEDSGADMTL DPRTQLQNHT TAEAIMDELV CNSSAQLEEN ERIPASVAAC  840
SEESNGIFAE EKMDFDMTIG TQTKNATSEE PKPTSLIPID QPIPAVIRKY SRTRRESYSA  900
EKFCNGNEAY SSKDNKEREC NESNLEDPSF SAGKGRKRNR ELERLTENKF NGSGFIRSPC  960
EGLRSRAGKD AANTSEVDIR KIAEKRATKT MRNRESVPAP CQDKKKILKG HHRCDLDGCR  1020
MSFETKRELS LHKRNRCPHE GCGKRFSSHK YAIIHQRVHD DERPLKCPWK GCSMSFKWAW  1080
ARTEHIRVHT GERPYKCKFE GCGLSFRFVS DISRHRRKTG HYENLSA*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6a57_A2e-521012112123132Lysine-specific demethylase REF6
6a58_A2e-521012112123132Lysine-specific demethylase REF6
6a59_A2e-521012112123132Lysine-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-131ELF6_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-134C2H2 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]