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 orange1.1g000392m
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: 1582aa    MW: 175857 Da    PI: 6.3108
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
orange1.1g000392mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H211.40.0009814901513223
                         EET..TTTEEESSHHHHHHHHHHT CS
            zf-C2H2    2 kCp..dCgksFsrksnLkrHirtH 23  
                         +Cp   Cgk+Fs++ +   H+r+H
  orange1.1g000392m 1490 RCPheGCGKRFSSHKYAIIHQRVH 1513
                         69999*****************99 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.5E-152060IPR003349JmjN domain
PROSITE profilePS5118314.1322162IPR003349JmjN domain
PfamPF023758.2E-162255IPR003349JmjN domain
SMARTSM005587.9E-47296465IPR003347JmjC domain
SuperFamilySSF511978.51E-27296460No hitNo description
PROSITE profilePS5118434.552299465IPR003347JmjC domain
PfamPF023733.8E-37329448IPR003347JmjC domain
SMARTSM003551814661488IPR015880Zinc finger, C2H2-like
SuperFamilySSF576671.83E-614891526No hitNo description
PROSITE profilePS5015712.44514891518IPR007087Zinc finger, C2H2
SMARTSM003550.04614891513IPR015880Zinc finger, C2H2-like
Gene3DG3DSA:3.30.160.601.4E-614901517IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028014911513IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.602.2E-1015181543IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015711.94615191548IPR007087Zinc finger, C2H2
SMARTSM003550.001615191543IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028015211543IPR007087Zinc finger, C2H2
SuperFamilySSF576672.87E-1015291572No hitNo description
Gene3DG3DSA:3.30.160.601.2E-1115441572IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS501579.49415491575IPR007087Zinc finger, C2H2
SMARTSM003550.7415491575IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028015511575IPR007087Zinc 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: 1582 aa     Download sequence    Send to blast
MGNNSNNNVE IPKWLQGLPL APVFYPTDTE FADPIAYISR IEKEASAFGI CKIVPPLPKP  60
SKKYVFGNLN KSLSKCSELG SDVNLPDAGT VATVGCCERG NEGEARAVFT TRHQELGQSV  120
KRIKGVDNKD NLQLGAQKQV WQSGEVYTLE QFESKSKAFA RSLLSVIKEV SPLVIEALFW  180
KAASEKPVYV EYANDVPGSG FGEPEGQFRY FHRRRRKVTS WKSYRNRGKA DEKNIELESA  240
RNCHNDQITH SCDKNDLETP TSSTPSSTLP FDENSRSSRR KSVTGSNDVE GTAGWKLSNS  300
PWNLQVISRS PGSLTRFMPD DIPGVTSPMV YIGMLFSWFA WHVEDHELHS MNFLHTGAPK  360
TWYAIPGDYA FTFEEVIRNE AYGGDIDRLA ALSLLGEKTT LISPEVIAAS GIPCCRLVQN  420
PGEFVVTFPR AYHAGFSHGF NCGEAANFGT PQWLMVAKEA AVRRAAMNYL PMLSHQQLLY  480
LLTMSFISRV PRSLLPGARS SRLRDRQKEE RELLVKKAFV EDILKENNIL SVLLGRQSTF  540
NAVLWNADLL PCQSKESQMP SANETVSTTP GETVPNNPYE KHNDHNNLLD EMNVYMEALN  600
DPYMGDDDIS RDFHIDSGAL ACVACGILGF PFMSVVQLSE RASIELLADL VKEGPGVSEL  660
KNTHHHTNLD GSVKSSVSDD LCLVPDISLL QKDLSVPSIT KSSRIWNTSN KYLRPRIFCL  720
EHAAQIEEIL QSKGGAEILV ICHSDYQKIK AHAAAVAEEI GSPFNYIDVP LDAASEEDLH  780
LIDLAIDDGE LDECREDWTS KLGINLRHCV KVRKNSPSMR VQHALSLGDL FSEKSLSSDF  840
SKIKWQFRRS RSKIKLYGRA HSKPCQNIEI KKDEVTGRKL DGATVKKEEK LIQYSRRKFK  900
QKPDLSTGAC GDQVHPRELL PEVSAATCDH LDGHNRSDFE INPDGTGNSG SISAGSIHSP  960
IGMSEGLHDI PVREATSNLS LNYSPSRVAD SLATATLVVD SIVQNDTESM KELNIEGDIF  1020
HMATCKSAEM QQNSGTDVTS EKTEISHHTV ASNEGSIIMR SDQITESMTI KNEKCNLASE  1080
GHCRKIEDLA PDNSCMISEA CDHMISDNEV RQNVQSTNGG NDVEPISCDH KLIDEPPAST  1140
GESCEDMREI STAESLQDNL QHERNIGNGS NEELVSSSVT MMIQPTSAPM EISEVPSKEC  1200
AAADLLNVGT KQKLISSCVS RMEVDQPSPL KVGGCSEVPI EICTKEDSGA DMTLDPRTQL  1260
QNHTTAEAIM DELVCNSSAQ LEENERIPAS VAACSEESNG IFAEEKMDFD MTIGTQTKNA  1320
TSEEPKPTSL IPIDQPIPAV IRKYSRTRRE SYSAEKFCNG NEAYSSKDNK ERECNESNLE  1380
DPSFSAGKGR KRNRELERLT ENKFNGSGFI RSPCEGLRSR AGKDAANTSE VDIRKIAEKR  1440
ATKTMRNRES VPAPCQDKKK ILKGHHRCDL DGCRMSFETK RELSLHKRNR CPHEGCGKRF  1500
SSHKYAIIHQ RVHDDERPLK CPWKGCSMSF KWAWARTEHI RVHTGERPYK CKFEGCGLSF  1560
RFVSDISRHR RKTGHYENLS A*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A5e-58279479137346Transcription factor jumonji (Jmj) family protein
6ip4_A5e-58279479137346Arabidopsis JMJ13
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
SwissprotQ6BDA00.0ELF6_ARATH; Probable lysine-specific demethylase ELF6
TrEMBLV4TDP10.0V4TDP1_9ROSI; Uncharacterized protein
STRINGXP_006485645.10.0(Citrus sinensis)
STRINGXP_006436450.10.0(Citrus clementina)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM115202731
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G04240.10.0C2H2 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]