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 XP_009122623.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family C2H2
Protein Properties Length: 1151aa    MW: 129337 Da    PI: 7.2985
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009122623.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H213.20.0002710631086223
                      EET..TTTEEESSHHHHHHHHHHT CS
         zf-C2H2    2 kCp..dCgksFsrksnLkrHirtH 23  
                      +C+   Cgk F+ + +L+ H+r+H
  XP_009122623.1 1063 RCTheGCGKKFRAHKYLVLHQRVH 1086
                      588889****************99 PP
2zf-C2H211.40.00111221148123
                      EEET..TTTEEESSHHHHHHHHHH..T CS
         zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                      ykC+   Cg sF+  s++ rH r+  H
  XP_009122623.1 1122 YKCKveECGLSFRFVSDYSRHRRKtgH 1148
                      99*********************9777 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005452.3E-141757IPR003349JmjN domain
PROSITE profilePS5118314.3261859IPR003349JmjN domain
PfamPF023754.1E-161952IPR003349JmjN domain
SMARTSM005588.7E-46242411IPR003347JmjC domain
PROSITE profilePS5118435.242245411IPR003347JmjC domain
SuperFamilySSF511971.02E-25257409No hitNo description
PfamPF023732.6E-37275394IPR003347JmjC domain
SMARTSM0035516010391061IPR015880Zinc finger, C2H2-like
SuperFamilySSF576678.38E-810501099No hitNo description
SMARTSM003550.05710621086IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.46410621091IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.2E-610631085IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028010641086IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.5E-910861113IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.06610921116IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.42710921121IPR007087Zinc finger, C2H2
PROSITE patternPS00028010941116IPR007087Zinc finger, C2H2
SuperFamilySSF576673.39E-1011031144No hitNo description
Gene3DG3DSA:3.30.160.605.4E-1011141145IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003554.811221148IPR015880Zinc finger, C2H2-like
PROSITE profilePS501579.95111221151IPR007087Zinc finger, C2H2
PROSITE patternPS00028011241148IPR007087Zinc 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
MGSSNVEIPN WLKAMPLAPV FRPTDTEFAD PIAYISKIEK QASAFGICKI IPPIPKPSKK  60
YVFCNLNKSL LRCPELASGV DVSKLGQEDR AVFTTRQQEL GQARKKSRGG EGGDVKQVWQ  120
SGGVYTLEQF ESKSKAFYKS QLGTVKEVSP VVVEALFWRA ASEKPMYIEY ANDVPGSAFG  180
EPEGHFRHFR QRKRRGRGFY QRKNGESSLP VVSPSLSAQD PSKKKNMDVV VVDEMEGTAG  240
WKLSNSSWNL QMIARSPGSV TRFMPDDIPG VTSPMVYIGM LFSWFAWHVE DHELHSMNYL  300
HTGSPKTWYA VPGDYALDFE EVIRKNSYGS NLDQLAALTQ LGEKTTLVSP EIIVSSDIPC  360
CRLVQNPGEF VVTFPRSYHV GFSHGFNCGE AANFGTPQWL NVAKEAAVRR AAMNYLPMLS  420
HQQLLYLLTM SFVSRVPRSL LPGGRSSRLR DRQREEREFL VKKAFVEDIL NENKNLSVLL  480
GEPGSRLVMW DPDLLPRHSV LALAATGVAT TPAVSSPAEA KSEIENKEEN PSLLEELSLF  540
MEKLKDVYYD DDDGQLNDFQ IDSGTLPCVA CGVLGFPFMS VVQPSENALK DLSERQGEID  600
ALEDKAESSE KSNCEWNTSS RYIRPRIFCL EHTIELQRLL QSRGGLKFLV ICHKDFQKFK  660
AHAAIVAEEV KVPFRYDDVL LESASKEELS LIDLAIEGEE NNEYGADWTS KLGINLRYCV  720
KVRKNSPTNK IQHALSLGGL FSDSSHVLDM STIKWLQRKS RSKAKPCSTT SGFTSRERLE  780
VKAERRLGEK EEVESQGGRK EEKIIQYSRK KKLNPNANRS RHASAVDSEM NNEIGDSADL  840
TSVTREHQGH SVALEPRTTN ANSEEEEQSQ VVLPTNREAV SEDIRHTEQQ EEQTHSSAQV  900
GLEVSETNIA SEKIVVDMVR DDDPLASNGD EASSSGLQAA DDENSMESEV ASSGNTKVIV  960
EAKKKRKIEL ESETNDYHPE SSIGFIKSPC EGLRSRGKRK VTCEETSSNL NEASDEEKKH  1020
TAKRLKKTPN TGSTTTQHNL CYQEGCKMTF KSKADLAAHK RNRCTHEGCG KKFRAHKYLV  1080
LHQRVHNDER PLACPWKGCS MNFKWQWART EHLRLHTGER PYKCKVEECG LSFRFVSDYS  1140
RHRRKTGHYV T
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A3e-72114258346Transcription factor jumonji (Jmj) family protein
6ip4_A3e-72114258346Arabidopsis JMJ13
Search in ModeBase
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009122623.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY6645000.0AY664500.1 Arabidopsis thaliana early flowering 6 (ELF6) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009122623.10.0PREDICTED: probable lysine-specific demethylase ELF6 isoform X1
RefseqXP_009122624.10.0PREDICTED: probable lysine-specific demethylase ELF6 isoform X2
SwissprotQ6BDA00.0ELF6_ARATH; Probable lysine-specific demethylase ELF6
TrEMBLA0A397XPG80.0A0A397XPG8_BRACM; Uncharacterized protein
STRINGBra009474.1-P0.0(Brassica rapa)
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]