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 Rsa1.0_03997.1_g00003.1
Organism
Raphanus sativus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family C2H2
Protein Properties Length: 1197aa    MW: 133836 Da    PI: 7.2456
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_03997.1_g00003.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H2130.000311091132223
                               EET..TTTEEESSHHHHHHHHHHT CS
                  zf-C2H2    2 kCp..dCgksFsrksnLkrHirtH 23  
                               +C+   Cgk F+ + +L+ H+r+H
  Rsa1.0_03997.1_g00003.1 1109 RCTheGCGKKFRAHKYLVLHQRVH 1132
                               588889****************99 PP
2zf-C2H211.50.0009211681194123
                               EEET..TTTEEESSHHHHHHHHHH..T CS
                  zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                               ykC+   Cg sF+  s++ rH r+  H
  Rsa1.0_03997.1_g00003.1 1168 YKCKvdGCGLSFRFVSDYSRHRRKtgH 1194
                               99*********************9777 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005451.1E-141656IPR003349JmjN domain
PROSITE profilePS5118314.3261758IPR003349JmjN domain
PfamPF023753.7E-161851IPR003349JmjN domain
SMARTSM005585.6E-46262431IPR003347JmjC domain
PROSITE profilePS5118434.973265431IPR003347JmjC domain
SuperFamilySSF511978.51E-26276429No hitNo description
PfamPF023732.0E-37295414IPR003347JmjC domain
SMARTSM003556010851107IPR015880Zinc finger, C2H2-like
SMARTSM003550.05711081132IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.46411081137IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.609.2E-811091136IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028011101132IPR007087Zinc finger, C2H2
SuperFamilySSF576671.24E-1011241166No hitNo description
Gene3DG3DSA:3.30.160.602.4E-1011371162IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.01511381162IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.80111381167IPR007087Zinc finger, C2H2
PROSITE patternPS00028011401162IPR007087Zinc finger, C2H2
SuperFamilySSF576673.64E-911561190No hitNo description
Gene3DG3DSA:3.30.160.602.2E-1011631191IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.2811681194IPR015880Zinc finger, C2H2-like
PROSITE profilePS501579.30711681197IPR007087Zinc finger, C2H2
PROSITE patternPS00028011701194IPR007087Zinc 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: 1197 aa     Download sequence    Send to blast
MGINVEIPNW LKAMPLAPVF RPTDTEFADP IAYISKIEKQ ASAFGICKIV PPIPKPSKKY  60
VFCNLNKSLL RCPELASGVD VSKLLLRQED RAVFTTRQQE LGQARKKNKG GGGEGGGGVK  120
QVWQSGGVYT LEQFESKSKA FYKSQLGTVK EVSSVVVEAL FWKAASEKPI YIEYANDVPG  180
SAFGEPEGHF RHFRQRKRRG RGFYQRKAVI NDSQEPSCKN GEETLPEVAK ASLASPSLLS  240
QDQSKNKNVD VIDEMEGTAG WKLSNSSWNL QMIARSPGSV TRFMPDDIPG VTSPMVYIGM  300
LFSWFAWHVE DHELHSMNYL HTGSPKTWYA VPGDYALDFE EVIRKNSYGR NLDQLAALTQ  360
LGEKTTLVSP EMIVSSDIPC CRLVQNPGEF VVTFPRSYHV GFSHGFNCGE AANFGTPQWL  420
NVAKEAAVRR AAMNYLPMLS HQQLLYLLTI VPRSLLPGGR SSRLRDRQRE EREFLVKKAF  480
VEDILNENKN LSVLLGEPGS RLVMWDPDLL PRHSALTLAA TGVDATSAVS CPAEAKNEVE  540
NGHSGTQNEE KTTLLEELSL FMEKLKDVYY DDDDGQLNDF QIDSGTLPCV ACGVLGFPFM  600
SVVQPSENAL EDLSERQEEI DAQEITAQSP EKTNNSEWNT SSRYVRPRIF CLEHTIELQR  660
LLQSRGGLKF LVICHKDFQK FKAHAAIVAE EVKVPFRYDD VLLESASKEE LSLIDLAIEG  720
EENNEHGADW TSKLGINLRY CVKVRKNSAN NKIQHALSLG GLFSDTSHML DMSTIKWLQR  780
KSRSKAKPCS TSCFTPREHL EVKGDRKLGE KEEEDESQAG RKEEKIIQYS RKKKLNPSAN  840
RSGHHGRAVH SEMNIGIGDS ADLTSVTREH QGNSMTSDNN NGSNSDSHVV DLVLSPTMLA  900
STVDNHNGTP MKMMCGELVC SDVDEAAEMS GQEFKELGST NANIEVPETN IASEKIVVDM  960
VRDDEPLASN GDQASSSGFQ AADNQNSVES VVGSSGNTEV KKKRKLELDC ETNDIPESSI  1020
GFIKSPCEGL RSRGKRKVTC ETSFDLNEAS DEEKKKPTAK RLKKTPTTRS GTHGQEEAST  1080
ATHHNRCYLE GCKMTFKSKT DLTAHKRNRC THEGCGKKFR AHKYLVLHQR VHNDERPFVC  1140
PWKGCTMNFK WQWARTEHLR LHTGERPYKC KVDGCGLSFR FVSDYSRHRR KTGHYVT
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A2e-56104458346Transcription factor jumonji (Jmj) family protein
6ip4_A2e-56104458346Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
110001005KKKRKL
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
PlantRegMapRsa1.0_03997.1_g00003.1
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_018446140.10.0PREDICTED: LOW QUALITY PROTEIN: probable lysine-specific demethylase ELF6
SwissprotQ6BDA00.0ELF6_ARATH; Probable lysine-specific demethylase ELF6
TrEMBLA0A0D3EHY90.0A0A0D3EHY9_BRAOL; Uncharacterized protein
STRINGBo9g181310.10.0(Brassica oleracea)
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]