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 RrC1477_p6
Organism
Raphanus raphanistrum
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: 1235aa    MW: 138481 Da    PI: 7.0658
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC1477_p6genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H2130.0003111471170223
                  EET..TTTEEESSHHHHHHHHHHT CS
     zf-C2H2    2 kCp..dCgksFsrksnLkrHirtH 23  
                  +C+   Cgk F+ + +L+ H+r+H
  RrC1477_p6 1147 RCTheGCGKKFRAHKYLVLHQRVH 1170
                  588889****************99 PP
2zf-C2H211.50.0009612061232123
                  EEET..TTTEEESSHHHHHHHHHH..T CS
     zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                  ykC+   Cg sF+  s++ rH r+  H
  RrC1477_p6 1206 YKCKvdGCGLSFRFVSDYSRHRRKtgH 1232
                  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
PfamPF023753.8E-161851IPR003349JmjN domain
SMARTSM005585.6E-46258427IPR003347JmjC domain
PROSITE profilePS5118434.973261427IPR003347JmjC domain
SuperFamilySSF511978.79E-26272425No hitNo description
PfamPF023732.1E-37291410IPR003347JmjC domain
SMARTSM003556811231145IPR015880Zinc finger, C2H2-like
SMARTSM003550.05711461170IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015713.46411461175IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.1E-711471174IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028011481170IPR007087Zinc finger, C2H2
SuperFamilySSF576679.1E-1111621204No hitNo description
Gene3DG3DSA:3.30.160.601.8E-1011751200IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE profilePS5015712.09211761205IPR007087Zinc finger, C2H2
SMARTSM003550.009511761200IPR015880Zinc finger, C2H2-like
PROSITE patternPS00028011781200IPR007087Zinc finger, C2H2
SuperFamilySSF576673.78E-911941228No hitNo description
Gene3DG3DSA:3.30.160.603.0E-1012011229IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.2812061232IPR015880Zinc finger, C2H2-like
PROSITE profilePS501579.30712061235IPR007087Zinc finger, C2H2
PROSITE patternPS00028012081232IPR007087Zinc 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: 1235 aa     Download sequence    Send to blast
MGMNVEIPNW LKAMPLAPVF RPTDTEFADP IAYISKIEKQ ASAFGICKIV PPIPKPSKKY  60
VFCNLNKSLL RCPELASGVD VSKLLLRQED RAVFTTRQQE LGQARKKSKG GEGGGGVKQV  120
WQSGGVYTLE QFESKSKAFY KSQLGTVKEV SPVVVEALFW KAAEEKPIYI EYANDVPGSA  180
FGEPEGHFRH FRQRKRRGRG FYQRKAEDSQ EPSCKNGEET LPEVAKASLT SPSLLSQDQS  240
KKKNVDVIDE MEGTAGWKLS NSSWNLQMIA RSPGSVTRFM PDDIPGVTSP MVYIGMLFSW  300
FAWHVEDHEL HSMNYLHTGS PKTWYAVPGD YALDFEEVIR KNSYGRNLDQ LAALTQLGEK  360
TTLVSPEMIV SSDIPCCRLV QNPGEFVVTF PRSYHVGFSH GFNCGEAANF GTPQWLNVAK  420
EAAVRRAAMN YLPMLSHQQL LYLLTMSFVS RQISIVPLVP RSLLPGGRSS RLRDRQREER  480
EFLVKKAFVE DILNENKNLS VLLGEPGSRL VMWYPDLLPR HSALALAATG VDATSAVSCP  540
AEAKNEVENG HSGTQNEEKT TLLEELSLFM EKLKDVYYDD DDGQLNDFQI DSGTLPCVAC  600
GVLGFPFMSV VQPSENALKD LSERQEDIDA QEITAQSSEK TNNSEWNTSS RYIRPRIFCL  660
EHTIELQRLL QSRGGLKFLV ICHKDFQKFK AHAAIVAEEV KVPFRYDDVL LESASKEELS  720
LIDLAIEGEE NNEHGADWTS KLGINLRYCV KVRKNSANNK IQHALSLGGL FSDTSHMLDM  780
STIKWLQRKS RSKAKPCSTS CFTLREHLEV KADRKLGEKE EDESQAGRKE EKIIQYSRKK  840
KLNPNANRAV QSEMNIGIGD SADLTSVTRE HQGHSMMTSD NNNGSNSDSH VVDLVVSPTV  900
LASTVDNHNG TPMKMMCGEF DCRDVDEAAE MSGQEFKELR STNANIEEEE QSQVVQPTNR  960
EAVSENIMHT EQEAHSSAQL GLEVPETSIA SEKLVVDIVR DDEPLASNGD QASSSGFQAA  1020
DNQNSVESVV GSSGNTEAKK KRKLELDCET NDIPESSIGF IKSPCEGLRS RGKRKVTCET  1080
SFDLNEASDE EKKKHTAKKL KKTSTTRSGT HGQEEASTAT HHNRCYLEGC KMTFKSKTDL  1140
AAHKRNRCTH EGCGKKFRAH KYLVLHQRVH NDERPFVCPW KGCSMNFKWQ WARTEHLRLH  1200
TGERPYKCKV DGCGLSFRFV SDYSRHRRKT GHYVT
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A7e-57104578366Transcription factor jumonji (Jmj) family protein
6ip4_A7e-57104578366Arabidopsis JMJ13
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
110381043KKKRKL
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_018446140.10.0PREDICTED: LOW QUALITY PROTEIN: probable lysine-specific demethylase ELF6
SwissprotQ6BDA00.0ELF6_ARATH; Probable lysine-specific demethylase ELF6
TrEMBLA0A3P6E3C60.0A0A3P6E3C6_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]