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 28507.m000165
Common NameRCOM_0263520
Organism
Ricinus communis
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Euphorbiaceae; Acalyphoideae; Acalypheae; Ricinus
Family C2H2
Protein Properties Length: 1554aa    MW: 174290 Da    PI: 6.8895
Description C2H2 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
28507.m000165genomeJCVIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-C2H211.60.0008314391464123
                     EEET..TTTEEESSHHHHHHHHHH.T CS
        zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt.H 23  
                     ykC    C++sF ++ +L  H r+ +
  28507.m000165 1439 YKCDleGCPMSFETRAELLLHKRNrC 1464
                     99********************9877 PP
2zf-C2H213.50.0002215221548123
                     EEET..TTTEEESSHHHHHHHHHH..T CS
        zf-C2H2    1 ykCp..dCgksFsrksnLkrHirt..H 23  
                     ykC+   Cg++F+  s++ rH r+  H
  28507.m000165 1522 YKCKveGCGRTFRFVSDFSRHRRKtgH 1548
                     99*********************9777 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SMARTSM005456.1E-131757IPR003349JmjN domain
PROSITE profilePS5118313.5361859IPR003349JmjN domain
PfamPF023752.8E-141952IPR003349JmjN domain
SuperFamilySSF511972.53E-26294463No hitNo description
SMARTSM005585.6E-45297466IPR003347JmjC domain
PROSITE profilePS5118432.911300466IPR003347JmjC domain
PfamPF023733.0E-35331449IPR003347JmjC domain
SMARTSM003558.714391461IPR015880Zinc finger, C2H2-like
SMARTSM003550.1414621486IPR015880Zinc finger, C2H2-like
SuperFamilySSF576673.92E-514621498No hitNo description
PROSITE profilePS5015710.88714621491IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.6E-414631490IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
PROSITE patternPS00028014641486IPR007087Zinc finger, C2H2
Gene3DG3DSA:3.30.160.601.6E-1014911516IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003557.5E-414921516IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015712.65314921521IPR007087Zinc finger, C2H2
PROSITE patternPS00028014941516IPR007087Zinc finger, C2H2
SuperFamilySSF576671.54E-1115021544No hitNo description
Gene3DG3DSA:3.30.160.602.4E-1215171545IPR013087Zinc finger C2H2-type/integrase DNA-binding domain
SMARTSM003550.06515221548IPR015880Zinc finger, C2H2-like
PROSITE profilePS5015711.5115221553IPR007087Zinc finger, C2H2
PROSITE patternPS00028015241548IPR007087Zinc 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: 1554 aa     Download sequence    Send to blast
MGMGNVEIPK WLKDLPLAPE FHPTDTEFAD PIAYISKIEK KATAFGICKI IPPLPKPSKR  60
YVFGNLNKSL SKCPELGDSV NLSNASSLKK GLQDIGNDGE ARAVFTTRHQ ELGQDIKKTK  120
GTIKENPQLG VHKQVWQSGE IYTLDQFESK SKAFAKSLLG MFKEISPLVI ETLFWKAASD  180
KPIHVEYAND VPGSAFGEPE DQFKYFHIRR RKRASYKSYR RSAGSSDCKE KEIDNVNNLD  240
NDEMKGTAMK NEPSMSSETI SRSSITSSVV LSEEILRSSK RKSVNANNDM EGTAGWKLSN  300
SPWNLQVIAR SPGSLTRFMP DDIPGVTSPM IYIGMLFSWF AWHVEDHELH SMNFLHTGSA  360
KTWYAVPGDH AFTFEEVIRM QAYGGGIDRL AALTLLGEKT TLLSPEVIVS SGIPCCRLIQ  420
NPGEFVVTFP RAYHVGFSHG FNCGEAANFG TPQWLKVAKE AAVRRAAMNY LPMLSHQQLL  480
YLLTMSFVSR VPRSLLPGAR SSRLRDRLKE ERELSVKKAF IEDMLKENNI LSALLGKDSI  540
CNVVIWNPDL LPCANKDFQV PSTVTATTEE IVSSFHSKDN SSTTENDLFK EMSLYMETLN  600
DLYVDDDGDL SDDFQVDSGT LACVACGILG FPFMSVVQPS DTALAGLLDH PLVQEGSIEE  660
SGNLPLSRGW NNSSKFLRPR IFCLEHGVQI EELLRSKGGA NMLLICHSDY QKIRAHAAAI  720
AEEIDTPFNY NEIPLESASQ EDLNLIYIAI DSEDHDDCGE DWTSKLAINL RYCVKVRKNS  780
PSNKVQHALA LGGLFSDETS SDFLNIKWQS RRSRSRIKLN RPAHCKPQNR VETNKENILG  840
KTSDNVIVKT ENKLIQYTRR KYKVKIDCSA RWNQGCPRKH TMEQVSGANC EDLVKHTRKT  900
SKITPAVEIS RSDAAGSCMS PIGMSGVLHE VQVLEATDEM CLNSASLHVT GPVLTANPAI  960
ERVVRQVEIP LEKSNRFENV STVSARVSFK IQHEEKVNGV IIEDEDSSGT NLCSQCVTAA  1020
ERSEMEGEYH TTKNISLTNE AREIFCEGQY KILGDRDVLA NELLILLTQL VYMFLTLLDT  1080
LKDQHAVSLE ESTECLQETC AEEDKLQHEI EITSGINKEL IPNIVMNDQN HVSVAESSEI  1140
LKQPCISANL FNVTLKRGMQ QGIQFTKERK KEHCSCSITQ MGIDQPNAVS EETISEALGG  1200
TSAKNLWTGS ILDFDMLLKV PTVNRSKVEN IIPNSTNQIQ DPVIPVIVEE YSEVPRASSV  1260
FSVGLNLETK LQKPIHSDDV VYRDDEVHEV CQTPRETNEE RLLSHITQIS QQSPAQIKRC  1320
FGTEEESYST GNVFKGQDDC SSHELESAES AVVDPRSTVG KGRKRKNEVE HLTENKLNNN  1380
GFIISPCEGL RPRAGKDATF RNGVDIRKSA QENPMTKKAR KPVNSVPNAK KKEIAKRSYK  1440
CDLEGCPMSF ETRAELLLHK RNRCPYEGCR KRFNSHRYAI IHQRVHEDDR PLKCPWKDCS  1500
MSFKWAWART EHMRVHTGEK PYKCKVEGCG RTFRFVSDFS RHRRKTGHCV NTPA
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6ip0_A2e-56280480137346Transcription factor jumonji (Jmj) family protein
6ip4_A2e-56280480137346Arabidopsis JMJ13
Search in ModeBase
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
PlantRegMap28507.m000165
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_025015315.10.0LOW QUALITY PROTEIN: probable lysine-specific demethylase ELF6
SwissprotQ6BDA00.0ELF6_ARATH; Probable lysine-specific demethylase ELF6
TrEMBLB9T0B70.0B9T0B7_RICCO; Uncharacterized protein
STRINGXP_002531686.10.0(Ricinus communis)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF80313034
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]