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 Csa15g002520.1
Organism
Camelina sativa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Camelina
Family C3H
Protein Properties Length: 1298aa    MW: 144070 Da    PI: 6.8725
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Csa15g002520.1genomeCSGPView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH32.71.2e-10934960127
                     --S---SGGGGTS--TTTTT-SS-SSS CS
         zf-CCCH   1 yktelCrffartGtCkyGdrCkFaHgp 27 
                     ++++ C+++ rtG C++G++C+F+H++
  Csa15g002520.1 934 PGEPDCSYYIRTGLCRFGSTCRFNHPR 960
                     5789*********************96 PP
2zf-CCCH35.71.5e-119811005327
                      S---SGGGGTS--TTTTT-SS-SSS CS
         zf-CCCH    3 telCrffartGtCkyGdrCkFaHgp 27  
                      +++C ++++tGtCk+G +CkF+H++
  Csa15g002520.1  981 QPECEYYLKTGTCKFGVTCKFHHPR 1005
                      799********************96 PP
3zf-CCCH31.82.4e-1010271051327
                      S---SGGGGTS--TTTTT-SS-SSS CS
         zf-CCCH    3 telCrffartGtCkyGdrCkFaHgp 27  
                      ++ C +f rtG+Ck+G++CkF+H++
  Csa15g002520.1 1027 EVDCAYFIRTGHCKFGGTCKFNHPQ 1051
                      578********************97 PP
4zf-CCCH35.22.1e-1111701196127
                      --S---SGGGGTS--TTTTT-SS-SSS CS
         zf-CCCH    1 yktelCrffartGtCkyGdrCkFaHgp 27  
                      +++++C+f+++tG Ck+G  CkF+H++
  Csa15g002520.1 1170 PGQPECQFYMKTGDCKFGTVCKFHHPR 1196
                      5789*********************96 PP
5zf-CCCH33.57.3e-1112161242127
                      --S---SGGGGTS--TTTTT-SS-SSS CS
         zf-CCCH    1 yktelCrffartGtCkyGdrCkFaHgp 27  
                      ++++lC f+ r+G+Ck+G++CkF H++
  Csa15g002520.1 1216 PGEPLCVFYTRYGICKFGPSCKFDHPM 1242
                      589**********************95 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF579033.32E-8665IPR011011Zinc finger, FYVE/PHD-type
Gene3DG3DSA:3.30.40.108.0E-61062IPR013083Zinc finger, RING/FYVE/PHD-type
PROSITE profilePS500168.5911263IPR019787Zinc finger, PHD-finger
SMARTSM002492.5E-51461IPR001965Zinc finger, PHD-type
PROSITE patternPS0135901560IPR019786Zinc finger, PHD-type, conserved site
Gene3DG3DSA:3.30.40.105.4E-19128206IPR013083Zinc finger, RING/FYVE/PHD-type
SuperFamilySSF578508.84E-14137206No hitNo description
PfamPF139208.5E-7142187No hitNo description
CDDcd001622.03E-8144187No hitNo description
PROSITE profilePS5008910.453145184IPR001841Zinc finger, RING-type
SMARTSM001840.037145183IPR001841Zinc finger, RING-type
SuperFamilySSF886971.79E-65247443IPR015947PUA-like domain
SMARTSM004665.6E-75267425IPR003105SRA-YDG
PROSITE profilePS5101552.586272421IPR003105SRA-YDG
PfamPF021829.3E-46275424IPR003105SRA-YDG
Gene3DG3DSA:2.30.280.101.8E-64283450IPR003105SRA-YDG
Gene3DG3DSA:3.30.40.101.5E-18501628IPR013083Zinc finger, RING/FYVE/PHD-type
SuperFamilySSF578503.28E-12511601No hitNo description
CDDcd001626.33E-4516577No hitNo description
PROSITE profilePS5008910.498517573IPR001841Zinc finger, RING-type
PfamPF134451.2E-8517559IPR027370RING-type zinc-finger, LisH dimerisation motif
SMARTSM001844.0E-7517573IPR001841Zinc finger, RING-type
PROSITE patternPS005180532541IPR017907Zinc finger, RING-type, conserved site
SuperFamilySSF577561.57E-7664685IPR001878Zinc finger, CCHC-type
Gene3DG3DSA:4.10.60.105.4E-6665682IPR001878Zinc finger, CCHC-type
SMARTSM003434.5E-6666682IPR001878Zinc finger, CCHC-type
PfamPF000982.2E-7666682IPR001878Zinc finger, CCHC-type
PROSITE profilePS5015811.301667682IPR001878Zinc finger, CCHC-type
ProDomPD0896394.0E-38714799IPR012923Chromosome segregation in meiosis protein 3
PfamPF079621.2E-11748797IPR012923Chromosome segregation in meiosis protein 3
PROSITE profilePS5010314.699933961IPR000571Zinc finger, CCCH-type
SMARTSM003567.0E-5933960IPR000571Zinc finger, CCCH-type
PfamPF006423.6E-7935960IPR000571Zinc finger, CCCH-type
SuperFamilySSF902294.06E-5938961IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010314.1089781006IPR000571Zinc finger, CCCH-type
SMARTSM003562.6E-59781005IPR000571Zinc finger, CCCH-type
PfamPF006424.6E-99811005IPR000571Zinc finger, CCCH-type
SuperFamilySSF902291.7E-59821007IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.106.8E-49841005IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010314.0810241052IPR000571Zinc finger, CCCH-type
SMARTSM003561.8E-410241051IPR000571Zinc finger, CCCH-type
PfamPF006422.6E-710271051IPR000571Zinc finger, CCCH-type
SuperFamilySSF902293.14E-510271053IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010314.2211691197IPR000571Zinc finger, CCCH-type
SMARTSM003561.6E-511691196IPR000571Zinc finger, CCCH-type
PfamPF006428.3E-811711196IPR000571Zinc finger, CCCH-type
SuperFamilySSF902293.14E-511731198IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.108.2E-411751197IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010315.18712151243IPR000571Zinc finger, CCCH-type
SMARTSM003563.9E-712151242IPR000571Zinc finger, CCCH-type
PfamPF006428.1E-812171242IPR000571Zinc finger, CCCH-type
SuperFamilySSF902295.36E-512181242IPR000571Zinc finger, CCCH-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006974Biological Processcellular response to DNA damage stimulus
GO:0007049Biological Processcell cycle
GO:0048478Biological Processreplication fork protection
GO:0005634Cellular Componentnucleus
GO:0003676Molecular Functionnucleic acid binding
GO:0008270Molecular Functionzinc ion binding
GO:0042393Molecular Functionhistone binding
Sequence ? help Back to Top
Protein Sequence    Length: 1298 aa     Download sequence    Send to blast
MARDIQFPCD GDGVCMRCKS TPPPEESLTC GTCVTPWHVS CLSSPPETLA STLQWHCPDC  60
SGEVDPLPVS GVAAGYGAVG SDLVAAIRAI EADETLSTVE KAKKRQQLLS GSKGVDEDDE  120
EEKKKGKGKN ANLDVLSALG DNLMCSFCMQ LPERPVTKPC GHNACLKCFE KWMGQGKRTC  180
GKCRSIVPEK MARNPRINSS LVSAIRFARV SRSAAAGTSK VYHFVSNQDR PDKAFTTERA  240
KKTGKANAAS GRIYVTIPPD HFGPIPAEND PVRSQGLLVG ESWEDRLECR QWGAHFPHVA  300
GIAGQASYGA QSVALSGGYE DDEDHGEWFL YTGSGGRDLS GNKRTNKDQS FDQKFEKSNE  360
ALRLSCKLGY PVRVVRSHKE KRSAYAPEEG VRYDGVYRIE KCWRKVGIQG SFKVCRYLFV  420
RCDNEPAPWT SDEHGDHPRP LPNIPELNMA TDLFERKESP SWDFDEGEGC WKWIKPPPAS  480
KKSVNVLDPE ERKSLKKAIK AAHSNTVRAR LLKEFKCQIC HQVMTLPVTT PCAHNFCKAC  540
LEAKFAGKTL VRERSRGGRT LRAQKNVMNC PCCPTDISDF LQNPQVNREV MEVIERLKNQ  600
EEDDAKPVDE EGEGSGTDPE EEMQVVSEEA EQPKKRIKLD TDVLELNLVG LIESSGDLIQ  660
VKTPTGCFKC GRPGHWSRDC PSSAPVAAGN NSVSSSSAPA QIPNNDNQRF SKKSGTSIGP  720
VPKLTKTRVQ RPKLTPELLL SEDGLGYVSD LGNMIRLYSE WHSHLLPYYS FDQFVHKVQQ  780
VASTKRVKNC INELRERVAS GVDPNKLYEK QEENTGPYDD DQGNVDMDQP SHDEENIPSR  840
SVDVDADVDP NVDAFQDSML NDIFDNASKL PSDEQNKDKS SELTEEQRER MEANRLKAME  900
KAHNISEEQR VHAMWQMNLG SEETMETGSY PERPGEPDCS YYIRTGLCRF GSTCRFNHPR  960
DRELVIATAR MRGEYPERIG QPECEYYLKT GTCKFGVTCK FHHPRNKAGI AGRVSLNMLG  1020
YPLRSNEVDC AYFIRTGHCK FGGTCKFNHP QPQPTNMMVP TSGQQSYPWS RASFIASPRW  1080
QDPSTYPSLI MPQGVVPVQG WNPYSGQLGS VSPSGTGNDL NYNRSLQQQS ETKESGSQSQ  1140
GSFSGFNPGS SVPLGGFYAL PRENVFPERP GQPECQFYMK TGDCKFGTVC KFHHPRDRQA  1200
PPPDCLLSSI GLPLRPGEPL CVFYTRYGIC KFGPSCKFDH PMRVFAYDNT ASETDEVVET  1260
SSSGHSRRIS VSETRQAAAT TTTSSGKDTT TIIDTQQ*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
2pb7_A3e-462554327189E3 ubiquitin-protein ligase UHRF1
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtE3 ubiquitin-protein ligase. Participates in CpG methylation-dependent transcriptional regulation and epigenetic transcriptional silencing. Mediates ubiquitination with the E2 ubiquitin-conjugating enzyme UBC11. Promotes methylation-mediated gene silencing leading, for example, to early flowering. Associates with methylated DNA, and can bind to CpG, CpNpG, and CpNpN DNA motifs, with a strong preference for methylated forms, and with highest affinity for CpG substrate. Probably acts at the DNA methylation?histone interface to maintain centromeric heterochromatin. {ECO:0000269|PubMed:17239600, ECO:0000269|PubMed:17242155, ECO:0000269|PubMed:18643997, ECO:0000269|PubMed:18704160}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapCsa15g002520.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY0654380.0AY065438.1 Arabidopsis thaliana putative transcription factor (At1g57820) mRNA, complete cds.
GenBankAY1172350.0AY117235.1 Arabidopsis thaliana putative transcription factor (At1g57820) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010463707.10.0PREDICTED: E3 ubiquitin-protein ligase ORTHRUS 2-like
SwissprotQ8VYZ00.0ORTH2_ARATH; E3 ubiquitin-protein ligase ORTHRUS 2
TrEMBLD7KYM70.0D7KYM7_ARALL; Uncharacterized protein
STRINGXP_010463707.10.0(Camelina sativa)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G02830.10.0zinc finger protein 1
Publications ? help Back to Top
  1. Yogeeswaran K, et al.
    Comparative genome analyses of Arabidopsis spp.: inferring chromosomal rearrangement events in the evolutionary history of A. thaliana.
    Genome Res., 2005. 15(4): p. 505-15
    [PMID:15805492]
  2. Johnson LM, et al.
    The SRA methyl-cytosine-binding domain links DNA and histone methylation.
    Curr. Biol., 2007. 17(4): p. 379-84
    [PMID:17239600]
  3. Woo HR,Pontes O,Pikaard CS,Richards EJ
    VIM1, a methylcytosine-binding protein required for centromeric heterochromatinization.
    Genes Dev., 2007. 21(3): p. 267-77
    [PMID:17242155]
  4. Liu S, et al.
    Plant SET- and RING-associated domain proteins in heterochromatinization.
    Plant J., 2007. 52(5): p. 914-26
    [PMID:17892444]
  5. Woo HR,Dittmer TA,Richards EJ
    Three SRA-domain methylcytosine-binding proteins cooperate to maintain global CpG methylation and epigenetic silencing in Arabidopsis.
    PLoS Genet., 2008. 4(8): p. e1000156
    [PMID:18704160]
  6. Woo HR,Richards EJ
    Natural variation in DNA methylation in ribosomal RNA genes of Arabidopsis thaliana.
    BMC Plant Biol., 2008. 8: p. 92
    [PMID:18783613]
  7. Yao Q,Song CX,He C,Kumaran D,Dunn JJ
    Heterologous expression and purification of Arabidopsis thaliana VIM1 protein: in vitro evidence for its inability to recognize hydroxymethylcytosine, a rare base in Arabidopsis DNA.
    Protein Expr. Purif., 2012. 83(1): p. 104-11
    [PMID:22459921]
  8. Heyndrickx KS,Vandepoele K
    Systematic identification of functional plant modules through the integration of complementary data sources.
    Plant Physiol., 2012. 159(3): p. 884-901
    [PMID:22589469]
  9. Shook MS,Richards EJ
    VIM proteins regulate transcription exclusively through the MET1 cytosine methylation pathway.
    Epigenetics, 2014. 9(7): p. 980-6
    [PMID:24762702]
  10. Kim J,Kim JH,Richards EJ,Chung KM,Woo HR
    Arabidopsis VIM proteins regulate epigenetic silencing by modulating DNA methylation and histone modification in cooperation with MET1.
    Mol Plant, 2014. 7(9): p. 1470-1485
    [PMID:25009302]