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 Carubv10012799m
Common NameCARUB_v10012799mg
Organism
Capsella rubella
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family C3H
Protein Properties Length: 1805aa    MW: 196939 Da    PI: 4.4044
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Carubv10012799mgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH24.16.1e-0817801803225
                       -S---SGGGGTS--TTTTT-SS-S CS
          zf-CCCH    2 ktelCrffartGtCkyGdrCkFaH 25  
                       +++ C+ff++ G+C+ G++C++ H
  Carubv10012799m 1780 GQRVCKFFREDGYCRKGASCNYLH 1803
                       6899******************** PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.40.101.2E-9633692IPR013083Zinc finger, RING/FYVE/PHD-type
SuperFamilySSF579031.73E-7634692IPR011011Zinc finger, FYVE/PHD-type
PROSITE profilePS500168.609636702IPR019787Zinc finger, PHD-finger
CDDcd155687.55E-21638683No hitNo description
SMARTSM002492.5E-7638684IPR001965Zinc finger, PHD-type
PROSITE patternPS013590639699IPR019786Zinc finger, PHD-type, conserved site
SuperFamilySSF475923.49E-19841920IPR003121SWIB/MDM2 domain
Gene3DG3DSA:1.10.245.106.1E-22842927IPR003121SWIB/MDM2 domain
PfamPF022014.3E-12864919IPR003121SWIB/MDM2 domain
SMARTSM007198.1E-559811090IPR004343Plus-3 domain
PROSITE profilePS5136030.7049811113IPR004343Plus-3 domain
SuperFamilySSF1590423.79E-359821110IPR004343Plus-3 domain
PfamPF031261.1E-249861088IPR004343Plus-3 domain
SuperFamilySSF552774.84E-1813161382IPR003169GYF domain
CDDcd000723.76E-1913291386No hitNo description
PROSITE profilePS5082916.51813291383IPR003169GYF domain
SMARTSM004441.3E-2313301385IPR003169GYF domain
PfamPF022131.4E-1313311370IPR003169GYF domain
Gene3DG3DSA:3.30.1490.401.8E-1713311383IPR003169GYF domain
Gene3DG3DSA:4.10.1000.101.5E-517751804IPR000571Zinc finger, CCCH-type
PROSITE profilePS5010314.51117781804IPR000571Zinc finger, CCCH-type
PfamPF006429.1E-617801803IPR000571Zinc finger, CCCH-type
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010964Biological Processregulation of chromatin silencing by small RNA
GO:0032776Biological ProcessDNA methylation on cytosine
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0008270Molecular Functionzinc ion binding
GO:0042393Molecular Functionhistone binding
Sequence ? help Back to Top
Protein Sequence    Length: 1805 aa     Download sequence    Send to blast
MDSDSARVSV ESVKDDSECV NVSNEPNLTE TCGDEGGGGD GVRDVNSSAA ASELVPLESV  60
SVDGNGEGVI LNSVADDVVE GGTPVDVVVS SELSPVVTEV GGGGEKNAAF NVQEMDSVGG  120
EASAVEAVPL KPSLVVGGGG EDEGAASMVK EENFSAQGSD SQANLSGDRL EENKEVAMEE  180
EPPSHEVNVV DSQNAEEKRE VGEQVVCEGM AGEESSQARE SELGQNIESE KDKVDVMEEE  240
TTAQAASLVN DIEIPDDKEV ACVAGFTEIP SEDKVLDDSV RNSGSEFVKE EPLKEELQIG  300
ERAKDLTDGD AKEGVDVTED AMDIQVLKQS EEEEKLDGAA VSVIETNPRE MDDVATEASE  360
KIAVPVDISS AVVTQLAGET NEKATVMDDA KEDVEKDSEA GKLLDIHVPE AAEEVETDAM  420
YGAGIEKEDG GVVGAGEAGQ AVELEESREE NQELSQELAK DETKISEVSE ETETRIGDEN  480
QEKDNDMTDL AEDVKPHGDS AVADIEEGKE DHDNLRVTET TETHEETVTG LVDGTKKAEV  540
SEETETRIED EDQEKDDEMT DVAEGVETHG DSSIADIEEA KENHENITET QEERVMAEMS  600
DEEPEEVDEE NKSAGGKRKR GRNIKTVKGA VKKKEEDVCF MCFDGGDLVL CDRRGCPKAY  660
HPSCVDRDEA FFQSKGKWNC GWHLCSKCEK TATYLCYTCM FSLCKGCAKD AVFFCIRGNK  720
GLCETCMETV KLIERKEQEK EPAQLDFDDK TSWEYLFKDY WIDLKTQLSL SPEELDQAKS  780
PRKGHESNAS KQGTAGETDS VTDGGSDSDS TPKKRKTRSR SKSGSAEKIL SPSDKNLSGD  840
TMEWASKELL DVVMHMRRGD RSFLPQLEAQ NLLLAYIKRY NLRDPRRKSQ VICDSRLQNL  900
FGKSHVGHFE MLNLLDSHFL IKEKNQADDI QGDIVDTEEA NHMDVDENLD HPMKSGKDKK  960
RKTRKKSVRK GRQSNLDDFA AVDMHNINLI YLRRSLVEDL LEDSTAFEDK VASAFVRLRI  1020
SGNQKQDLYR LVQVVGTSKA PEPYKVGKKT TDFVLEILNL DKTEVVSIDI ISNQDFTEDE  1080
CKRLKQSIKC GLINRLTVGD IQEKAIALQE VRVKNLLEAE ILRFSHLRDR ASDMGRRKEL  1140
RECVEKLQLL KSPEERQRRL EEIPEIHADP KMDPECESED EDEKEEKEKE KQLRPRSSSF  1200
NRRVRDPISP RKVGFGSNES WTGTSNYSNT SANRELGRSY SGRGSTGRGD YLGSSDDMVS  1260
ESMWTSGRER EVQPSLSSEK PRSVSIPETT ARSSRAIAPL ELSPRIAPEI LTAPPAIVPQ  1320
PVSKSNESEK IWHYKDPSGK VQGPFSMAQL RKWNNTGYFP AKLEIWKAKE SPLDSILLTD  1380
ALAGLFHKQP QAVDNSYMKA QVAAYSGQSS QSEPNLGSTA RTAPSTIEIP RNSQDTWSQG  1440
GSLPSPTPNQ ITTPTAKRRN FESRWSPTKP TSHSAIQSMN YPAAQPGQSQ TSRIDIPVAV  1500
NSAGALQPQT YPIPTSDSIN VSVNHSATLH SPTPAGGKQS WGSMQTDKFD SHGHGGSDTP  1560
SSQNSSMSYG TTTPSVLPSQ SQPGFPPSDS WKVAIPSQPM AQTQAQASWG MNTVNNQNSG  1620
QAPANQNTSW GQGTVNPNMG WGGPAQAGMN VNWPGSSAPS NGQGIPNSSW GGPVQGQPQA  1680
YPNPGWGVTA VPQAQPQAQV QAPVSNTGSG GWIQPGQGMQ SGNNNQNWGT QNQMVIPSGG  1740
SGGNQAGFWG NQQNQNGDSG YGWNRQSSGS GGQNNNNFKG QRVCKFFRED GYCRKGASCN  1800
YLHN*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4gnd_A2e-19623712288Histone-lysine N-methyltransferase NSD3
4gnd_C2e-19623712288Histone-lysine N-methyltransferase NSD3
4gne_A2e-19623712288Histone-lysine N-methyltransferase NSD3
4gnf_A2e-19623712288Histone-lysine N-methyltransferase NSD3
4gng_A2e-19623712288Histone-lysine N-methyltransferase NSD3
4gng_D2e-19623712288Histone-lysine N-methyltransferase NSD3
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtPlays a central role in integrating RNA silencing and chromatin signals in 21 nt siRNA-dependent DNA methylation on cytosine pathway leading to transcriptional gene silencing of specific sequences. Involved in a chromatin-based RNA silencing pathway that encompasses both post-transcriptional gene silencing (PTGS) (e.g. RDR1, RDR6 and AGO2) and transcriptional gene silencing (TGS) (e.g. siRNA-dependent DNA methylation and histone H3) components. Mediates siRNA accumulation at specific chromatin loci. Binds H3K4me0 through its PHD to enforce low levels of H3K4 methylation and gene silencing at a subset of genomic loci. {ECO:0000269|PubMed:22940247}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapCarubv10012799m
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC0070470.0AC007047.7 Arabidopsis thaliana chromosome 2 clone F16F14 map mi398, complete sequence.
GenBankCP0026850.0CP002685.1 Arabidopsis thaliana chromosome 2, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006296817.10.0zinc finger CCCH domain-containing protein 19
SwissprotQ9SIV50.0C3H19_ARATH; Zinc finger CCCH domain-containing protein 19
TrEMBLR0HWB10.0R0HWB1_9BRAS; Uncharacterized protein
STRINGXP_006296817.10.0(Capsella rubella)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM54221620
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G16485.10.0nucleic acid binding;zinc ion binding;DNA binding