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 XP_009112389.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family C3H
Protein Properties Length: 1872aa    MW: 203955 Da    PI: 4.3165
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009112389.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH19.61.6e-0618481871225
                      -S---SGGGGTS--TTTTT-SS-S CS
         zf-CCCH    2 ktelCrffartGtCkyGdrCkFaH 25  
                      +++ C+f++++G C+ G+ C++ H
  XP_009112389.1 1848 GQRVCKFHRENGNCRKGAACTYLH 1871
                      6899******************** PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.40.102.6E-10703763IPR013083Zinc finger, RING/FYVE/PHD-type
SuperFamilySSF579033.99E-8705768IPR011011Zinc finger, FYVE/PHD-type
PROSITE profilePS500168.689707773IPR019787Zinc finger, PHD-finger
CDDcd155681.15E-21709754No hitNo description
SMARTSM002491.8E-8709755IPR001965Zinc finger, PHD-type
PROSITE patternPS013590710770IPR019786Zinc finger, PHD-type, conserved site
Gene3DG3DSA:1.10.245.104.0E-24904997IPR003121SWIB/MDM2 domain
SMARTSM001510.0058909994IPR019835SWIB domain
SuperFamilySSF475923.27E-20913994IPR003121SWIB/MDM2 domain
PfamPF022011.3E-12931989IPR003121SWIB/MDM2 domain
PROSITE profilePS5136030.58710501182IPR004343Plus-3 domain
SMARTSM007192.9E-5410501159IPR004343Plus-3 domain
SuperFamilySSF1590424.32E-3510511179IPR004343Plus-3 domain
PfamPF031262.5E-2410551157IPR004343Plus-3 domain
SuperFamilySSF552777.85E-1913861453IPR003169GYF domain
CDDcd000721.55E-1914001457No hitNo description
PROSITE profilePS5082916.8114001454IPR003169GYF domain
SMARTSM004441.8E-2314011456IPR003169GYF domain
Gene3DG3DSA:3.30.1490.401.7E-1714011454IPR003169GYF domain
PfamPF022133.0E-1414021443IPR003169GYF domain
PROSITE profilePS5010313.13118461872IPR000571Zinc finger, CCCH-type
PfamPF006422.0E-418481871IPR000571Zinc 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: 1872 aa     Download sequence    Send to blast
MDSDSAKASV ESMRDDPKCI HVSNDPNLAG TCGESSVAAE EGGGCDGATG AKGIDAVDTA  60
AAVLNPVAEM SGVVDAVVSA DLSPVAAEGG GEEDASFIAQ ECGSLDLVGG GAAVEVVSPV  120
VGEGGEEDRA AEQSDSAANL LGLGCEKVSI SGDNLEESKE EEPSASEVNG DDSLREGSQE  180
VVCGGMADEK SSQAIESKLD VMEEDTAAQA ASLEDIVSVD IDIPDVKDVA SVAGFTEISS  240
QDKGLGDSVP LEQEPLKELQ IVEEAKDLTD GDAKEDMDVA EGAMGNLMTE EEEKPDDITV  300
LEIKTKPQDV DDVANEGTEK NETRVGESSV DKETVMDDVK EDVEKDPEAG KSVDMHVPES  360
AEEVETYVKY GDGIEEEGEG MACVGEAEQT VDLEETQKLS EELAKVDETK IAEASEEIGT  420
VIRHGDDMTD MTEDVKIHGN SSVADIEGGR EDLEEMGVTE ALEETVMDKV EGTKIAEVSE  480
ETETRIEDED QEKDDDMTDV KTHADSLVAD IEEGKEIQEE MGLADMTETQ EETVEGKAVR  540
TKVAEASEET ETRSVDVDQE KDENMMDVKT LGDSSVADTE EEKKRQEEMG MAEMTETQEE  600
TVEGKVDGTK ASELSEETEA RTEDEDEEKD ENMTDAETHV DSSLADIEEG KESQEEIEMT  660
ELSATQDESV TAETGDEDAE DVEEENKGVG GKRKRVRNTK TGKKKEEDVC FICFDGGDLV  720
LCDRRGCPKA YHPSCVNQDE DFFRSKGKWN CGWHQCSKCE KTATYLCYTC VFSLCKGCAK  780
DAVFFCIRGN KGFCETCMET IKLIEREEQE KKEPAQLDFD DKTSWESLFK DYWIDLKTQL  840
SISPEELDQA KSPQKGNKSN AGKQGTAREI DYGTDEGSDS DSSPKKRKTR SRSKSGSAEK  900
NQSPANKSSS GETWASKELL DVVAHMRRGD RSFLPSTEVH ALLLDYIKKY NLRDPRRKSQ  960
VVCDSRLKNL FGKSHVGHFE MLNILDTHFL DKEQQQADNI QGSIVDTDPD YVDLDENVDH  1020
PVKSAKDKKR KTRKKGARKG RQSNLDDFAA VDMHNINLIY LRRSLVEDLL EDSTAFEEKV  1080
ASAFVRLRIS GNQKQDLYRL VQVVGTSKAP EPYKVGKKTT DYVLEILNLD KTEVISIDII  1140
SNQDFTEDEC NRLRQSIKCG LINRLTVGDI QEKAIALQEV RVKNLLDAEI LRFSHLRDRA  1200
SDMGHRKELR ECVEKVQLLK SPEERQRRLE EIPEIHADPK MDPDYESEDE DEKEEKEKEK  1260
SLRRRSSSFN RRGRDPISPR KGGFSSNESW TGTSNYSSTS ANRELSRSYS GRGSNGRGDY  1320
LGSSDDKVSD SLWNSGRERE KDMQQYLGTE KPRTVSLPEP PPRSSRAVAP PELSPRIAPV  1380
ISTPPPPVVP QPAPKSNESE KMWHYKDPSG KVQGPFSMAQ LRKWNNTGYF PAKLEIWKAN  1440
ESSLDSVLLT DALAGLFQKQ GQSVDNSYTK AYSGQSSQSE PNIGSSARTA PSVLDIPKNS  1500
QDTWSSGGSL PSPTPTQMTT PTAKRRSFES RWSPTKPSAQ SAVQSMSFPS AQSVPSQASR  1560
TDIPVVVNTA SALQPGTHPI PTPDRANVSV NHYGSSGPLP SPTPVGGMQS WGNMQTDKFD  1620
LHGRGRGDAP FSSQNSSASY GTTTPSALTS QSQPGFPASD PWRAPVPSQS NTQTQAPAWA  1680
MNTSQNSGQP QAPTNQNSSW GQATVVNPNM GWAGPPQAGM SVNWAASSVP PTGQGMPNPG  1740
WGGPAQVQQP QAYPNSGWGV TGQAQSQAQV QAPGSSTSSG WMQTGQGMQS GNSNQNWGTQ  1800
NQTAMPSGGS GGNQTGYWGN QQNQNGDSGY GWNRQSSGSG GHNNNFKGQR VCKFHRENGN  1860
CRKGAACTYL HN
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4gnd_A3e-19697783488Histone-lysine N-methyltransferase NSD3
4gnd_C3e-19697783488Histone-lysine N-methyltransferase NSD3
4gne_A3e-19697783488Histone-lysine N-methyltransferase NSD3
4gnf_A3e-19697783488Histone-lysine N-methyltransferase NSD3
4gng_A3e-19697783488Histone-lysine N-methyltransferase NSD3
4gng_D3e-19697783488Histone-lysine N-methyltransferase NSD3
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.211550.0bud| root
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in seedlings, mostly in the vasculature and shoot apices of young seedlings. {ECO:0000269|PubMed:22940247}.
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
PlantRegMapXP_009112389.1
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_009112389.10.0PREDICTED: zinc finger CCCH domain-containing protein 19
SwissprotQ9SIV50.0C3H19_ARATH; Zinc finger CCCH domain-containing protein 19
TrEMBLM4F8880.0M4F888_BRARP; Uncharacterized protein
STRINGBra037299.1-P0.0(Brassica rapa)
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