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 Tp3g29760
Organism
Thellungiella parvula
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassicaceae incertae sedis; Schrenkiella
Family C3H
Protein Properties Length: 1868aa    MW: 203871 Da    PI: 4.3987
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Tp3g29760genomethellungiellaView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH22.81.6e-0718441867225
                 -S---SGGGGTS--TTTTT-SS-S CS
    zf-CCCH    2 ktelCrffartGtCkyGdrCkFaH 25  
                 +++ C+f++++G+C+ G+ C++ H
  Tp3g29760 1844 GQRVCKFYRENGHCRKGAACNYLH 1867
                 6899******************** PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.30.40.102.0E-9711771IPR013083Zinc finger, RING/FYVE/PHD-type
SuperFamilySSF579034.21E-8713769IPR011011Zinc finger, FYVE/PHD-type
PROSITE profilePS500168.609715781IPR019787Zinc finger, PHD-finger
CDDcd155681.00E-20717762No hitNo description
SMARTSM002494.6E-6717763IPR001965Zinc finger, PHD-type
PROSITE patternPS013590718778IPR019786Zinc finger, PHD-type, conserved site
Gene3DG3DSA:1.10.245.102.5E-24893987IPR003121SWIB/MDM2 domain
SuperFamilySSF475921.42E-21895985IPR003121SWIB/MDM2 domain
PfamPF022012.7E-12921979IPR003121SWIB/MDM2 domain
PROSITE profilePS5136030.70410401172IPR004343Plus-3 domain
SMARTSM007191.3E-5410401149IPR004343Plus-3 domain
SuperFamilySSF1590424.84E-3510411169IPR004343Plus-3 domain
PfamPF031262.6E-2410451147IPR004343Plus-3 domain
SuperFamilySSF552773.53E-1813851449IPR003169GYF domain
PROSITE profilePS5082916.48913961450IPR003169GYF domain
CDDcd000726.41E-1913961453No hitNo description
Gene3DG3DSA:3.30.1490.404.3E-1713971450IPR003169GYF domain
SMARTSM004443.6E-2313971452IPR003169GYF domain
PfamPF022134.3E-1413981438IPR003169GYF domain
PROSITE profilePS5010314.26718421868IPR000571Zinc finger, CCCH-type
PfamPF006422.9E-518441867IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.102.5E-418461868IPR000571Zinc 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: 1868 aa     Download sequence    Send to blast
MDSDSPKASV ESMQNDSERI HVSNEPNLTG TCGDSSVPEE EEGGDVGGCE VVTGMKGIDA  60
VDTAAASGLG ASVGEGEGAI FNSVAEISDG LEGRSPVAVV SSELSPAVME GGGGGEENEA  120
FVVQEKDSMD LVGGSAAVEV VPLESSSVVA EGGEEDQIGS IVQEGDSAAE HSDSPANFSG  180
LGGEKDSISG DNLEENKEVS MEEEPPSLDL PASEANGDDS LRKEAQQVVC GGMADEKNSQ  240
AIESELGQHT ESEKEKFDVM EDTTAQAASL EDKVSVDIEI PDVKEVASVA GFTELPSQDK  300
GLNDSVLNSG SEFVEEEPLE DLQIGEGAKD QTDGDSKEDV NVAEDAMGNQ VLAKTEEEEK  360
HDAVTVLEIQ TMPQEVDDVT NEVSDKNETP VGKSSADKEA VMDDVKEDVE KEGSEAGKSV  420
DIHVPEAAEE VETDVKYGDG IEKEGERMGG VGEGNQSVDL EETRKLSEEL AKVDKTKLAE  480
VSEETETVIR DEDEEKVDGM TDMEEDVKTH EDSSVVDIEE GREDREEMGM TEILEETVMR  540
NVDGIKIAEV SEETETRIKD EDQEKDDGMA DVETHGDSSV ADIEERREDH EKMGMAEMTE  600
TQEETVVGKA EGRKIAETSE ETETRTEDED EEKDENMTDV ETHGDSSVAD IEEERESHEE  660
MEMTELTETQ EESVMAETGD EEPEEVEEEN KGAGRKRKRV INTKTVKGTG KKKEEDVCFM  720
CFDGGDLVLC DRRGCPKAYH PSCVDRDEAF FHSKGKWNCG WHLCSKCEKT ATYLCYTCMF  780
SLCKGCAKDA VFFCVRGNKG LCETCMETVK LIEREEQEKK EPAQLDFNDK TSWESLFKDY  840
WIDLKTQLSL SPEELDQAKS PQKGNESHAA LQKKRKTRSR SKSGSAEKIL SPANKNSSAE  900
TVEWASKELL DVVAHMRRGD RSFLPHSEVH GLLLDYIKRY NLRDPRRKSQ VVCDSRLKNL  960
FGKSHVGHFE MLNLLDTHFL KKEQQHADDV QGSIVDTEPD YVDVDENLDH PVKSGKDKKR  1020
KARKKGVKKG RQSNLDDFAA VDMHNINLIY LRRSLVEDLL EDSTAFEEKV ASAFVRLRIS  1080
GNQKQDLYRL VQVVGTSKAP EPYKVGKKTT DYVLEILNLD KTEVISIDII SNQDFTEDEC  1140
KRLRQSIKCG LINRLTVGDI QEKAIALQEV RVKNLLEAEI LRFGHLRDRA SDMGRRKEYP  1200
YLLELSKCVE KVQLLKSPEE RQRRLEEIPE IHADPKMDPD CESEDEDEKE EKEKDKNLRP  1260
RSSTFNRRGR DPISPRRGGF SSNESWTGTS NYSNTSANRE LTRSYSGRGS TGRGDYLGSS  1320
EDKVSESMWN SGREREREMQ QSVGSEKPRS VTLPEPSPRS SRAIAPRELS PRVVPEISMA  1380
APVVVPQPAP KSNESEKMWH YKDPSGKVQG PFSMAQLRKW NNTGYFPAKL EIWKATESPL  1440
DSVLLSDALA GLFQKQAHSL DNSYTKAQVA AYSGQSSQSE ANLGSSARTA PSILDIPRNS  1500
QDTWSSGGSL PSPTPNQITT PTAKRRNFES RWSPTKPSAQ SAVQSMSFPS AQSGLSQASR  1560
DIPVVVNSAG ALQPGIHPIP TPDSTNVSVI HYGSSAPLPS PTPVGGKQSW GNMQTDKFDS  1620
HGRGGGDAPS SSQNSSASYG TTPGVLPSQS QPGFPSSDSW RVPVPSQSNT QAQAPAWGMN  1680
NSQNSGQPPA PANQNSSWGQ GAVNPNMGWA GPAQAGMNVN WAGSSVPPTG QGMPNPGWGG  1740
PVQVQPQAYP NAGWGVTGQA QSQAQVQAPG SSTSSGWMQP GQGMQSGNSN QNWGTQNQTA  1800
IPGGGSGGNQ AGFWGNQQSQ NGDSGYGWNR QSSGSGGHSN NFKGQRVCKF YRENGHCRKG  1860
AACNYLHN
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4gnd_A2e-19702791288Histone-lysine N-methyltransferase NSD3
4gnd_C2e-19702791288Histone-lysine N-methyltransferase NSD3
4gne_A2e-19702791288Histone-lysine N-methyltransferase NSD3
4gnf_A2e-19702791288Histone-lysine N-methyltransferase NSD3
4gng_A2e-19702791288Histone-lysine N-methyltransferase NSD3
4gng_D2e-19702791288Histone-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
PlantRegMapTp3g29760
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_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