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 Bostr.18351s0110.1.p
Organism
Boechera stricta
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Boechereae; Boechera
Family C3H
Protein Properties Length: 1810aa    MW: 197350 Da    PI: 4.3549
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Bostr.18351s0110.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH24.16.1e-0817851808225
                            -S---SGGGGTS--TTTTT-SS-S CS
               zf-CCCH    2 ktelCrffartGtCkyGdrCkFaH 25  
                            +++ C+ff++ G+C+ G++C++ H
  Bostr.18351s0110.1.p 1785 GQRVCKFFREDGYCRKGASCNYLH 1808
                            6899******************** PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF579036.87E-8625698IPR011011Zinc finger, FYVE/PHD-type
Gene3DG3DSA:3.30.40.108.8E-10645705IPR013083Zinc finger, RING/FYVE/PHD-type
PROSITE profilePS500168.609649715IPR019787Zinc finger, PHD-finger
SMARTSM002492.5E-7651697IPR001965Zinc finger, PHD-type
CDDcd155687.57E-21651696No hitNo description
PROSITE patternPS013590652712IPR019786Zinc finger, PHD-type, conserved site
SuperFamilySSF475921.96E-20853937IPR003121SWIB/MDM2 domain
Gene3DG3DSA:1.10.245.101.6E-23853940IPR003121SWIB/MDM2 domain
SMARTSM001510.0077872937IPR019835SWIB domain
PfamPF022011.4E-12876932IPR003121SWIB/MDM2 domain
SMARTSM007193.5E-549941103IPR004343Plus-3 domain
PROSITE profilePS5136029.4519941126IPR004343Plus-3 domain
SuperFamilySSF1590424.45E-349951123IPR004343Plus-3 domain
PfamPF031261.8E-249991101IPR004343Plus-3 domain
SuperFamilySSF552772.35E-1813291395IPR003169GYF domain
CDDcd000721.91E-1913421399No hitNo description
PROSITE profilePS5082916.28513421396IPR003169GYF domain
SMARTSM004441.3E-2313431398IPR003169GYF domain
PfamPF022131.3E-1313441384IPR003169GYF domain
Gene3DG3DSA:3.30.1490.401.4E-1713441396IPR003169GYF domain
PROSITE profilePS5010314.51117831809IPR000571Zinc finger, CCCH-type
PfamPF006429.1E-617851808IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.103.3E-517871809IPR000571Zinc 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: 1810 aa     Download sequence    Send to blast
MDSDSARTYM ESIKDDSECV HDSNEPNLTG TCGDSSVGEE EGGGEEVTDV NSSAAASELV  60
PPEPVSPDGK GEGAVLNSVP ENSDVVERRA PVDVVVSSEL SPVVTEVGGG GEENAAFNVQ  120
EMDSVGGVAA VVEVVPLKPS SVVGEGGEEE GAASIVKEGD FTAEGSDSQA NLSGDRLDQN  180
KDVSMEEEPP IHDLSGYEVN GVDSLNAEEK REEGEQVVCG GMAGEESSQA IESELGQNTE  240
SEKEKVDVME QETTAQAASL VNDIEIPDDK EVACVAGFTE IPSQDKVLDD SVRNSGSEFV  300
EEKPVKELQI GEGAKDLTEG DAKEGVDVIE DAMDIQILKK SEEEEKVDGA AVSEIETKPQ  360
EVDDVATEVS DKIAVPVDIS SAVVTQFAGE TSNDKEIIMD DVKEDVEKDS EAGKSLDIHV  420
PEAAEEVETD VKYGAGIEKE GDGVGGAGEA GQTVDLEESR EENQELSQEL AKVDETKISE  480
VSEETETMIG DEDQEKDDDM TDFTEDVETR GNSSVADFEE GREDHEDMGV TEMTETQEET  540
VVGKVDGTKI AEVSEETETR IEDEDREKDD VMTDVAEDVK THRDSSVADI EEGRENQEEM  600
TETQEESAVA EMGDEEPEEV EEENKSAGGK RKRGRNTKTV KGTGKKKEED VCFMCFDGGD  660
LVLCDRRGCP KAYHPSCVDR DEAFFQSKGK WNCGWHLCSK CEKTATYLCY TCMFSLCKGC  720
AKDAVFFCIR GNKGLCETCM ETVKLIERKE QEKEPAQLDF DDKTSWEYLF KDYWIDLKTQ  780
LSLSPEELDQ AKSPRKGHES NASKQGTASE TDYVTDGGSD SDSAPKKRKT RSRSKSGSAE  840
KILSPADKNL SGETMEWASK ELLDVVVHMR RGDRSFLPQL EVQNLLLAYI KRYNLRDPRR  900
KSQVICDSRL QNLFGKSHVG HFEMLNLLDS HFLKKEQNQA DDIQGDIVDT EEPNHVNVDE  960
NLDHPMKSGK GKKRKTRKKS VRKGRQSNLD DFAAVDMHNI NLIYLRRSLV EDLLEDSAAF  1020
EEKVASAFVR LRISGNQKQD LYRLVQVVGT SKAPEPYKVG KKTTDFVLEI LNLDKTEVVS  1080
IDIISNQDFT EDECKRLKQS IKCGLINRLT VGDIHDKAIA LQEVRVKNLL EAEILRFSHL  1140
RDRASDMGRR KELRECVEKL QLLKSPEERQ RRLEEIPEIH ADPKMDPDCE SEDEDEKEEK  1200
EKEKQLRPRS SSFNRRGRDP ISPRKGGFSS NESWTGTSNY SNTSANRELS RSYSGRGSTG  1260
RVDYLGSSDD MVSESMWTSA REREVQPSLG SEKPRSVSIP ETTAKSSRAV APLELSPRIA  1320
SESSTAPPAV VPQPVPKSNE SEKIWHYKDP SGKVQGPFSM AQLRKWNNTG YFPAKLEIWK  1380
AKESPLDSIL LNDALAGLFQ KQIQAVDNSY TKAQVAAYSG QSSQSEPNLG TTARTAPSTI  1440
EIPRNSQDTW SQGGSLPSPT PNQITTPTAK KRNFESRWSP TKPSPQSANQ LMNYSVAQSG  1500
QSQASRIDIP VVVNSAGALQ PQTYPIPTSD SINVSVIHPA TLPSPTPAGG KQSWGSMQTD  1560
HGGSDALSSQ NSSTSYGTTT PSVLPSQSQP GFPPSDSWKV AVPSQPNAQA QTQWGMNMVN  1620
NNQNSGQPQA PANQNSSWGQ GTVNPNMGWV GPAQAGANVN WAGSSVPSTG QGIPNSGWGG  1680
PVQGQPQAYP NPGWGVTGLP QSQSQAQVQA QAGTTGSGWM QPGQGIQSGN SNTNWGTQNQ  1740
TAIPSGGSGG NQAGFWGNQQ NQNGDSGYGW NRQSSGSGGQ NNFKGQRVCK FFREDGYCRK  1800
GASCNYLHN*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4gnd_A1e-19636725288Histone-lysine N-methyltransferase NSD3
4gnd_C1e-19636725288Histone-lysine N-methyltransferase NSD3
4gne_A1e-19636725288Histone-lysine N-methyltransferase NSD3
4gnf_A1e-19636725288Histone-lysine N-methyltransferase NSD3
4gng_A1e-19636725288Histone-lysine N-methyltransferase NSD3
4gng_D1e-19636725288Histone-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
PlantRegMapBostr.18351s0110.1.p
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_019092708.10.0PREDICTED: zinc finger CCCH domain-containing protein 19-like
SwissprotQ9SIV50.0C3H19_ARATH; Zinc finger CCCH domain-containing protein 19
TrEMBLR0HWB10.0R0HWB1_9BRAS; Uncharacterized protein
STRINGBostr.18351s0110.1.p0.0(Boechera stricta)
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