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 Araha.10997s0001.1.p
Organism
Arabidopsis halleri
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family C3H
Protein Properties Length: 1304aa    MW: 144218 Da    PI: 5.8183
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Araha.10997s0001.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH24.64.3e-0812791302225
                            -S---SGGGGTS--TTTTT-SS-S CS
               zf-CCCH    2 ktelCrffartGtCkyGdrCkFaH 25  
                            +++ C+ff++ G+C+ G++C++ H
  Araha.10997s0001.1.p 1279 GQRVCKFFREDGYCRKGASCNYLH 1302
                            6899******************** PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF579037.31E-8119190IPR011011Zinc finger, FYVE/PHD-type
Gene3DG3DSA:3.30.40.105.9E-10137197IPR013083Zinc finger, RING/FYVE/PHD-type
PROSITE profilePS500168.609141207IPR019787Zinc finger, PHD-finger
SMARTSM002492.5E-7143189IPR001965Zinc finger, PHD-type
CDDcd155684.87E-21143188No hitNo description
PROSITE patternPS013590144204IPR019786Zinc finger, PHD-type, conserved site
Gene3DG3DSA:1.10.245.108.1E-24345432IPR003121SWIB/MDM2 domain
SuperFamilySSF475924.36E-21345429IPR003121SWIB/MDM2 domain
SMARTSM001510.0059364429IPR019835SWIB domain
PfamPF022011.5E-13366424IPR003121SWIB/MDM2 domain
PROSITE profilePS5136030.82486618IPR004343Plus-3 domain
SMARTSM007191.1E-54486595IPR004343Plus-3 domain
SuperFamilySSF1590423.79E-35487615IPR004343Plus-3 domain
PfamPF031261.6E-24491593IPR004343Plus-3 domain
SuperFamilySSF552778.89E-18821887IPR003169GYF domain
CDDcd000722.90E-18834891No hitNo description
PROSITE profilePS5082916.431834888IPR003169GYF domain
SMARTSM004443.1E-22835890IPR003169GYF domain
Gene3DG3DSA:3.30.1490.404.1E-17836888IPR003169GYF domain
PfamPF022131.1E-13836876IPR003169GYF domain
PROSITE profilePS5010314.51112771303IPR000571Zinc finger, CCCH-type
PfamPF006426.4E-612791302IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.101.2E-512811303IPR000571Zinc 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: 1304 aa     Download sequence    Send to blast
MDSDSERASL DSIKDDSEYH EDMGVTETQE ETVMGKVDGT KIAEVSEETE TRIEDEDQEK  60
DDEMTDVAED VKTHGDSSVA DIEQGRENHE EMTETQEESV MAELGDEETD EVEEENKSAG  120
GKRKRGRNTK TVKGTGKKKE EDVCFMCFDG GDLVLCDRRG CPKAYHPSCV DRDEAFFQSK  180
GKWNCGWHLC SKCEKTATYL CYTCMFSLCK GCAKDAVFFC IRGNKGLCET CMETVKLIER  240
KEQEKEPAQL DFDDKTSWEY LFKDYWIDLK TQLSLSPEEL DQAKRPLKGH ETNASKQGTA  300
SETDYVTDGG SDSDSSPKKR KTRSRSKSGS AEKILSPADK NLSGETMEWA SKELLDLVVH  360
MRRGDRSFLP MTEVQTLLLA YIKRYNLRDP RRKSQVICDS RLQNLFGKSH VGHFEMLNLL  420
DSHFLKKEQN QADDIQGDIV DTEEPNHVDV DENLDHPMKS GKDKKRKTRK KNVRKGRQSN  480
LDDFAAVDMH NINLIYLRRS LVEDLLEDST AFEEKVASAF VRLRISGNQK QDLYRLVQVV  540
GTSKAPEPYK VGKKTTDYVL EILNLDKTEV ISIDIISNQD FTEDECKRLK QSIKCGLINR  600
LTVGDIQEKA IALQEVRVKN LLEAEILRFS HLRDRASDMG HRKELRECVE KLQLLKSPEE  660
RQRRLEEIPE IHADPKMDPD CESEDEDEKE EKEKEKQLRP RSSSFNRRGR DPISPRKGGF  720
SSNESWTGTN NYSNTSANRE LTRSYSGRGS TGRGDYLGSS DDKVSESMWT SAREREVQPS  780
LGPEKPRSVS IPETTPRSSR AVAPPQLSPR IASEISTAPP AVVPQPVPKA NESEKIWHYK  840
DPSGKVQGPF SMAQLRKWNN TGYFPAKLEI WKAKESALDS VLLTDALAGL FQKQTQAVDN  900
SYTKAQVAAY SGQSSQSEPN LGSTARTAPS TIEIPRNSQD TWSQGGSLPS PTPNQITTPT  960
AKRRNFESRW SPTKPSPQSA NQSMNYSVAQ SGQSQASRID IPVVVNSAGT LQPQAYSIPT  1020
PDLINVSVNH SATLHSPTPA GGKQSWGSMQ TDHGGSNAPS SQNSSTSYGT PSPSVLPSQS  1080
QPGFPPSDTW KVAVPSQPNA QAQAQAQAQW GMNMVNNNQN SGQPQALANQ NSSWGQGTVN  1140
PNMGWVGPAQ AGVNVNWGGS SVPLTGQGIP NSGWGGPVQG QTQAYPNPGW GATGHPQAQP  1200
QAQVQAQAGT TSAGWMQPGQ GIQSGNGNQN WGTQNQTAIP SGGSGGNQAG YWGNQQQSQN  1260
GDSGYGWNRQ SSGQNNFKGQ RVCKFFREDG YCRKGASCNY LHN*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4gnd_A3e-19128217288Histone-lysine N-methyltransferase NSD3
4gnd_C3e-19128217288Histone-lysine N-methyltransferase NSD3
4gne_A3e-19128217288Histone-lysine N-methyltransferase NSD3
4gnf_A3e-19128217288Histone-lysine N-methyltransferase NSD3
4gng_A3e-19128217288Histone-lysine N-methyltransferase NSD3
4gng_D3e-19128217288Histone-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
PlantRegMapAraha.10997s0001.1.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_020886241.10.0zinc finger CCCH domain-containing protein 19 isoform X2
SwissprotQ9SIV50.0C3H19_ARATH; Zinc finger CCCH domain-containing protein 19
TrEMBLA0A1P8B1D00.0A0A1P8B1D0_ARATH; GW repeat-and PHD finger-containing protein NERD
STRINGAT2G16485.10.0(Arabidopsis thaliana)
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