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 319845
Common NameARALYDRAFT_319845
Organism
Arabidopsis lyrata
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: 673aa    MW: 72287.6 Da    PI: 8.8309
Description C3H family protein
Gene Model
Gene Model ID Type Source Coding Sequence
319845genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH23.78.2e-08648671225
              -S---SGGGGTS--TTTTT-SS-S CS
  zf-CCCH   2 ktelCrffartGtCkyGdrCkFaH 25 
              +++ C+ff++ G+C+ G++C++ H
   319845 648 GQRVCKFFREDGHCRKGASCNYLH 671
              6899******************** PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF552773.14E-18180246IPR003169GYF domain
CDDcd000721.16E-17193250No hitNo description
PROSITE profilePS5082916.431193247IPR003169GYF domain
SMARTSM004443.1E-22194249IPR003169GYF domain
Gene3DG3DSA:3.30.1490.401.8E-17195247IPR003169GYF domain
PfamPF022134.8E-14195235IPR003169GYF domain
PROSITE profilePS5010314.587646672IPR000571Zinc finger, CCCH-type
PfamPF006421.5E-5648671IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.101.6E-5650672IPR000571Zinc 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:0042393Molecular Functionhistone binding
GO:0046872Molecular Functionmetal ion binding
Sequence ? help Back to Top
Protein Sequence    Length: 673 aa     Download sequence    Send to blast
MFTLRECVEK LQLLKSPEER QRRLEEIPEI HDDPKMDPDC ESEDEDEKEE KEKEKQLRPR  60
SSSFNRRGRD PISPRKGGFS SNESWTGTSN YSNTSANREL TRSYSGRGST GRGDYLGSSD  120
DKVSESMWTS ARERDVQPSL GPEKPRSVSI PETTTRSSRA VAPPELSPRF ASEISTAPPA  180
VVPQPVPKSN ESEKIWHYKD PSGKVQGPFS MAQLRKWNNT GYFPAKLEIW KAKESALDSV  240
LLTDALAGLF QKQTQAVDNS YTKAQVAAYS GQSSQSEPNL GSTARTAPST IEIPRNSQDT  300
WSQSGSLPSP TPNQITTPTA KRRNFESRWS PTKPSPQSAN QSMNYSVAQS VQSHASRIDI  360
PVVVNSAGTL QPQAYPVPTP DLINVSVNHS ATLHSPTPAG GKQSWGSLQT DHGGSNAPSS  420
QNSSTSYGTP SPSVLHSQSQ PGFPPSDPWK VAVPSQPNVQ AQAQAQAQAQ AQAQAQWGIN  480
MVNNNQNSGQ PQAQAPANQN SSWGQGTVNP NMGWVGPAQA GVNVNWGGSS APSTGQGIPN  540
SGWGGPVQGQ TQAYPNPGWG AIGHPQAQPQ AQVQAQAGTT SAGWMQPGQG IQSGNSNQNW  600
GTQNQTAIPS GGSGGNQAGY WGNQQQSQNG DSGYGWNRQS SGQNNFKGQR VCKFFREDGH  660
CRKGASCNYL HN*
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
PlantRegMap319845
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_002886232.20.0zinc finger CCCH domain-containing protein 19 isoform X1
SwissprotQ9SIV50.0C3H19_ARATH; Zinc finger CCCH domain-containing protein 19
TrEMBLD7L1W50.0D7L1W5_ARALL; Zinc finger (CCCH-type) family protein
STRINGfgenesh1_pm.C_scaffold_30028610.0(Arabidopsis lyrata)
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