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 AT2G16485.1
Common NameF16F14, NERD
Organism
Arabidopsis thaliana
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: 1773aa    MW: 195051 Da    PI: 4.4204
Description nucleic acid binding;zinc ion binding;DNA binding
Gene Model
Gene Model ID Type Source Coding Sequence
AT2G16485.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1zf-CCCH23.41e-0717491772225
                   -S---SGGGGTS--TTTTT-SS-S CS
      zf-CCCH    2 ktelCrffartGtCkyGdrCkFaH 25  
                   +++ C+ff+++G+C+ G++C++ H
  AT2G16485.1 1749 GQRVCKFFRENGHCRKGASCNYLH 1772
                   6899******************** PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF579031.17E-7575648IPR011011Zinc finger, FYVE/PHD-type
Gene3DG3DSA:3.30.40.103.4E-9595655IPR013083Zinc finger, RING/FYVE/PHD-type
PROSITE profilePS500168.618599665IPR019787Zinc finger, PHD-finger
CDDcd155684.21E-20601646No hitNo description
SMARTSM002491.4E-6601647IPR001965Zinc finger, PHD-type
PROSITE patternPS013590602662IPR019786Zinc finger, PHD-type, conserved site
SuperFamilySSF475929.81E-21797887IPR003121SWIB/MDM2 domain
Gene3DG3DSA:1.10.245.106.6E-23802890IPR003121SWIB/MDM2 domain
SMARTSM001510.0096816887IPR019835SWIB domain
PfamPF022011.1E-12825882IPR003121SWIB/MDM2 domain
PROSITE profilePS5136030.829441076IPR004343Plus-3 domain
SMARTSM007191.1E-549441053IPR004343Plus-3 domain
SuperFamilySSF1590425.62E-359451073IPR004343Plus-3 domain
PfamPF031262.4E-249491051IPR004343Plus-3 domain
SuperFamilySSF552771.83E-1812931360IPR003169GYF domain
CDDcd000725.55E-2013071364No hitNo description
PROSITE profilePS5082916.76613071361IPR003169GYF domain
SMARTSM004444.4E-2413081363IPR003169GYF domain
Gene3DG3DSA:3.30.1490.401.7E-1713091361IPR003169GYF domain
PfamPF022131.2E-1313091348IPR003169GYF domain
PROSITE profilePS5010314.66217471773IPR000571Zinc finger, CCCH-type
PfamPF006421.8E-517491772IPR000571Zinc finger, CCCH-type
Gene3DG3DSA:4.10.1000.103.4E-517511773IPR000571Zinc 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
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000005anatomycultured plant cell
PO:0000293anatomyguard cell
Sequence ? help Back to Top
Protein Sequence    Length: 1773 aa     Download sequence    Send to blast
MDSDSERASL ESIKDNSECV HVSNEPNLTA TCVDSSVGEE GVTDVNSSAA VSELVPPEQG  60
EGALLNSVPE ISERGIPVDV VSSVDGGGEE NAAFNIQEID SVGGDAAAVE EVPLKSSSVV  120
GEGREEEAGA SIVKEEDFVA EANLSGDRLE ENKEVSMEEE PSSHELSVCE VNGVDSLNDE  180
ENREVGEQIV CGSMGGEEIE SDLESKKEKV DVIEEETTAQ AASLVNAIEI PDDKEVACVA  240
GFTEISSQDK GLDESGNGFL DEEPVKELQI GEGAKDLTDG DAKEGVDVTE DEMDIQVLKK  300
SKEEEKVDST TELEIETMRL EVHDVATEMS DKTVISSAVV TQFTGETSND KETVMDDVKE  360
DVDKDSEAGK SLDIHVPEAT EEVDTDVNYG VGIEKEGDGV GGAEEAGQTV DLEEIREENQ  420
ELSKELAQVD ETKISEMSEV TETMIKDEDQ EKDDNMTDLA EDVENHRDSS VADIEEGRED  480
HEDMGVTETQ KETVLGKVDR TKIAEVSEET DTRIEDEDQE KDDEMTDVAE DVKTHGDSSV  540
ADIEEGRESQ EEMTETQEDS VMADEEPEEV EEENKSAGGK RKRGRNTKTV KGTGKKKEED  600
VCFMCFDGGD LVLCDRRGCT KAYHPSCVDR DEAFFQTKGK WNCGWHLCSK CEKTATYLCY  660
TCMFSLCKGC AKDAVFFCIR GNKGLCETCM ETVKLIERKQ QEKEPAQLDF NDKTSWEYLF  720
KDYWIDLKTQ LSLSPEELDQ AKRPLKGHET NASKQGTASE TDYVTDGGSD SDSSPKKRKT  780
RSRSKSGSAE KILSSGDKNL SDETMEWASK ELLDLVVHMR RGDRSFLPML EVQTLLLAYI  840
KRYNLRDPRR KSQVICDSRL QNLFGKSHVG HFEMLNLLDS HFLKKEQNQA DDIQGDIVDT  900
EEPNHVDVDE NLDHPVKSGK DKKRKTRKKN VRKGRQSNLD DFAAVDMHNI NLIYLRRSLV  960
EDLLEDSTAF EEKVASAFVR LRISGNQKQD LYRLVQVVGT SKAPEPYKVG KKTTDYVLEI  1020
LNLDKTEVIS IDIISNQDFT EDECKRLKQS IKCGLINRLT VGDIQEKAIA LQEVRVKNLL  1080
EAEILRFSHL RDRASDMGRR KEYPYLLKLS NSLTMLTLRE CVEKLQLLKS PEERQRRLEE  1140
IPEIHADPKM DPDCESEDED EKEEKEKEKQ LRPRSSSFNR RGRDPISPRK GGFSSNESWT  1200
GTSNYSNTSA NRELSRSYSG RGSTGRGDYL GSSDDKVSDS MWTSAREREV QPSLGSEKPR  1260
SVSIPETPAR SSRAIAPPEL SPRIASEISM APPAVVSQPV PKSNDSEKIW HYKDPSGKVQ  1320
GPFSMAQLRK WNNTGYFPAK LEIWKANESP LDSVLLTDAL AGLFQKQTQA VDNSYMKAQV  1380
AAFSGQSSQS EPNLGFAARI APTTIEIPRN SQDTWSQGGS LPSPTPNQIT TPTAKRRNFE  1440
SRWSPTKPSP QSANQSMNYS VAQSGQSQTS RIDIPVVVNS AGALQPQTYP IPTPDPINVS  1500
VNHSATLHSP TPAGGKQSWG SMQTDHGGSN TPSSQNNSTS YGTPSPSVLP SQSQPGFPPS  1560
DSWKVAVPSQ PNAQAQAQWG MNMVNNNQNS AQPQAPANQN SSWGQGTVNP NMGWVGPAQT  1620
GVNVNWGGSS VPSTVQGITH SGWVAPVQGQ TQAYPNPGWG PTGHPQSQSQ SQVQAQAGTT  1680
GSGWMQPGQG IQSGNSNQNW GTQNQTAIPS GGSGGNQAGY WGNQQQSQNG DSGYGWNRQS  1740
GGQQNNFKGQ RVCKFFRENG HCRKGASCNY LHN
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4gnd_A2e-18586675288Histone-lysine N-methyltransferase NSD3
4gnd_C2e-18586675288Histone-lysine N-methyltransferase NSD3
4gne_A2e-18586675288Histone-lysine N-methyltransferase NSD3
4gnf_A2e-18586675288Histone-lysine N-methyltransferase NSD3
4gng_A2e-18586675288Histone-lysine N-methyltransferase NSD3
4gng_D2e-18586675288Histone-lysine N-methyltransferase NSD3
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.402690.0flower| leaf| root| seed
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO2402544610.0
Genevisible263605_at0.0
Expression AtlasAT2G16485-
AtGenExpressAT2G16485-
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}.
Function -- GeneRIF ? help Back to Top
  1. A central role for NERD in integrating RNA silencing and chromatin signals in transcriptional silencing is supported by data showing that it binds both to histone H3 and AGO2 proteins and contributes to siRNA accumulation at a NERD-targeted locus. [NERD]
    [PMID: 22940247]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT2G16485.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Silencing-deficience characterized by a lower siRNA accumulation and a transcriptional up-regulation of specific loci that correlates with a local loss of cytosine methylation on DNA and an increased methylation of histone H3 'Lys-4' (e.g. H3K4me2, H3K4me3) and 'Lys-36' (e.g. H3K36me3). {ECO:0000269|PubMed:22940247}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT2G16485
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.
GenBankDQ4465070.0DQ446507.1 Arabidopsis thaliana clone pENTR221-At2g16485 unknown (At2g16485) gene, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_179241.40.0GW repeat- and PHD finger-containing protein NERD
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
Representative plantOGRP1807911
Publications ? help Back to Top
  1. Underwood BA,Vanderhaeghen R,Whitford R,Town CD,Hilson P
    Simultaneous high-throughput recombinational cloning of open reading frames in closed and open configurations.
    Plant Biotechnol. J., 2006. 4(3): p. 317-24
    [PMID:17147637]
  2. Wang D, et al.
    Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice.
    BMC Genomics, 2008. 9: p. 44
    [PMID:18221561]
  3. Jones AM, et al.
    Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis thaliana.
    J Proteomics, 2009. 72(3): p. 439-51
    [PMID:19245862]
  4. Ito J, et al.
    Analysis of the Arabidopsis cytosolic proteome highlights subcellular partitioning of central plant metabolism.
    J. Proteome Res., 2011. 10(4): p. 1571-82
    [PMID:21166475]
  5. Pontier D, et al.
    NERD, a plant-specific GW protein, defines an additional RNAi-dependent chromatin-based pathway in Arabidopsis.
    Mol. Cell, 2012. 48(1): p. 121-32
    [PMID:22940247]