PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

AT2G16485.1

Common Name

F16F14, NERD

Organism

Arabidopsis thaliana

Taxonomic ID

3702

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
AT2G16485.1	genome	TAIR	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	zf-CCCH	23.4	1e-07	1749	1772	2	25
-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

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF57903	1.17E-7	575	648	IPR011011	Zinc finger, FYVE/PHD-type
Gene3D	G3DSA:3.30.40.10	3.4E-9	595	655	IPR013083	Zinc finger, RING/FYVE/PHD-type
PROSITE profile	PS50016	8.618	599	665	IPR019787	Zinc finger, PHD-finger
CDD	cd15568	4.21E-20	601	646	No hit	No description
SMART	SM00249	1.4E-6	601	647	IPR001965	Zinc finger, PHD-type
PROSITE pattern	PS01359	0	602	662	IPR019786	Zinc finger, PHD-type, conserved site
SuperFamily	SSF47592	9.81E-21	797	887	IPR003121	SWIB/MDM2 domain
Gene3D	G3DSA:1.10.245.10	6.6E-23	802	890	IPR003121	SWIB/MDM2 domain
SMART	SM00151	0.0096	816	887	IPR019835	SWIB domain
Pfam	PF02201	1.1E-12	825	882	IPR003121	SWIB/MDM2 domain
PROSITE profile	PS51360	30.82	944	1076	IPR004343	Plus-3 domain
SMART	SM00719	1.1E-54	944	1053	IPR004343	Plus-3 domain
SuperFamily	SSF159042	5.62E-35	945	1073	IPR004343	Plus-3 domain
Pfam	PF03126	2.4E-24	949	1051	IPR004343	Plus-3 domain
SuperFamily	SSF55277	1.83E-18	1293	1360	IPR003169	GYF domain
CDD	cd00072	5.55E-20	1307	1364	No hit	No description
PROSITE profile	PS50829	16.766	1307	1361	IPR003169	GYF domain
SMART	SM00444	4.4E-24	1308	1363	IPR003169	GYF domain
Gene3D	G3DSA:3.30.1490.40	1.7E-17	1309	1361	IPR003169	GYF domain
Pfam	PF02213	1.2E-13	1309	1348	IPR003169	GYF domain
PROSITE profile	PS50103	14.662	1747	1773	IPR000571	Zinc finger, CCCH-type
Pfam	PF00642	1.8E-5	1749	1772	IPR000571	Zinc finger, CCCH-type
Gene3D	G3DSA:4.10.1000.10	3.4E-5	1751	1773	IPR000571	Zinc finger, CCCH-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010964	Biological Process	regulation of chromatin silencing by small RNA
GO:0032776	Biological Process	DNA methylation on cytosine
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0008270	Molecular Function	zinc ion binding
GO:0042393	Molecular Function	histone binding

Plant Ontology ? help Back to Top
PO Term	PO Category	PO Description
PO:0000005	anatomy	cultured plant cell
PO:0000293	anatomy	guard 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

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

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4gnd_A	2e-18	586	675	2	88	Histone-lysine N-methyltransferase NSD3
4gnd_C	2e-18	586	675	2	88	Histone-lysine N-methyltransferase NSD3
4gne_A	2e-18	586	675	2	88	Histone-lysine N-methyltransferase NSD3
4gnf_A	2e-18	586	675	2	88	Histone-lysine N-methyltransferase NSD3
4gng_A	2e-18	586	675	2	88	Histone-lysine N-methyltransferase NSD3
4gng_D	2e-18	586	675	2	88	Histone-lysine N-methyltransferase NSD3
Search in ModeBase

Expression -- UniGene ? help Back to Top
UniGene ID	E-value	Expressed in
At.40269	0.0	flower\| leaf\| root\| seed

Expression -- Microarray ? help Back to Top
Source	ID	E-value
GEO	240254461	0.0
Genevisible	263605_at	0.0
Expression Atlas	AT2G16485	-
AtGenExpress	AT2G16485	-

Expression -- Description ? help Back to Top
Source	Description
Uniprot	TISSUE 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
UniProt	Plays 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
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
Source	Link
PlantRegMap	AT2G16485.1

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	-

Phenotype -- Disruption Phenotype ? help Back to Top
Source	Description
UniProt	DISRUPTION 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 Express	AT2G16485

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC007047	0.0	AC007047.7 Arabidopsis thaliana chromosome 2 clone F16F14 map mi398, complete sequence.
GenBank	CP002685	0.0	CP002685.1 Arabidopsis thaliana chromosome 2, complete sequence.
GenBank	DQ446507	0.0	DQ446507.1 Arabidopsis thaliana clone pENTR221-At2g16485 unknown (At2g16485) gene, complete cds.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	NP_179241.4	0.0	GW repeat- and PHD finger-containing protein NERD
Swissprot	Q9SIV5	0.0	C3H19_ARATH; Zinc finger CCCH domain-containing protein 19
TrEMBL	A0A1P8B1D0	0.0	A0A1P8B1D0_ARATH; GW repeat-and PHD finger-containing protein NERD
STRING	AT2G16485.1	0.0	(Arabidopsis thaliana)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM5422	16	20
Representative plant	OGRP1807	9	11

Link Out ? help Back to Top
Phytozome	AT2G16485.1
Entrez Gene	816147
iHOP	AT2G16485
wikigenes	AT2G16485

Publications ? help Back to Top
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] Wang D, et al. Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice. BMC Genomics, 2008. 9: p. 44 [PMID:18221561] Jones AM, et al. Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis thaliana. J Proteomics, 2009. 72(3): p. 439-51 [PMID:19245862] 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] 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]