UniProtKB - Q9SIV5 (C3H19_ARATH)
Protein
Zinc finger CCCH domain-containing protein 19
Gene
NERD
Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Functioni
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.1 Publication
Regions
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Zinc fingeri | 599 – 665 | PHD-typePROSITE-ProRule annotationAdd BLAST | 67 | |
Zinc fingeri | 1747 – 1773 | C3H1-typePROSITE-ProRule annotationAdd BLAST | 27 |
GO - Molecular functioni
- DNA binding Source: UniProtKB-KW
- histone binding Source: UniProtKB
- metal ion binding Source: UniProtKB-KW
- RNA polymerase II C-terminal domain phosphoserine binding Source: GO_Central
GO - Biological processi
- DNA methylation on cytosine Source: UniProtKB
- gene silencing by RNA Source: UniProtKB-KW
- regulation of heterochromatin assembly by small RNA Source: UniProtKB
Keywordsi
Molecular function | DNA-binding |
Biological process | RNA-mediated gene silencing, Transcription, Transcription regulation |
Ligand | Metal-binding, Zinc |
Names & Taxonomyi
Protein namesi | Recommended name: Zinc finger CCCH domain-containing protein 19Short name: AtC3H19 Alternative name(s): Protein Needed for RDR2-independent DNA methylation |
Gene namesi | Name:NERD Ordered Locus Names:At2g16485/At2g16480/At2g16470 ORF Names:F16F14 |
Organismi | Arabidopsis thaliana (Mouse-ear cress) |
Taxonomic identifieri | 3702 [NCBI] |
Taxonomic lineagei | Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliopsida › eudicotyledons › Gunneridae › Pentapetalae › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis |
Proteomesi |
|
Organism-specific databases
Araporti | AT2G16485 |
TAIRi | locus:2827287, AT2G16485 |
Subcellular locationi
Nucleus
- Nucleus 1 Publication
Cytosol
- cytosol Source: TAIR
Nucleus
- Cdc73/Paf1 complex Source: GO_Central
- nucleus Source: UniProtKB
Keywords - Cellular componenti
NucleusPathology & Biotechi
Disruption phenotypei
Silencing-deficiency 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).1 Publication
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000371978 | 1 – 1773 | Zinc finger CCCH domain-containing protein 19Add BLAST | 1773 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 1281 | PhosphoserineCombined sources | 1 |
Keywords - PTMi
PhosphoproteinProteomic databases
PaxDbi | Q9SIV5 |
PRIDEi | Q9SIV5 |
ProteomicsDBi | 239086 |
PTM databases
iPTMneti | Q9SIV5 |
Expressioni
Tissue specificityi
Expressed in seedlings, mostly in the vasculature and shoot apices of young seedlings.1 Publication
Gene expression databases
ExpressionAtlasi | Q9SIV5, baseline and differential |
Genevisiblei | Q9SIV5, AT |
Interactioni
Subunit structurei
Interacts with unmethylated histone H3 and AGO2. The interaction with AGO2 in required to direct DNA methylation and silencing.
1 PublicationGO - Molecular functioni
- histone binding Source: UniProtKB
- RNA polymerase II C-terminal domain phosphoserine binding Source: GO_Central
Protein-protein interaction databases
STRINGi | 3702.AT2G16485.1 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 801 – 884 | SWIB/MDM2PROSITE-ProRule annotationAdd BLAST | 84 | |
Domaini | 944 – 1076 | Plus3PROSITE-ProRule annotationAdd BLAST | 133 | |
Domaini | 1307 – 1361 | GYFPROSITE-ProRule annotationAdd BLAST | 55 |
Coiled coil
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Coiled coili | 196 – 218 | Sequence analysisAdd BLAST | 23 | |
Coiled coili | 403 – 437 | Sequence analysisAdd BLAST | 35 |
Motif
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Motifi | 581 – 588 | Nuclear localization signal 1By similarity | 8 | |
Motifi | 921 – 928 | Nuclear localization signal 2By similarity | 8 |
Compositional bias
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Compositional biasi | 122 – 573 | Glu-richAdd BLAST | 452 |
Domaini
The PHD-type zinc finger (599-665) binds to unmethylated histone H3 'Lys-4' (H3K4me0).1 Publication
Zinc finger
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Zinc fingeri | 599 – 665 | PHD-typePROSITE-ProRule annotationAdd BLAST | 67 | |
Zinc fingeri | 1747 – 1773 | C3H1-typePROSITE-ProRule annotationAdd BLAST | 27 |
Keywords - Domaini
Coiled coil, Repeat, Zinc-fingerPhylogenomic databases
eggNOGi | KOG1081, Eukaryota KOG1862, Eukaryota KOG1946, Eukaryota |
HOGENOMi | CLU_236474_0_0_1 |
InParanoidi | Q9SIV5 |
OrthoDBi | 85697at2759 |
Family and domain databases
CDDi | cd00072, GYF, 1 hit |
Gene3Di | 1.10.245.10, 1 hit 2.170.260.30, 1 hit 3.30.1490.40, 1 hit 3.30.40.10, 1 hit |
InterProi | View protein in InterPro IPR003169, GYF IPR035445, GYF-like_dom_sf IPR004343, Plus-3_dom IPR036128, Plus3-like_sf IPR019835, SWIB_domain IPR036885, SWIB_MDM2_dom_sf IPR003121, SWIB_MDM2_domain IPR019786, Zinc_finger_PHD-type_CS IPR000571, Znf_CCCH IPR011011, Znf_FYVE_PHD IPR001965, Znf_PHD IPR019787, Znf_PHD-finger IPR013083, Znf_RING/FYVE/PHD |
Pfami | View protein in Pfam PF02213, GYF, 1 hit PF03126, Plus-3, 1 hit PF02201, SWIB, 1 hit PF00642, zf-CCCH, 1 hit |
SMARTi | View protein in SMART SM00444, GYF, 1 hit SM00249, PHD, 1 hit SM00719, Plus3, 1 hit SM00151, SWIB, 1 hit |
SUPFAMi | SSF159042, SSF159042, 1 hit SSF47592, SSF47592, 1 hit SSF55277, SSF55277, 1 hit SSF57903, SSF57903, 1 hit |
PROSITEi | View protein in PROSITE PS50829, GYF, 1 hit PS51360, PLUS3, 1 hit PS51925, SWIB_MDM2, 1 hit PS50103, ZF_C3H1, 1 hit PS01359, ZF_PHD_1, 1 hit PS50016, ZF_PHD_2, 1 hit |
(1+)i Sequence
Sequence statusi: Complete.
This entry has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All
Q9SIV5-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MDSDSERASL ESIKDNSECV HVSNEPNLTA TCVDSSVGEE GVTDVNSSAA
60 70 80 90 100
VSELVPPEQG EGALLNSVPE ISERGIPVDV VSSVDGGGEE NAAFNIQEID
110 120 130 140 150
SVGGDAAAVE EVPLKSSSVV GEGREEEAGA SIVKEEDFVA EANLSGDRLE
160 170 180 190 200
ENKEVSMEEE PSSHELSVCE VNGVDSLNDE ENREVGEQIV CGSMGGEEIE
210 220 230 240 250
SDLESKKEKV DVIEEETTAQ AASLVNAIEI PDDKEVACVA GFTEISSQDK
260 270 280 290 300
GLDESGNGFL DEEPVKELQI GEGAKDLTDG DAKEGVDVTE DEMDIQVLKK
310 320 330 340 350
SKEEEKVDST TELEIETMRL EVHDVATEMS DKTVISSAVV TQFTGETSND
360 370 380 390 400
KETVMDDVKE DVDKDSEAGK SLDIHVPEAT EEVDTDVNYG VGIEKEGDGV
410 420 430 440 450
GGAEEAGQTV DLEEIREENQ ELSKELAQVD ETKISEMSEV TETMIKDEDQ
460 470 480 490 500
EKDDNMTDLA EDVENHRDSS VADIEEGRED HEDMGVTETQ KETVLGKVDR
510 520 530 540 550
TKIAEVSEET DTRIEDEDQE KDDEMTDVAE DVKTHGDSSV ADIEEGRESQ
560 570 580 590 600
EEMTETQEDS VMADEEPEEV EEENKSAGGK RKRGRNTKTV KGTGKKKEED
610 620 630 640 650
VCFMCFDGGD LVLCDRRGCT KAYHPSCVDR DEAFFQTKGK WNCGWHLCSK
660 670 680 690 700
CEKTATYLCY TCMFSLCKGC AKDAVFFCIR GNKGLCETCM ETVKLIERKQ
710 720 730 740 750
QEKEPAQLDF NDKTSWEYLF KDYWIDLKTQ LSLSPEELDQ AKRPLKGHET
760 770 780 790 800
NASKQGTASE TDYVTDGGSD SDSSPKKRKT RSRSKSGSAE KILSSGDKNL
810 820 830 840 850
SDETMEWASK ELLDLVVHMR RGDRSFLPML EVQTLLLAYI KRYNLRDPRR
860 870 880 890 900
KSQVICDSRL QNLFGKSHVG HFEMLNLLDS HFLKKEQNQA DDIQGDIVDT
910 920 930 940 950
EEPNHVDVDE NLDHPVKSGK DKKRKTRKKN VRKGRQSNLD DFAAVDMHNI
960 970 980 990 1000
NLIYLRRSLV EDLLEDSTAF EEKVASAFVR LRISGNQKQD LYRLVQVVGT
1010 1020 1030 1040 1050
SKAPEPYKVG KKTTDYVLEI LNLDKTEVIS IDIISNQDFT EDECKRLKQS
1060 1070 1080 1090 1100
IKCGLINRLT VGDIQEKAIA LQEVRVKNLL EAEILRFSHL RDRASDMGRR
1110 1120 1130 1140 1150
KEYPYLLKLS NSLTMLTLRE CVEKLQLLKS PEERQRRLEE IPEIHADPKM
1160 1170 1180 1190 1200
DPDCESEDED EKEEKEKEKQ LRPRSSSFNR RGRDPISPRK GGFSSNESWT
1210 1220 1230 1240 1250
GTSNYSNTSA NRELSRSYSG RGSTGRGDYL GSSDDKVSDS MWTSAREREV
1260 1270 1280 1290 1300
QPSLGSEKPR SVSIPETPAR SSRAIAPPEL SPRIASEISM APPAVVSQPV
1310 1320 1330 1340 1350
PKSNDSEKIW HYKDPSGKVQ GPFSMAQLRK WNNTGYFPAK LEIWKANESP
1360 1370 1380 1390 1400
LDSVLLTDAL AGLFQKQTQA VDNSYMKAQV AAFSGQSSQS EPNLGFAARI
1410 1420 1430 1440 1450
APTTIEIPRN SQDTWSQGGS LPSPTPNQIT TPTAKRRNFE SRWSPTKPSP
1460 1470 1480 1490 1500
QSANQSMNYS VAQSGQSQTS RIDIPVVVNS AGALQPQTYP IPTPDPINVS
1510 1520 1530 1540 1550
VNHSATLHSP TPAGGKQSWG SMQTDHGGSN TPSSQNNSTS YGTPSPSVLP
1560 1570 1580 1590 1600
SQSQPGFPPS DSWKVAVPSQ PNAQAQAQWG MNMVNNNQNS AQPQAPANQN
1610 1620 1630 1640 1650
SSWGQGTVNP NMGWVGPAQT GVNVNWGGSS VPSTVQGITH SGWVAPVQGQ
1660 1670 1680 1690 1700
TQAYPNPGWG PTGHPQSQSQ SQVQAQAGTT GSGWMQPGQG IQSGNSNQNW
1710 1720 1730 1740 1750
GTQNQTAIPS GGSGGNQAGY WGNQQQSQNG DSGYGWNRQS GGQQNNFKGQ
1760 1770
RVCKFFRENG HCRKGASCNY LHN
Computationally mapped potential isoform sequencesi
There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basketA0A1P8B1D0 | A0A1P8B1D0_ARATH | GW repeat-and PHD finger-containing... | NERD At2g16485, F16F14.1, F16F14_1 | 1,758 | Annotation score: |
Sequence cautioni
The sequence AAD22293 differs from that shown. Reason: Erroneous gene model prediction. Was originally thought to correspond to three different genes At2g16470, At2g16480 and At2g16485.Curated
The sequence AAD22314 differs from that shown. Reason: Erroneous gene model prediction. Was originally thought to correspond to three different genes At2g16470, At2g16480 and At2g16485.Curated
The sequence AAM15362 differs from that shown. Reason: Erroneous gene model prediction. Was originally thought to correspond to three different genes At2g16470, At2g16480 and At2g16485.Curated
The sequence ABE65448 differs from that shown. Reason: Erroneous gene model prediction.Curated
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AC007047 Genomic DNA Translation: AAD22314.1 Sequence problems. AC007047 Genomic DNA Translation: AAD22293.1 Sequence problems. AC007047 Genomic DNA Translation: AAM15362.1 Sequence problems. CP002685 Genomic DNA Translation: AEC06501.1 DQ446507 Genomic DNA Translation: ABE65448.1 Sequence problems. |
PIRi | F84540 G84540 |
RefSeqi | NP_179241.4, NM_127202.5 |
Genome annotation databases
EnsemblPlantsi | AT2G16485.1; AT2G16485.1; AT2G16485 |
GeneIDi | 816147 |
Gramenei | AT2G16485.1; AT2G16485.1; AT2G16485 |
KEGGi | ath:AT2G16485 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AC007047 Genomic DNA Translation: AAD22314.1 Sequence problems. AC007047 Genomic DNA Translation: AAD22293.1 Sequence problems. AC007047 Genomic DNA Translation: AAM15362.1 Sequence problems. CP002685 Genomic DNA Translation: AEC06501.1 DQ446507 Genomic DNA Translation: ABE65448.1 Sequence problems. |
PIRi | F84540 G84540 |
RefSeqi | NP_179241.4, NM_127202.5 |
3D structure databases
SMRi | Q9SIV5 |
ModBasei | Search... |
Protein-protein interaction databases
STRINGi | 3702.AT2G16485.1 |
PTM databases
iPTMneti | Q9SIV5 |
Proteomic databases
PaxDbi | Q9SIV5 |
PRIDEi | Q9SIV5 |
ProteomicsDBi | 239086 |
Genome annotation databases
EnsemblPlantsi | AT2G16485.1; AT2G16485.1; AT2G16485 |
GeneIDi | 816147 |
Gramenei | AT2G16485.1; AT2G16485.1; AT2G16485 |
KEGGi | ath:AT2G16485 |
Organism-specific databases
Araporti | AT2G16485 |
TAIRi | locus:2827287, AT2G16485 |
Phylogenomic databases
eggNOGi | KOG1081, Eukaryota KOG1862, Eukaryota KOG1946, Eukaryota |
HOGENOMi | CLU_236474_0_0_1 |
InParanoidi | Q9SIV5 |
OrthoDBi | 85697at2759 |
Miscellaneous databases
PROi | PR:Q9SIV5 |
Gene expression databases
ExpressionAtlasi | Q9SIV5, baseline and differential |
Genevisiblei | Q9SIV5, AT |
Family and domain databases
CDDi | cd00072, GYF, 1 hit |
Gene3Di | 1.10.245.10, 1 hit 2.170.260.30, 1 hit 3.30.1490.40, 1 hit 3.30.40.10, 1 hit |
InterProi | View protein in InterPro IPR003169, GYF IPR035445, GYF-like_dom_sf IPR004343, Plus-3_dom IPR036128, Plus3-like_sf IPR019835, SWIB_domain IPR036885, SWIB_MDM2_dom_sf IPR003121, SWIB_MDM2_domain IPR019786, Zinc_finger_PHD-type_CS IPR000571, Znf_CCCH IPR011011, Znf_FYVE_PHD IPR001965, Znf_PHD IPR019787, Znf_PHD-finger IPR013083, Znf_RING/FYVE/PHD |
Pfami | View protein in Pfam PF02213, GYF, 1 hit PF03126, Plus-3, 1 hit PF02201, SWIB, 1 hit PF00642, zf-CCCH, 1 hit |
SMARTi | View protein in SMART SM00444, GYF, 1 hit SM00249, PHD, 1 hit SM00719, Plus3, 1 hit SM00151, SWIB, 1 hit |
SUPFAMi | SSF159042, SSF159042, 1 hit SSF47592, SSF47592, 1 hit SSF55277, SSF55277, 1 hit SSF57903, SSF57903, 1 hit |
PROSITEi | View protein in PROSITE PS50829, GYF, 1 hit PS51360, PLUS3, 1 hit PS51925, SWIB_MDM2, 1 hit PS50103, ZF_C3H1, 1 hit PS01359, ZF_PHD_1, 1 hit PS50016, ZF_PHD_2, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | C3H19_ARATH | |
Accessioni | Q9SIV5Primary (citable) accession number: Q9SIV5 Secondary accession number(s): F4IKD7, Q8S8E0, Q9SIV4 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | May 5, 2009 |
Last sequence update: | June 13, 2012 | |
Last modified: | April 7, 2021 | |
This is version 113 of the entry and version 3 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Plant Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
Reference proteomeDocuments
- Arabidopsis thaliana
Arabidopsis thaliana: entries and gene names