RDM16_ARATH
ID RDM16_ARATH Reviewed; 786 AA.
AC Q9C7E7; Q8H0S1;
DT 18-JAN-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 03-AUG-2022, entry version 126.
DE RecName: Full=Protein RDM16 {ECO:0000303|PubMed:24068953};
DE AltName: Full=Pre-mRNA-splicing factor RDM16 {ECO:0000305};
DE AltName: Full=Protein RNA-directed DNA methylation 16 {ECO:0000303|PubMed:24068953};
GN Name=RDM16 {ECO:0000303|PubMed:24068953};
GN OrderedLocusNames=At1g28060 {ECO:0000312|Araport:AT1G28060};
GN ORFNames=F13K9.16 {ECO:0000312|EMBL:AAG51492.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [4]
RP FUNCTION, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX PubMed=24068953; DOI=10.1371/journal.pgen.1003779;
RA Huang C.F., Miki D., Tang K., Zhou H.R., Zheng Z., Chen W., Ma Z.Y.,
RA Yang L., Zhang H., Liu R., He X.J., Zhu J.K.;
RT "A Pre-mRNA-splicing factor is required for RNA-directed DNA methylation in
RT Arabidopsis.";
RL PLoS Genet. 9:E1003779-E1003779(2013).
CC -!- FUNCTION: Functions in the RNA-directed DNA methylation (RdDM) pathway.
CC Acts as a pre-mRNA splicing factor, likely by affecting Pol V
CC transcripts. Affects DNA methylation of transposable elements (TEs) and
CC preferentially influences NRPD1- and ROS1-targeted loci.
CC {ECO:0000269|PubMed:24068953}.
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleoplasm
CC {ECO:0000269|PubMed:24068953}.
CC -!- DISRUPTION PHENOTYPE: Embryonic lethality when homozygous.
CC {ECO:0000269|PubMed:24068953}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AC069471; AAG51492.1; -; Genomic_DNA.
DR EMBL; CP002684; AEE30907.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM58978.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM58979.1; -; Genomic_DNA.
DR EMBL; AY126993; AAM83220.1; -; mRNA.
DR EMBL; BT002294; AAN72305.1; -; mRNA.
DR PIR; C86406; C86406.
DR RefSeq; NP_001319094.1; NM_001332796.1.
DR RefSeq; NP_001321377.1; NM_001332797.1.
DR RefSeq; NP_174127.1; NM_102571.3.
DR AlphaFoldDB; Q9C7E7; -.
DR SMR; Q9C7E7; -.
DR STRING; 3702.AT1G28060.1; -.
DR iPTMnet; Q9C7E7; -.
DR PaxDb; Q9C7E7; -.
DR PRIDE; Q9C7E7; -.
DR ProteomicsDB; 235053; -.
DR EnsemblPlants; AT1G28060.1; AT1G28060.1; AT1G28060.
DR EnsemblPlants; AT1G28060.2; AT1G28060.2; AT1G28060.
DR EnsemblPlants; AT1G28060.3; AT1G28060.3; AT1G28060.
DR GeneID; 839699; -.
DR Gramene; AT1G28060.1; AT1G28060.1; AT1G28060.
DR Gramene; AT1G28060.2; AT1G28060.2; AT1G28060.
DR Gramene; AT1G28060.3; AT1G28060.3; AT1G28060.
DR KEGG; ath:AT1G28060; -.
DR Araport; AT1G28060; -.
DR TAIR; locus:2010519; AT1G28060.
DR eggNOG; KOG2769; Eukaryota.
DR HOGENOM; CLU_015750_1_0_1; -.
DR InParanoid; Q9C7E7; -.
DR OMA; ANQTHIL; -.
DR OrthoDB; 1322299at2759; -.
DR PhylomeDB; Q9C7E7; -.
DR PRO; PR:Q9C7E7; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q9C7E7; baseline and differential.
DR GO; GO:0005654; C:nucleoplasm; IDA:UniProtKB.
DR GO; GO:0046540; C:U4/U6 x U5 tri-snRNP complex; IBA:GO_Central.
DR GO; GO:0009793; P:embryo development ending in seed dormancy; IMP:UniProtKB.
DR GO; GO:0006397; P:mRNA processing; IMP:UniProtKB.
DR GO; GO:0000398; P:mRNA splicing, via spliceosome; IBA:GO_Central.
DR GO; GO:0044030; P:regulation of DNA methylation; IMP:UniProtKB.
DR InterPro; IPR013881; Pre-mRNA_splic_Prp3.
DR InterPro; IPR027104; Prp3.
DR InterPro; IPR010541; Prp3_C.
DR PANTHER; PTHR14212; PTHR14212; 2.
DR Pfam; PF06544; DUF1115; 1.
DR Pfam; PF08572; PRP3; 1.
PE 2: Evidence at transcript level;
KW mRNA processing; mRNA splicing; Nucleus; Reference proteome.
FT CHAIN 1..786
FT /note="Protein RDM16"
FT /id="PRO_0000438694"
FT REGION 1..223
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 255..283
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 532..557
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 616..642
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..139
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 144..193
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 208..223
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 261..283
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 535..549
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 461
FT /note="Q -> P (in Ref. 3; AAN72305)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 786 AA; 88638 MW; 0F89AB3BC352CCE7 CRC64;
MDKERYSRSH RDDRDRDSSP DHSPQREGGR RRDRDVDSKR RDSDHYRSSR RGDREDERDR
TKDRRGRSVE RGEREGSRDR EKHHHERSHE GSKEKESRSK RKDREEENGA RDGKKKSRFA
DGNGERRSRF EDVAIEVENK DAQVSEGSGA TNPTSGVTMG ASTYSSIPSE ASAAPSQTLL
TKVSSISTTD ENKASVVRSH EVPGKSSTDG RPLSTAGKSS ANLPLDSSAL AAKARKALQL
QKGLADRLKN LPLLKKATKP TSEGSPHTRV PPSTTTPAVS TGTSFASTLP HTGLAGFGSI
ANIEAVKRAQ ELAANMGFHQ DREFAPVINL FPGQAPSDMT VAQRPEKPPV LRVDALGREI
DEHGNVISVT KPSNLSTLKV NINKKKKDAF QILKPQLEAD LKENPYFDTR MGIDEKKILR
PKRMSFQFVE EGKWTRDAEN LKFKSHFGEA KAKELKVKQA QLAKANDDIN PNLIEVSERV
PRKEKPKEPI PDVEWWDANV LTNGEYGEIT DGTITESHLK IEKLTHYIEH PRPIEPPAEA
APPPPQPLKL TKKEQKKLRT QRRLAKEKEK QEMIRQGLLE PPKAKVKMSN LMKVLGSEAT
QDPTKLEKEI RTAAAEREQA HTDRNAARKL TPAEKREKKE RKLFDDPTTV ETIVSVYKIK
KLSHPKTRFK VEMNARENRL TGCSVMTDEM SVVVVEGKSK AIKRYGKLMM KRINWEEAER
KEGNEDEEEE VNGGNKCWLV WQGSIGKPSF HRFHVHECVT ESTAKKVFMD AGVVHYWDLA
VNYSDD
