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Protein RTF1 homolog (Protein VERNALIZATION INDEPENDENCE 5)

 VIP5_ARATH              Reviewed;         643 AA.
Q9C950; Q8RWR3;
29-APR-2015, integrated into UniProtKB/Swiss-Prot.
01-JUN-2001, sequence version 1.
25-APR-2018, entry version 106.
RecName: Full=Protein RTF1 homolog {ECO:0000305};
AltName: Full=Protein VERNALIZATION INDEPENDENCE 5 {ECO:0000303|PubMed:15472079};
Name=VIP5 {ECO:0000303|PubMed:15472079};
OrderedLocusNames=At1g61040 {ECO:0000312|Araport:AT1G61040};
ORFNames=T7P1.17 {ECO:0000312|EMBL:AAG51642.1};
Arabidopsis thaliana (Mouse-ear cress).
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
Arabidopsis.
NCBI_TaxID=3702;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=11130712; DOI=10.1038/35048500;
Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S.,
White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y.,
Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W.,
Chung M.K., Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K.,
Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y.,
Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L.,
Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E.,
Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B.,
Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P.,
Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A.,
Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I.,
Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D.,
Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M.,
Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M.,
Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.;
"Sequence and analysis of chromosome 1 of the plant Arabidopsis
thaliana.";
Nature 408:816-820(2000).
[2]
GENOME REANNOTATION.
STRAIN=cv. Columbia;
PubMed=27862469; DOI=10.1111/tpj.13415;
Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
Town C.D.;
"Araport11: a complete reannotation of the Arabidopsis thaliana
reference genome.";
Plant J. 89:789-804(2017).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
STRAIN=cv. Columbia;
PubMed=14593172; DOI=10.1126/science.1088305;
Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
"Empirical analysis of transcriptional activity in the Arabidopsis
genome.";
Science 302:842-846(2003).
[4]
DISRUPTION PHENOTYPE.
PubMed=12750345;
Zhang H., Ransom C., Ludwig P., van Nocker S.;
"Genetic analysis of early flowering mutants in Arabidopsis defines a
class of pleiotropic developmental regulator required for expression
of the flowering-time switch flowering locus C.";
Genetics 164:347-358(2003).
[5]
FUNCTION.
PubMed=15472079; DOI=10.1105/tpc.104.026062;
Oh S., Zhang H., Ludwig P., van Nocker S.;
"A mechanism related to the yeast transcriptional regulator Paf1c is
required for expression of the Arabidopsis FLC/MAF MADS box gene
family.";
Plant Cell 16:2940-2953(2004).
[6]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-87, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19376835; DOI=10.1104/pp.109.138677;
Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
Grossmann J., Gruissem W., Baginsky S.;
"Large-scale Arabidopsis phosphoproteome profiling reveals novel
chloroplast kinase substrates and phosphorylation networks.";
Plant Physiol. 150:889-903(2009).
[7]
IDENTIFICATION IN THE PAF1 COMPLEX, FUNCTION, AND SUBCELLULAR
LOCATION.
PubMed=20363855; DOI=10.1104/pp.110.155838;
Park S., Oh S., Ek-Ramos J., van Nocker S.;
"PLANT HOMOLOGOUS TO PARAFIBROMIN is a component of the PAF1 complex
and assists in regulating expression of genes within H3K27ME3-enriched
chromatin.";
Plant Physiol. 153:821-831(2010).
[8]
FUNCTION, AND DISRUPTION PHENOTYPE.
PubMed=21799800; DOI=10.1371/journal.pone.0022241;
Liu Y., Geyer R., van Zanten M., Carles A., Li Y., Horold A.,
van Nocker S., Soppe W.J.;
"Identification of the Arabidopsis REDUCED DORMANCY 2 gene uncovers a
role for the polymerase associated factor 1 complex in seed
dormancy.";
PLoS ONE 6:E22241-E22241(2011).
[9]
ACETYLATION [LARGE SCALE ANALYSIS] AT GLY-2, CLEAVAGE OF INITIATOR
METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS
SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=22223895; DOI=10.1074/mcp.M111.015131;
Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C.,
Meinnel T., Giglione C.;
"Comparative large-scale characterisation of plant vs. mammal proteins
reveals similar and idiosyncratic N-alpha acetylation features.";
Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
-!- FUNCTION: Component of the PAF1 complex (PAF1C) which is involved
in histone modifications such as methylation on histone H3 'Lys-4'
(H3K4me3) (PubMed:20363855). Involved in regulation of flowering
time. Required for the expression of the flowering repressors and
FLC and MADS-box genes of the MAF family (PubMed:15472079).
Involved in the control of seed dormancy and germination
(PubMed:21799800). {ECO:0000269|PubMed:15472079,
ECO:0000269|PubMed:20363855, ECO:0000269|PubMed:21799800}.
-!- SUBUNIT: Component of the nuclear PAF1 complex (PAF1C), which
consists of VIP2/ELF7/PAF1, VIP3/SKI8/WDR61, VIP4/LEO1, VIP5/RTF1,
VIP6/ELF8/CTR9 and CDC73. {ECO:0000269|PubMed:20363855}.
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:20363855}.
-!- DISRUPTION PHENOTYPE: Early flowering, reduced plant size and
defects in floral morphology in whorls 1-3, but fully fertile
flowers (PubMed:12750345). Reduced seed dormancy and increased
germination rate of freshly harvested seeds (PubMed:21799800).
{ECO:0000269|PubMed:12750345, ECO:0000269|PubMed:21799800}.
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EMBL; AC018908; AAG51642.1; -; Genomic_DNA.
EMBL; CP002684; AEE33770.1; -; Genomic_DNA.
EMBL; CP002684; ANM60373.1; -; Genomic_DNA.
EMBL; CP002684; ANM60374.1; -; Genomic_DNA.
EMBL; AY091764; AAM10312.1; -; mRNA.
PIR; A96636; A96636.
RefSeq; NP_001322666.1; NM_001333927.1.
RefSeq; NP_001322667.1; NM_001333926.1.
RefSeq; NP_176299.1; NM_104784.4.
UniGene; At.36545; -.
ProteinModelPortal; Q9C950; -.
SMR; Q9C950; -.
STRING; 3702.AT1G61040.1; -.
iPTMnet; Q9C950; -.
PaxDb; Q9C950; -.
PRIDE; Q9C950; -.
EnsemblPlants; AT1G61040.1; AT1G61040.1; AT1G61040.
EnsemblPlants; AT1G61040.2; AT1G61040.2; AT1G61040.
EnsemblPlants; AT1G61040.3; AT1G61040.3; AT1G61040.
GeneID; 842395; -.
Gramene; AT1G61040.1; AT1G61040.1; AT1G61040.
Gramene; AT1G61040.2; AT1G61040.2; AT1G61040.
Gramene; AT1G61040.3; AT1G61040.3; AT1G61040.
KEGG; ath:AT1G61040; -.
Araport; AT1G61040; -.
TAIR; locus:2205996; AT1G61040.
eggNOG; KOG2402; Eukaryota.
eggNOG; COG5296; LUCA.
KO; K15178; -.
OMA; SGCKSAV; -.
OrthoDB; EOG0936076D; -.
PhylomeDB; Q9C950; -.
PRO; PR:Q9C950; -.
Proteomes; UP000006548; Chromosome 1.
ExpressionAtlas; Q9C950; baseline and differential.
Genevisible; Q9C950; AT.
GO; GO:0016593; C:Cdc73/Paf1 complex; IDA:UniProtKB.
GO; GO:0005634; C:nucleus; IDA:UniProtKB.
GO; GO:0003677; F:DNA binding; IEA:InterPro.
GO; GO:1990269; F:RNA polymerase II C-terminal domain phosphoserine binding; IBA:GO_Central.
GO; GO:0001076; F:transcription factor activity, RNA polymerase II transcription factor binding; IBA:GO_Central.
GO; GO:0009908; P:flower development; IEA:UniProtKB-KW.
GO; GO:0016570; P:histone modification; IEA:InterPro.
GO; GO:0009910; P:negative regulation of flower development; IMP:TAIR.
GO; GO:0045893; P:positive regulation of transcription, DNA-templated; IMP:TAIR.
GO; GO:0006368; P:transcription elongation from RNA polymerase II promoter; IEA:InterPro.
Gene3D; 2.170.260.30; -; 1.
InterPro; IPR004343; Plus-3_dom.
InterPro; IPR036128; Plus3-like_sf.
InterPro; IPR031102; Rtf1.
PANTHER; PTHR13115; PTHR13115; 1.
Pfam; PF03126; Plus-3; 1.
SMART; SM00719; Plus3; 1.
SUPFAM; SSF159042; SSF159042; 1.
PROSITE; PS51360; PLUS3; 1.
1: Evidence at protein level;
Acetylation; Complete proteome; Flowering; Nucleus; Phosphoprotein;
Reference proteome; Transcription; Transcription regulation.
INIT_MET 1 1 Removed. {ECO:0000244|PubMed:22223895}.
CHAIN 2 643 Protein RTF1 homolog.
/FTId=PRO_0000432761.
DOMAIN 261 396 Plus3. {ECO:0000255|PROSITE-
ProRule:PRU00693}.
COMPBIAS 206 242 Ser-rich. {ECO:0000255|PROSITE-
ProRule:PRU00016}.
COMPBIAS 530 560 Ala-rich. {ECO:0000255|PROSITE-
ProRule:PRU00001}.
MOD_RES 2 2 N-acetylglycine.
{ECO:0000244|PubMed:22223895}.
MOD_RES 87 87 Phosphoserine.
{ECO:0000244|PubMed:19376835}.
CONFLICT 22 22 R -> S (in Ref. 3; AAM10312).
{ECO:0000305}.
SEQUENCE 643 AA; 71320 MW; A098B6F38CE8C4AD CRC64;
MGDLENLLLE AAGRTNSAGR SRHPPSSRRR EGSYSDGSSD SRDDSDEDRG YASRKPSGSQ
VPLKKRLEAE REDRAARVEG GYGDGPSDRE GDSSEESDFG DDLYKNEEDR QKLAGMTEFQ
REMILSERAD KKGDKNFTEK LRSKRESEKT PVSKKETQPL PASRGVRSSA RSADRAAAKD
DALNELRAKR MKQQDPAALR KLRDASKGGS GSRDFSSTKR KPLASSNLSS SSQSDSDSRS
QSDDEGSNGG MLDSDDDRSD VPTFEDVKEV TIRRSKLAKW LMEPFFEELI VGCFVRVGIG
RSKSGPIYRL CWVKNVDATD PDKTYKLENK TTHKYLNVVW GNETSAARWQ MAMISDGHPL
EEEYRQWIRE VERTNGRMPT KQDISEKKEA IQRTNSFVYS AETVKQMLQE KKSASVRPMN
VAAEKDRLRK ELEIAQSKND EAGVERIKSK IKQLDASRNK KGVDKKALKL AEMNKKNRAE
NFKNASEVKS ITASLKAGEA GYDPFSRRWT RSSNYYNGKN KGKDGEENEA AVAAAVETNG
ADAGAGVEAT EAALEAAAEA GKLIDTRAPI GQGAEHNQLH NFELSLSLTA LQKYGGPQGV
QKAFMARKQL TEATVGCRVA ENDGKRHGLT LTVSDYKRRR GLL


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