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Protein LEO1 homolog (Protein VERNALIZATION INDEPENDENCE 4)

 VIP4_ARATH              Reviewed;         625 AA.
Q9FNQ0; B9DF97; Q8L5W5;
29-APR-2015, integrated into UniProtKB/Swiss-Prot.
01-MAR-2001, sequence version 1.
10-OCT-2018, entry version 108.
RecName: Full=Protein LEO1 homolog {ECO:0000305};
AltName: Full=Protein VERNALIZATION INDEPENDENCE 4 {ECO:0000303|PubMed:12207655};
Name=VIP4 {ECO:0000303|PubMed:12207655};
OrderedLocusNames=At5g61150 {ECO:0000312|Araport:AT5G61150};
ORFNames=MAF19.15 {ECO:0000312|EMBL:BAB10377.1};
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 [MRNA], FUNCTION, TISSUE SPECIFICITY, AND
DISRUPTION PHENOTYPE.
PubMed=12207655; DOI=10.1046/j.1365-313X.2002.01380.x;
Zhang H., van Nocker S.;
"The VERNALIZATION INDEPENDENCE 4 gene encodes a novel regulator of
FLOWERING LOCUS C.";
Plant J. 31:663-673(2002).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=cv. Columbia;
PubMed=9405937; DOI=10.1093/dnares/4.4.291;
Kotani H., Nakamura Y., Sato S., Kaneko T., Asamizu E., Miyajima N.,
Tabata S.;
"Structural analysis of Arabidopsis thaliana chromosome 5. II.
Sequence features of the regions of 1,044,062 bp covered by thirteen
physically assigned P1 clones.";
DNA Res. 4:291-300(1997).
[3]
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).
[4]
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).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-531.
STRAIN=cv. Columbia;
PubMed=19423640; DOI=10.1093/dnares/dsp009;
Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M.,
Seki M., Shinozaki K.;
"Analysis of multiple occurrences of alternative splicing events in
Arabidopsis thaliana using novel sequenced full-length cDNAs.";
DNA Res. 16:155-164(2009).
[6]
INTERACTION WITH VIP3 AND VIP6.
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).
[7]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-203; SER-570; SER-600;
SER-605 AND SER-622, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE
SCALE ANALYSIS].
TISSUE=Root;
PubMed=18433157; DOI=10.1021/pr8000173;
de la Fuente van Bentem S., Anrather D., Dohnal I., Roitinger E.,
Csaszar E., Joore J., Buijnink J., Carreri A., Forzani C.,
Lorkovic Z.J., Barta A., Lecourieux D., Verhounig A., Jonak C.,
Hirt H.;
"Site-specific phosphorylation profiling of Arabidopsis proteins by
mass spectrometry and peptide chip analysis.";
J. Proteome Res. 7:2458-2470(2008).
[8]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-548; SER-600 AND
SER-605, AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE
ANALYSIS].
STRAIN=cv. Columbia;
PubMed=19245862; DOI=10.1016/j.jprot.2009.02.004;
Jones A.M.E., MacLean D., Studholme D.J., Serna-Sanz A.,
Andreasson E., Rathjen J.P., Peck S.C.;
"Phosphoproteomic analysis of nuclei-enriched fractions from
Arabidopsis thaliana.";
J. Proteomics 72:439-451(2009).
[9]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-548; SER-600; SER-605
AND SER-622, 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).
[10]
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).
[11]
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).
-!- 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 repressor and
MADS box gene FLC (PubMed:12207655). Involved in the control of
seed dormancy and germination (PubMed:21799800).
{ECO:0000269|PubMed:12207655, 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 (PubMed:20363855). Interacts with VIP3
and VIP6 (PubMed:15472079). {ECO:0000269|PubMed:15472079,
ECO:0000269|PubMed:20363855}.
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:20363855}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=1;
Comment=A number of isoforms are produced. According to EST
sequences. {ECO:0000305};
Name=1;
IsoId=Q9FNQ0-1; Sequence=Displayed;
-!- TISSUE SPECIFICITY: Expressed in roots, shoot apices, stems,
cauline leaves, inflorescence apices and flowers.
{ECO:0000269|PubMed:12207655}.
-!- DISRUPTION PHENOTYPE: Early flowering, defects in floral
morphology in whorls 1-3, but fully fertile flowers
(PubMed:12207655). Reduced seed dormancy and increased germination
rate of freshly harvested seeds (PubMed:21799800).
{ECO:0000269|PubMed:12207655, ECO:0000269|PubMed:21799800}.
-!- SIMILARITY: Belongs to the LEO1 family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AF490422; AAM81969.1; -; mRNA.
EMBL; AB006696; BAB10377.1; -; Genomic_DNA.
EMBL; CP002688; AED97427.1; -; Genomic_DNA.
EMBL; BT002058; AAN72069.1; -; mRNA.
EMBL; BT008386; AAP37745.1; -; mRNA.
EMBL; AK316687; BAH19414.1; -; mRNA.
RefSeq; NP_851237.1; NM_180906.2. [Q9FNQ0-1]
UniGene; At.29120; -.
ProteinModelPortal; Q9FNQ0; -.
SMR; Q9FNQ0; -.
IntAct; Q9FNQ0; 2.
STRING; 3702.AT5G61150.1; -.
iPTMnet; Q9FNQ0; -.
PaxDb; Q9FNQ0; -.
EnsemblPlants; AT5G61150.1; AT5G61150.1; AT5G61150. [Q9FNQ0-1]
GeneID; 836236; -.
Gramene; AT5G61150.1; AT5G61150.1; AT5G61150. [Q9FNQ0-1]
KEGG; ath:AT5G61150; -.
Araport; AT5G61150; -.
TAIR; locus:2159466; AT5G61150.
eggNOG; KOG2428; Eukaryota.
eggNOG; ENOG410XRI0; LUCA.
HOGENOM; HOG000240426; -.
InParanoid; Q9FNQ0; -.
KO; K15177; -.
OMA; NTIRWRM; -.
OrthoDB; EOG09360BFR; -.
PhylomeDB; Q9FNQ0; -.
PRO; PR:Q9FNQ0; -.
Proteomes; UP000006548; Chromosome 5.
ExpressionAtlas; Q9FNQ0; baseline and differential.
Genevisible; Q9FNQ0; AT.
GO; GO:0016593; C:Cdc73/Paf1 complex; IDA:UniProtKB.
GO; GO:0005829; C:cytosol; IDA:TAIR.
GO; GO:0005634; C:nucleus; IDA:UniProtKB.
GO; GO:1990269; F:RNA polymerase II C-terminal domain phosphoserine 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:0032968; P:positive regulation of transcription elongation from RNA polymerase II promoter; IBA:GO_Central.
GO; GO:0006368; P:transcription elongation from RNA polymerase II promoter; IEA:InterPro.
GO; GO:0010048; P:vernalization response; IMP:TAIR.
InterPro; IPR007149; Leo1.
PANTHER; PTHR23146; PTHR23146; 1.
Pfam; PF04004; Leo1; 1.
1: Evidence at protein level;
Alternative splicing; Coiled coil; Complete proteome; Flowering;
Nucleus; Phosphoprotein; Reference proteome; Transcription;
Transcription regulation.
CHAIN 1 625 Protein LEO1 homolog.
/FTId=PRO_0000432760.
COILED 415 539 {ECO:0000255}.
COMPBIAS 20 248 Glu-rich. {ECO:0000255|PROSITE-
ProRule:PRU00007}.
COMPBIAS 518 604 Glu-rich. {ECO:0000255|PROSITE-
ProRule:PRU00007}.
MOD_RES 203 203 Phosphoserine.
{ECO:0000244|PubMed:18433157}.
MOD_RES 548 548 Phosphoserine.
{ECO:0000244|PubMed:19245862,
ECO:0000244|PubMed:19376835}.
MOD_RES 570 570 Phosphoserine.
{ECO:0000244|PubMed:18433157}.
MOD_RES 600 600 Phosphoserine.
{ECO:0000244|PubMed:18433157,
ECO:0000244|PubMed:19245862,
ECO:0000244|PubMed:19376835}.
MOD_RES 605 605 Phosphoserine.
{ECO:0000244|PubMed:18433157,
ECO:0000244|PubMed:19245862,
ECO:0000244|PubMed:19376835}.
MOD_RES 622 622 Phosphoserine.
{ECO:0000244|PubMed:18433157,
ECO:0000244|PubMed:19376835}.
CONFLICT 27 27 E -> Q (in Ref. 1; AAM81969).
{ECO:0000305}.
CONFLICT 206 206 D -> H (in Ref. 1; AAM81969).
{ECO:0000305}.
CONFLICT 318 318 T -> P (in Ref. 1; AAM81969).
{ECO:0000305}.
CONFLICT 474 474 N -> T (in Ref. 1; AAM81969).
{ECO:0000305}.
SEQUENCE 625 AA; 71758 MW; 8073ED1C25B3504D CRC64;
MVKGEKRSEM MLNLFGDNSE EEEIESEHEC NRRQPNYASD EAEGGVEPEG EGEAEVEVHG
EAEAESDGEQ GDVELDPGES EGEREQSSQE ADPQEESEAR DSDSDNKEEE HGGRVAKKRR
QEVVESGSER SGEKHYESED EEVDQTRSPR SPSEEKEEVQ VAQSDVNIRN VFGSSDDEDA
EEYVRNDVEQ DEHRSPIEDE EGSEKDLRPD DMVLDDIIPE EDPQYESEAE HVEARYRERP
VGPPLEVEVP FRPPPGDPVK MNMIKVSNIM GIDPKPFDAK TFVEEDTFMT DEPGAKNRIR
LDNNIVRHRF VKSRDGKTYS ESNARFVRWS DGSLQLLIGN EVLNITEQDA KEDQNHLFIK
HEKGILQSQG RILKKMRFTP SSLTSNSHRL LTAIVESRQK KAFKVKNCVT DIDPEREKEK
REKAESQNLK ASTKLSQARE KIKRKYPLPV ERRQLSTGYL EDALDEDDED YRSNRGYEED
LEAEAQRERR ILNAKKSHKG IPGRSSMTSA RPSRRQMEYS ESEREESEYE TEEEEEEKSP
ARGRGKDSED EYEEDAEEDE EERGKSNRYS DEDEEEEEVA GGRAEKDHRG SGRKRKGIES
DEEESPPRKA PTHRRKAVID DSDED


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