PUM6_ARATH
ID PUM6_ARATH Reviewed; 861 AA.
AC Q9C5E7; C0Z2M6; Q2V3E7; Q3E9W4; Q9SVZ7;
DT 30-NOV-2010, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 03-AUG-2022, entry version 127.
DE RecName: Full=Pumilio homolog 6, chloroplastic;
DE Short=APUM-6;
DE Short=AtPUM6;
DE Flags: Precursor;
GN Name=APUM6; OrderedLocusNames=At4g25880; ORFNames=F14M19.160;
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=10617198; DOI=10.1038/47134;
RA Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA Martienssen R., McCombie W.R.;
RT "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL Nature 402:769-777(1999).
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] (ISOFORM 1).
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 3).
RC STRAIN=cv. Columbia;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [5]
RP GENE FAMILY, FUNCTION, AND RNA-BINDING.
RX PubMed=19682068; DOI=10.1111/j.1742-4658.2009.07230.x;
RA Francischini C.W., Quaggio R.B.;
RT "Molecular characterization of Arabidopsis thaliana PUF proteins -- binding
RT specificity and target candidates.";
RL FEBS J. 276:5456-5470(2009).
RN [6]
RP GENE FAMILY.
RX PubMed=20214804; DOI=10.1186/1471-2229-10-44;
RA Tam P.P., Barrette-Ng I.H., Simon D.M., Tam M.W., Ang A.L., Muench D.G.;
RT "The Puf family of RNA-binding proteins in plants: phylogeny, structural
RT modeling, activity and subcellular localization.";
RL BMC Plant Biol. 10:44-44(2010).
CC -!- FUNCTION: Sequence-specific RNA-binding protein that regulates
CC translation and mRNA stability by binding the 3'-UTR of target mRNAs.
CC Binds the APUM-binding elements (APBEs) in the 3'-UTR mRNA sequence of
CC CLV1, PNH, WUS and FAS2. {ECO:0000269|PubMed:19682068}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000305}. Cytoplasm
CC {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=4;
CC Name=1;
CC IsoId=Q9C5E7-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9C5E7-2; Sequence=VSP_040179;
CC Name=3;
CC IsoId=Q9C5E7-3; Sequence=VSP_040180;
CC Name=4;
CC IsoId=Q9C5E7-4; Sequence=VSP_040179, VSP_040180;
CC -!- DOMAIN: The pumilio repeats mediate the association with RNA by packing
CC together to form a right-handed superhelix that approximates a half
CC donut. The number as well as the specific sequence of the repeats
CC determine the specificity for target mRNAs (By similarity).
CC {ECO:0000250}.
CC -!- MISCELLANEOUS: [Isoform 3]: May be due to a competing donor splice
CC site. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAH56955.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=CAB39609.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=CAB79443.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AL049480; CAB39609.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AL161564; CAB79443.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002687; AEE85127.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE85128.1; -; Genomic_DNA.
DR EMBL; CP002687; AEE85129.1; -; Genomic_DNA.
DR EMBL; CP002687; ANM68046.1; -; Genomic_DNA.
DR EMBL; CP002687; ANM68047.1; -; Genomic_DNA.
DR EMBL; AF360298; AAK26008.1; -; mRNA.
DR EMBL; AY133866; AAM91800.1; -; mRNA.
DR EMBL; AK318840; BAH56955.1; ALT_INIT; mRNA.
DR EMBL; AK319148; BAH57263.1; -; mRNA.
DR PIR; T04242; T04242.
DR RefSeq; NP_001031720.1; NM_001036643.2. [Q9C5E7-4]
DR RefSeq; NP_001329827.1; NM_001341767.1. [Q9C5E7-3]
DR RefSeq; NP_001329828.1; NM_001341768.1. [Q9C5E7-1]
DR RefSeq; NP_567733.1; NM_118721.3. [Q9C5E7-1]
DR RefSeq; NP_974618.2; NM_202889.3. [Q9C5E7-2]
DR AlphaFoldDB; Q9C5E7; -.
DR SMR; Q9C5E7; -.
DR STRING; 3702.AT4G25880.1; -.
DR iPTMnet; Q9C5E7; -.
DR PaxDb; Q9C5E7; -.
DR PRIDE; Q9C5E7; -.
DR ProteomicsDB; 226265; -. [Q9C5E7-1]
DR EnsemblPlants; AT4G25880.1; AT4G25880.1; AT4G25880. [Q9C5E7-1]
DR EnsemblPlants; AT4G25880.2; AT4G25880.2; AT4G25880. [Q9C5E7-2]
DR EnsemblPlants; AT4G25880.3; AT4G25880.3; AT4G25880. [Q9C5E7-4]
DR EnsemblPlants; AT4G25880.4; AT4G25880.4; AT4G25880. [Q9C5E7-3]
DR EnsemblPlants; AT4G25880.5; AT4G25880.5; AT4G25880. [Q9C5E7-1]
DR GeneID; 828694; -.
DR Gramene; AT4G25880.1; AT4G25880.1; AT4G25880. [Q9C5E7-1]
DR Gramene; AT4G25880.2; AT4G25880.2; AT4G25880. [Q9C5E7-2]
DR Gramene; AT4G25880.3; AT4G25880.3; AT4G25880. [Q9C5E7-4]
DR Gramene; AT4G25880.4; AT4G25880.4; AT4G25880. [Q9C5E7-3]
DR Gramene; AT4G25880.5; AT4G25880.5; AT4G25880. [Q9C5E7-1]
DR KEGG; ath:AT4G25880; -.
DR Araport; AT4G25880; -.
DR TAIR; locus:2117552; AT4G25880.
DR eggNOG; KOG1488; Eukaryota.
DR HOGENOM; CLU_004017_1_0_1; -.
DR InParanoid; Q9C5E7; -.
DR OMA; EMVHANK; -.
DR OrthoDB; 239732at2759; -.
DR PhylomeDB; Q9C5E7; -.
DR PRO; PR:Q9C5E7; -.
DR Proteomes; UP000006548; Chromosome 4.
DR ExpressionAtlas; Q9C5E7; baseline and differential.
DR Genevisible; Q9C5E7; AT.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005783; C:endoplasmic reticulum; IDA:TAIR.
DR GO; GO:0003729; F:mRNA binding; IDA:UniProtKB.
DR GO; GO:0010608; P:post-transcriptional regulation of gene expression; IBA:GO_Central.
DR GO; GO:0006417; P:regulation of translation; IEA:UniProtKB-KW.
DR CDD; cd07920; Pumilio; 1.
DR Gene3D; 1.25.10.10; -; 1.
DR InterPro; IPR011989; ARM-like.
DR InterPro; IPR016024; ARM-type_fold.
DR InterPro; IPR033133; PUM-HD.
DR InterPro; IPR033712; Pumilio_RNA-bd.
DR InterPro; IPR001313; Pumilio_RNA-bd_rpt.
DR Pfam; PF00806; PUF; 8.
DR SMART; SM00025; Pumilio; 8.
DR SUPFAM; SSF48371; SSF48371; 1.
DR PROSITE; PS50302; PUM; 8.
DR PROSITE; PS50303; PUM_HD; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Chloroplast; Cytoplasm; Phosphoprotein; Plastid;
KW Reference proteome; Repeat; RNA-binding; Transit peptide;
KW Translation regulation.
FT TRANSIT 1..23
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 24..861
FT /note="Pumilio homolog 6, chloroplastic"
FT /id="PRO_0000401388"
FT DOMAIN 512..852
FT /note="PUM-HD"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00318"
FT REPEAT 532..567
FT /note="Pumilio 1"
FT REPEAT 568..603
FT /note="Pumilio 2"
FT REPEAT 604..639
FT /note="Pumilio 3"
FT REPEAT 640..675
FT /note="Pumilio 4"
FT REPEAT 676..712
FT /note="Pumilio 5"
FT REPEAT 713..748
FT /note="Pumilio 6"
FT REPEAT 749..784
FT /note="Pumilio 7"
FT REPEAT 791..826
FT /note="Pumilio 8"
FT REGION 1..34
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 105..199
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 213..261
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 426..454
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..33
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 105..122
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 133..147
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 158..195
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 213..240
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 159
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9SS47"
FT VAR_SEQ 542..547
FT /note="Missing (in isoform 2 and isoform 4)"
FT /evidence="ECO:0000305"
FT /id="VSP_040179"
FT VAR_SEQ 855..861
FT /note="ENQELRR -> GMKFPNKTKN (in isoform 3 and isoform 4)"
FT /evidence="ECO:0000303|PubMed:19423640"
FT /id="VSP_040180"
FT CONFLICT 451
FT /note="N -> S (in Ref. 4; BAH56955)"
FT /evidence="ECO:0000305"
FT CONFLICT 613
FT /note="Missing (in Ref. 4; BAH56955)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 861 AA; 96105 MW; 44555848AAFCDE5A CRC64;
MATENPIRIS GSNERWSNSR KVSVPNRSGS APPNMEGSFL AVDNLLSRQG GSVYNNLMLP
RYGFEEPVTT HPSSKHSLNR IPSPPIYYPT EYQFIDNRVG RFRSNQGLNK VNSPIHLSQG
KLSTHKEVSE DESSQQLSVN SVSDRTDGLD IRLSPGSQSL ADFRQDDTSS GQTPQHSRSN
SSNGEVNTAD ESGNFSELSD DVVVKDNAAS TARASIGNEK SPDESTIISK MKSTNISGPG
TAKYPREPRY GQPERQPHQQ QNNATWIQGG SNMGSHGVND AVIGAGQFHY GQPYKFSGDG
QPVLQSSGFT PPLLYTATQT AYMTSPAHVY NMQSPAVYSP QYGYGPYTNM IPQFMPGYPS
HGSVPVVVSP DFIPQLSGPS AGSVVHGGEM QYAEKLYVPP GQPSFPDPMY MQYCQQSFGQ
MEPLAPRNHT NAPESQKDDP KFLRQIRGPS NSNMARPGMG VNYYGIQPNM GIMVQYLPTH
LGPPLSPGHV PYVEAYPGWQ PQGSLEGANG PRLCNFLEEL KSGKGRRFDL SDITGHIVEF
SADQHGSRFI QQKLENCKPE EKAAVFREIL PHACKLMTDV FGNYVIQKFF EYGNSTQRKE
LADQLMGQIV PLSLQMYGCR VIQKALDVIE PDQRVRLARE LDGQVMRCVR DQNGNHVIQK
CIENIPADKV GFMLYAFRGQ VSSLSMHPYG CRVIQRLLER CSHDHQCRFI TEEILESVCV
LSKDQYGNYV TQHVLEKGTS EERERIGRKL SGHIVQLSLH KFASNVIEKC LEYGGRVERD
LIIKEIAGPD ESYNSLLMMM KDQYGNYVVQ KIFETCTADQ RLTLFSRVRM HASALKKYTY
GKHIVSRLEQ PSIEENQELR R
