PR39A_ARATH
ID PR39A_ARATH Reviewed; 768 AA.
AC Q93ZR3; A0A178W5N7; O64496;
DT 23-FEB-2022, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 157.
DE RecName: Full=Pre-mRNA-processing factor 39-1 {ECO:0000303|PubMed:17380304};
DE Short=AtPRP39-1 {ECO:0000303|PubMed:17380304};
DE AltName: Full=PRP39 homolog A {ECO:0000305};
DE AltName: Full=Pre-mRNA-processing factor 39a {ECO:0000303|PubMed:28971960};
GN Name=PRP39-1 {ECO:0000303|PubMed:17380304};
GN Synonyms=PRP39a {ECO:0000303|PubMed:28971960};
GN OrderedLocusNames=At1g04080 {ECO:0000312|Araport:AT1G04080};
GN ORFNames=F20D22.14 {ECO:0000312|EMBL:AAC16751.1};
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=16807317; DOI=10.1093/nar/gkl429;
RA de la Fuente van Bentem S., Anrather D., Roitinger E., Djamei A.,
RA Hufnagl T., Barta A., Csaszar E., Dohnal I., Lecourieux D., Hirt H.;
RT "Phosphoproteomics reveals extensive in vivo phosphorylation of Arabidopsis
RT proteins involved in RNA metabolism.";
RL Nucleic Acids Res. 34:3267-3278(2006).
RN [6]
RP FUNCTION, DISRUPTION PHENOTYPE, AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia;
RX PubMed=17380304; DOI=10.1007/s00299-007-0336-5;
RA Wang C., Tian Q., Hou Z., Mucha M., Aukerman M., Olsen O.A.;
RT "The Arabidopsis thaliana AT PRP39-1 gene, encoding a tetratricopeptide
RT repeat protein with similarity to the yeast pre-mRNA processing protein
RT PRP39, affects flowering time.";
RL Plant Cell Rep. 26:1357-1366(2007).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19376835; DOI=10.1104/pp.109.138677;
RA Reiland S., Messerli G., Baerenfaller K., Gerrits B., Endler A.,
RA Grossmann J., Gruissem W., Baginsky S.;
RT "Large-scale Arabidopsis phosphoproteome profiling reveals novel
RT chloroplast kinase substrates and phosphorylation networks.";
RL Plant Physiol. 150:889-903(2009).
RN [8]
RP FUNCTION, DISRUPTION PHENOTYPE, GENE FAMILY, AND NOMENCLATURE.
RC STRAIN=cv. Columbia;
RX PubMed=28971960; DOI=10.1534/genetics.117.300149;
RA Kanno T., Lin W.-D., Fu J.L., Chang C.-L., Matzke A.J.M., Matzke M.;
RT "A genetic screen for pre-mRNA splicing mutants of Arabidopsis thaliana
RT identifies putative U1 snRNP components RBM25 and PRP39a.";
RL Genetics 207:1347-1359(2017).
CC -!- FUNCTION: Involved in pre-mRNA splicing (PubMed:28971960). Involved in
CC the determination of flowering time probably via the modulation of
CC flowering associated genes (e.g. FLC, FT and SOC1) expression
CC (PubMed:17380304). {ECO:0000269|PubMed:17380304,
CC ECO:0000269|PubMed:28971960}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:P39682}.
CC -!- TISSUE SPECIFICITY: Expressed ubiquitously at low levels, with highest
CC expression in seedling roots, developing siliques and germinating
CC seeds, and, to a lower extent, in flowers, shoot meristems,
CC inflorescence stems, developing seeds and leaves.
CC {ECO:0000269|PubMed:17380304}.
CC -!- DISRUPTION PHENOTYPE: Altered pre-messenger RNA (pre-mRNA) splicing
CC (PubMed:28971960). Delayed flowering under both long and short days,
CC and slightly reduced responsiveness to gibberellin (GA) and
CC vernalization treatment (PubMed:17380304, PubMed:28971960). Short
CC stature and reduced seed set (PubMed:28971960). Reduced levels of FLC
CC but increased levels of FT and SOC1 transcripts (PubMed:17380304).
CC {ECO:0000269|PubMed:17380304, ECO:0000269|PubMed:28971960}.
CC -!- SIMILARITY: Belongs to the PRP39 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC16751.1; Type=Erroneous gene model prediction; Note=The predicted gene At1g04090 has been split into 2 genes: At1g04080 and At1g04090.; Evidence={ECO:0000305};
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DR EMBL; AC002411; AAC16751.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE27652.1; -; Genomic_DNA.
DR EMBL; CP002684; ANM59954.1; -; Genomic_DNA.
DR EMBL; AY056321; AAL07170.1; -; mRNA.
DR EMBL; AY091187; AAM14126.1; -; mRNA.
DR EMBL; AY087878; AAM65430.1; -; mRNA.
DR PIR; T00964; T00964.
DR RefSeq; NP_001322270.1; NM_001331460.1.
DR RefSeq; NP_563700.1; NM_100289.4.
DR SMR; Q93ZR3; -.
DR iPTMnet; O64496; -.
DR PRIDE; Q93ZR3; -.
DR ProMEX; Q93ZR3; -.
DR ProteomicsDB; 181746; -.
DR EnsemblPlants; AT1G04080.1; AT1G04080.1; AT1G04080.
DR EnsemblPlants; AT1G04080.4; AT1G04080.4; AT1G04080.
DR EnsemblPlants; AT1G04090.1; AT1G04090.1; AT1G04090.
DR GeneID; 839314; -.
DR Gramene; AT1G04080.1; AT1G04080.1; AT1G04080.
DR Gramene; AT1G04080.4; AT1G04080.4; AT1G04080.
DR Gramene; AT1G04090.1; AT1G04090.1; AT1G04090.
DR Araport; AT1G04080; -.
DR HOGENOM; CLU_007434_1_0_1; -.
DR OMA; NYCAFKV; -.
DR PhylomeDB; Q93ZR3; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; Q93ZR3; baseline and differential.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0006397; P:mRNA processing; IDA:UniProtKB.
DR GO; GO:0048573; P:photoperiodism, flowering; IMP:UniProtKB.
DR GO; GO:0008380; P:RNA splicing; IEA:UniProtKB-KW.
DR Gene3D; 1.25.40.10; -; 2.
DR InterPro; IPR003107; HAT.
DR InterPro; IPR011990; TPR-like_helical_dom_sf.
DR SMART; SM00386; HAT; 7.
DR SUPFAM; SSF48452; SSF48452; 2.
PE 1: Evidence at protein level;
KW mRNA processing; mRNA splicing; Nucleus; Reference proteome; Repeat.
FT CHAIN 1..768
FT /note="Pre-mRNA-processing factor 39-1"
FT /id="PRO_0000454965"
FT REPEAT 116..148
FT /note="HAT 1"
FT /evidence="ECO:0000255"
FT REPEAT 150..182
FT /note="HAT 2"
FT /evidence="ECO:0000255"
FT REPEAT 185..220
FT /note="HAT 3"
FT /evidence="ECO:0000255"
FT REPEAT 222..255
FT /note="HAT 4"
FT /evidence="ECO:0000255"
FT REPEAT 341..373
FT /note="HAT 5"
FT /evidence="ECO:0000255"
FT REPEAT 375..407
FT /note="HAT 6"
FT /evidence="ECO:0000255"
FT REPEAT 444..477
FT /note="HAT 7"
FT /evidence="ECO:0000255"
FT REPEAT 479..517
FT /note="HAT 8"
FT /evidence="ECO:0000255"
FT REGION 278..314
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 668..688
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 297..311
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 768 AA; 85242 MW; 559058FC35178DE5 CRC64;
MGDSEAMVSE GYTSAPYGDY NASAATVEST GQETAPIVDA SHSVNNDSLV NGTAPVENGS
ATDNVAVTAP AAEHGDNTGS TLSTEEERLW NIVRANSLEF NAWTALIDET ERIAQDNIAK
IRKVYDAFLA EFPLCYGYWK KFADHEARVG AMDKVVEVYE RAVLGVTYSV DIWLHYCTFA
INTYGDPETI RRLFERALVY VGTDFLSSPL WDKYIEYEYM QQDWSRVALI YTRILENPIQ
NLDRYFSSFK ELAETRPLSE LRSAEESAAA AVAVAGDASE SAASESGEKA DEGRSQVDGS
TEQSPKLESA SSTEPEELKK YVGIREAMYI KSKEFESKII GYEMAIRRPY FHVRPLNVAE
LENWHNYLDF IERDGDFNKV VKLYERCVVT CANYPEYWIR YVTNMEASGS ADLAENALAR
ATQVFVKKQP EIHLFAARLK EQNGDIAGAR AAYQLVHSEI SPGLLEAVIK HANMEYRLGN
LDDAFSLYEQ VIAVEKGKEH STILPLLYAQ YSRFSYLVSR DAEKARRIIV EALDHVQPSK
PLMEALIHFE AIQPPPREID YLEPLVEKVI KPDADAQNIA SSTEREELSL IYIEFLGIFG
DVKSIKKAED QHVKLFYPHR STSELKKRSA DDFLASDRTK MAKTYNGTPP AQPVSNAYPN
AQAQWSGGYA AQPQTWPPAQ AAPAQPQQWN PAYGQQAAYG AYGGYPAGYT APQAPTPVPQ
AAAYGAYPAQ TYPTQSYAPP VAAAAPAAAP VQQPAAAVAP QAYYNTYY
