Y6344_ARATH
ID Y6344_ARATH Reviewed; 232 AA.
AC Q8GWQ6; A8MRN7; Q944I0; Q9FMV8;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 113.
DE RecName: Full=UPF0235 protein At5g63440;
GN OrderedLocusNames=At5g63440; ORFNames=MLE2.7;
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=9501997; DOI=10.1093/dnares/4.6.401;
RA Nakamura Y., Sato S., Kaneko T., Kotani H., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. III. Sequence
RT features of the regions of 1,191,918 bp covered by seventeen physically
RT assigned P1 clones.";
RL DNA Res. 4:401-414(1997).
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=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
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 [5]
RP SUBCELLULAR LOCATION, INTERACTION WITH CTN, AND DISRUPTION PHENOTYPE.
RX PubMed=23454656; DOI=10.1016/j.febslet.2013.02.041;
RA Baldwin K.L., Dinh E.M., Hart B.M., Masson P.H.;
RT "CACTIN is an essential nuclear protein in Arabidopsis and may be
RT associated with the eukaryotic spliceosome.";
RL FEBS Lett. 587:873-879(2013).
CC -!- FUNCTION: May play a role during early embryonic development. Probably
CC involved in pre-mRNA splicing (By similarity). {ECO:0000250}.
CC -!- SUBUNIT: Interacts with CTN. {ECO:0000269|PubMed:23454656}.
CC -!- INTERACTION:
CC Q8GWQ6; F4I2J8: CTN; NbExp=4; IntAct=EBI-8454619, EBI-8454629;
CC -!- SUBCELLULAR LOCATION: Nucleus speckle {ECO:0000269|PubMed:23454656}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1;
CC IsoId=Q8GWQ6-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8GWQ6-2; Sequence=VSP_054999, VSP_055000;
CC Name=3;
CC IsoId=Q8GWQ6-3; Sequence=VSP_054998;
CC -!- DISRUPTION PHENOTYPE: No visible phenotype.
CC {ECO:0000269|PubMed:23454656}.
CC -!- SIMILARITY: Belongs to the UPF0235 family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB08809.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AB007649; BAB08809.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED97747.1; -; Genomic_DNA.
DR EMBL; CP002688; AED97748.1; -; Genomic_DNA.
DR EMBL; CP002688; AED97749.1; -; Genomic_DNA.
DR EMBL; AK118693; BAC43287.1; -; mRNA.
DR EMBL; AF428410; AAL16178.1; -; mRNA.
DR EMBL; AY133627; AAM91457.1; -; mRNA.
DR RefSeq; NP_001078789.1; NM_001085320.1. [Q8GWQ6-3]
DR RefSeq; NP_568972.2; NM_125739.4. [Q8GWQ6-1]
DR RefSeq; NP_851256.1; NM_180925.2. [Q8GWQ6-2]
DR AlphaFoldDB; Q8GWQ6; -.
DR SMR; Q8GWQ6; -.
DR BioGRID; 21705; 1.
DR IntAct; Q8GWQ6; 1.
DR MINT; Q8GWQ6; -.
DR STRING; 3702.AT5G63440.2; -.
DR PaxDb; Q8GWQ6; -.
DR PRIDE; Q8GWQ6; -.
DR ProteomicsDB; 243172; -. [Q8GWQ6-1]
DR EnsemblPlants; AT5G63440.1; AT5G63440.1; AT5G63440. [Q8GWQ6-2]
DR EnsemblPlants; AT5G63440.2; AT5G63440.2; AT5G63440. [Q8GWQ6-1]
DR EnsemblPlants; AT5G63440.3; AT5G63440.3; AT5G63440. [Q8GWQ6-3]
DR GeneID; 836463; -.
DR Gramene; AT5G63440.1; AT5G63440.1; AT5G63440. [Q8GWQ6-2]
DR Gramene; AT5G63440.2; AT5G63440.2; AT5G63440. [Q8GWQ6-1]
DR Gramene; AT5G63440.3; AT5G63440.3; AT5G63440. [Q8GWQ6-3]
DR KEGG; ath:AT5G63440; -.
DR Araport; AT5G63440; -.
DR TAIR; locus:2167361; AT5G63440.
DR eggNOG; KOG3276; Eukaryota.
DR eggNOG; KOG4397; Eukaryota.
DR HOGENOM; CLU_075663_0_0_1; -.
DR InParanoid; Q8GWQ6; -.
DR OMA; ESASFIY; -.
DR PhylomeDB; Q8GWQ6; -.
DR PRO; PR:Q8GWQ6; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q8GWQ6; baseline and differential.
DR Genevisible; Q8GWQ6; AT.
DR GO; GO:0016607; C:nuclear speck; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IDA:TAIR.
DR GO; GO:0005681; C:spliceosomal complex; IEA:UniProtKB-KW.
DR GO; GO:0097167; P:circadian regulation of translation; IMP:TAIR.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0009640; P:photomorphogenesis; IMP:TAIR.
DR GO; GO:2000306; P:positive regulation of photomorphogenesis; IMP:TAIR.
DR GO; GO:0008380; P:RNA splicing; IEA:UniProtKB-KW.
DR Gene3D; 3.30.1200.10; -; 1.
DR HAMAP; MF_00634; UPF0235; 1.
DR InterPro; IPR003746; DUF167.
DR InterPro; IPR036591; YggU-like_sf.
DR Pfam; PF02594; DUF167; 1.
DR SMART; SM01152; DUF167; 1.
DR SUPFAM; SSF69786; SSF69786; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; mRNA processing; mRNA splicing; Nucleus;
KW Reference proteome; Spliceosome.
FT CHAIN 1..232
FT /note="UPF0235 protein At5g63440"
FT /id="PRO_0000429605"
FT VAR_SEQ 1..41
FT /note="MPKRTTHTYSSEDAAPDGPDSDLFVYYCKHCGSHVLITDTQ -> MDPTLIS
FT SYTTANTVVLMSLSL (in isoform 3)"
FT /evidence="ECO:0000305"
FT /id="VSP_054998"
FT VAR_SEQ 192..205
FT /note="LGLRLSQMTLQRGW -> PNQSVINHFLRFIL (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_054999"
FT VAR_SEQ 206..232
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14593172"
FT /id="VSP_055000"
SQ SEQUENCE 232 AA; 25693 MW; 8A6574783E9BDC26 CRC64;
MPKRTTHTYS SEDAAPDGPD SDLFVYYCKH CGSHVLITDT QLQKMPKRKT DRSNVLDKKT
HLARLNVSEG GKVLLKRGEG KMERQFRMNC IGCELFVCYR AEENLETASF IYIVDGALSA
VAAETNPQDA PVPPCISQLD GGLVQVAIEV EDRAQRSAIT RVNADDVRVT VAAPAARGEA
NNELLEFMGR VLGLRLSQMT LQRGWNSKSK LLVVEDLSAR QVYEKLLEAV VP
