YBOX3_MOUSE
ID YBOX3_MOUSE Reviewed; 361 AA.
AC Q9JKB3; Q80WG4; Q9EQF7; Q9EQF8;
DT 15-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 15-MAR-2005, sequence version 2.
DT 03-AUG-2022, entry version 159.
DE RecName: Full=Y-box-binding protein 3;
DE AltName: Full=Cold shock domain-containing protein A;
DE AltName: Full=DNA-binding protein A;
DE AltName: Full=Y-box protein 3;
GN Name=Ybx3; Synonyms=Csda, Msy4;
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), IDENTIFICATION IN A MRNP COMPLEX
RP WITH YBX2, RNA-BINDING, SUBCELLULAR LOCATION, AND TISSUE SPECIFICITY.
RC TISSUE=Testis;
RX PubMed=10772793; DOI=10.1006/dbio.2000.9658;
RA Davies H.G., Giorgini F., Fajardo M.A., Braun R.E.;
RT "A sequence-specific RNA binding complex expressed in murine germ cells
RT contains MSY2 and MSY4.";
RL Dev. Biol. 221:87-100(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), AND TISSUE SPECIFICITY.
RC STRAIN=CD-1; TISSUE=Testis;
RX PubMed=10956549; DOI=10.1093/molehr/6.9.779;
RA Mastrangelo M.-A., Kleene K.C.;
RT "Developmental expression of Y-box protein 1 mRNA and alternatively spliced
RT Y-box protein 3 mRNAs in spermatogenic cells in mice.";
RL Mol. Hum. Reprod. 6:779-788(2000).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
RC STRAIN=FVB/N; TISSUE=Colon, and Eye;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [4]
RP RNA-BINDING.
RX PubMed=11564883; DOI=10.1128/mcb.21.20.7010-7019.2001;
RA Giorgini F., Davies H.G., Braun R.E.;
RT "MSY2 and MSY4 bind a conserved sequence in the 3' untranslated region of
RT protamine 1 mRNA in vitro and in vivo.";
RL Mol. Cell. Biol. 21:7010-7019(2001).
RN [5]
RP FUNCTION IN TRANSLATIONAL REPRESSION, AND TISSUE SPECIFICITY.
RX PubMed=12117816; DOI=10.1242/dev.129.15.3669;
RA Giorgini F., Davies H.G., Braun R.E.;
RT "Translational repression by MSY4 inhibits spermatid differentiation in
RT mice.";
RL Development 129:3669-3679(2002).
RN [6]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-33; SER-52 AND SER-195, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Brown adipose tissue, Heart, Kidney, Liver, Lung, Pancreas, Spleen,
RC and Testis;
RX PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL Cell 143:1174-1189(2010).
RN [7]
RP METHYLATION [LARGE SCALE ANALYSIS] AT ARG-315, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Brain, and Embryo;
RX PubMed=24129315; DOI=10.1074/mcp.o113.027870;
RA Guo A., Gu H., Zhou J., Mulhern D., Wang Y., Lee K.A., Yang V., Aguiar M.,
RA Kornhauser J., Jia X., Ren J., Beausoleil S.A., Silva J.C., Vemulapalli V.,
RA Bedford M.T., Comb M.J.;
RT "Immunoaffinity enrichment and mass spectrometry analysis of protein
RT methylation.";
RL Mol. Cell. Proteomics 13:372-387(2014).
CC -!- FUNCTION: Binds to the GM-CSF promoter. Seems to act as a repressor (By
CC similarity). Binds also to full-length mRNA and to short RNA sequences
CC containing the consensus site 5'-UCCAUCA-3'. May have a role in
CC translation repression. {ECO:0000250, ECO:0000269|PubMed:12117816}.
CC -!- SUBUNIT: Found in a mRNP complex with YBX2 (PubMed:10772793). Interacts
CC with RRP1B (By similarity). {ECO:0000250|UniProtKB:P16989,
CC ECO:0000269|PubMed:10772793}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:10772793}. Nucleus
CC {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1; Synonyms=Msy3l;
CC IsoId=Q9JKB3-1; Sequence=Displayed;
CC Name=2; Synonyms=Msy3s;
CC IsoId=Q9JKB3-2; Sequence=VSP_013051;
CC -!- TISSUE SPECIFICITY: Expressed in oocytes, spermatocytes and spermatids
CC (at protein level). Expressed in skeletal muscle, kidney, brain,
CC spleen, liver, heart and spermatids. Isoform 2 is preferentially
CC expressed in somatic tissues (PubMed:10956549).
CC {ECO:0000269|PubMed:10772793, ECO:0000269|PubMed:10956549,
CC ECO:0000269|PubMed:12117816}.
CC -!- MISCELLANEOUS: Transgenic mice overexpressing Ybx3 exhibit disruption
CC of the normal completion of spermatogenesis, dominant sterility and
CC abnormal translation activation of repressed mRNA.
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DR EMBL; AF246224; AAF61741.1; -; mRNA.
DR EMBL; AF248546; AAG14418.1; -; mRNA.
DR EMBL; AF248547; AAG14419.1; -; mRNA.
DR EMBL; BC048242; AAH48242.1; -; mRNA.
DR EMBL; BC062377; AAH62377.1; -; mRNA.
DR CCDS; CCDS20605.1; -. [Q9JKB3-2]
DR CCDS; CCDS20606.1; -. [Q9JKB3-1]
DR RefSeq; NP_035863.1; NM_011733.2. [Q9JKB3-2]
DR RefSeq; NP_620817.2; NM_139117.2. [Q9JKB3-1]
DR AlphaFoldDB; Q9JKB3; -.
DR SMR; Q9JKB3; -.
DR BioGRID; 207989; 12.
DR DIP; DIP-42746N; -.
DR IntAct; Q9JKB3; 9.
DR MINT; Q9JKB3; -.
DR STRING; 10090.ENSMUSP00000032309; -.
DR iPTMnet; Q9JKB3; -.
DR PhosphoSitePlus; Q9JKB3; -.
DR EPD; Q9JKB3; -.
DR jPOST; Q9JKB3; -.
DR MaxQB; Q9JKB3; -.
DR PaxDb; Q9JKB3; -.
DR PeptideAtlas; Q9JKB3; -.
DR PRIDE; Q9JKB3; -.
DR ProteomicsDB; 299609; -. [Q9JKB3-1]
DR ProteomicsDB; 299610; -. [Q9JKB3-2]
DR Antibodypedia; 11792; 246 antibodies from 23 providers.
DR DNASU; 56449; -.
DR Ensembl; ENSMUST00000032309; ENSMUSP00000032309; ENSMUSG00000030189. [Q9JKB3-1]
DR Ensembl; ENSMUST00000087865; ENSMUSP00000085172; ENSMUSG00000030189. [Q9JKB3-2]
DR GeneID; 56449; -.
DR KEGG; mmu:56449; -.
DR UCSC; uc009eis.1; mouse. [Q9JKB3-1]
DR UCSC; uc009eit.1; mouse. [Q9JKB3-2]
DR CTD; 8531; -.
DR MGI; MGI:2137670; Ybx3.
DR VEuPathDB; HostDB:ENSMUSG00000030189; -.
DR eggNOG; KOG3070; Eukaryota.
DR GeneTree; ENSGT00940000159340; -.
DR HOGENOM; CLU_063071_2_0_1; -.
DR InParanoid; Q9JKB3; -.
DR OMA; ENHHEAN; -.
DR PhylomeDB; Q9JKB3; -.
DR TreeFam; TF317306; -.
DR BioGRID-ORCS; 56449; 0 hits in 74 CRISPR screens.
DR ChiTaRS; Ybx3; mouse.
DR PRO; PR:Q9JKB3; -.
DR Proteomes; UP000000589; Chromosome 6.
DR RNAct; Q9JKB3; protein.
DR Bgee; ENSMUSG00000030189; Expressed in seminiferous tubule of testis and 263 other tissues.
DR Genevisible; Q9JKB3; MM.
DR GO; GO:0005737; C:cytoplasm; IDA:MGI.
DR GO; GO:0005829; C:cytosol; ISO:MGI.
DR GO; GO:0005921; C:gap junction; ISO:MGI.
DR GO; GO:0005634; C:nucleus; IDA:MGI.
DR GO; GO:0003677; F:DNA binding; IDA:MGI.
DR GO; GO:0003730; F:mRNA 3'-UTR binding; IDA:MGI.
DR GO; GO:0003676; F:nucleic acid binding; IBA:GO_Central.
DR GO; GO:1905538; F:polysome binding; IDA:MGI.
DR GO; GO:0043021; F:ribonucleoprotein complex binding; IDA:MGI.
DR GO; GO:0000977; F:RNA polymerase II transcription regulatory region sequence-specific DNA binding; IDA:NTNU_SB.
DR GO; GO:0003697; F:single-stranded DNA binding; ISO:MGI.
DR GO; GO:0006915; P:apoptotic process; IMP:MGI.
DR GO; GO:0071474; P:cellular hyperosmotic response; ISO:MGI.
DR GO; GO:0071356; P:cellular response to tumor necrosis factor; ISO:MGI.
DR GO; GO:0035234; P:ectopic germ cell programmed cell death; IMP:MGI.
DR GO; GO:0009566; P:fertilization; IMP:MGI.
DR GO; GO:0001701; P:in utero embryonic development; IGI:MGI.
DR GO; GO:0008584; P:male gonad development; IMP:MGI.
DR GO; GO:0043066; P:negative regulation of apoptotic process; IMP:MGI.
DR GO; GO:0051093; P:negative regulation of developmental process; IMP:MGI.
DR GO; GO:1902219; P:negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress; ISO:MGI.
DR GO; GO:0060546; P:negative regulation of necroptotic process; ISO:MGI.
DR GO; GO:2000242; P:negative regulation of reproductive process; IMP:MGI.
DR GO; GO:0048642; P:negative regulation of skeletal muscle tissue development; IDA:MGI.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IDA:NTNU_SB.
DR GO; GO:0046622; P:positive regulation of organ growth; IMP:MGI.
DR GO; GO:0010468; P:regulation of gene expression; IBA:GO_Central.
DR GO; GO:0007283; P:spermatogenesis; IMP:MGI.
DR CDD; cd04458; CSP_CDS; 1.
DR Gene3D; 2.40.50.140; -; 1.
DR InterPro; IPR011129; CSD.
DR InterPro; IPR019844; CSD_1.
DR InterPro; IPR002059; CSP_DNA-bd.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR Pfam; PF00313; CSD; 1.
DR PRINTS; PR00050; COLDSHOCK.
DR SMART; SM00357; CSP; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR PROSITE; PS00352; CSD_1; 1.
DR PROSITE; PS51857; CSD_2; 1.
PE 1: Evidence at protein level;
KW Acetylation; Alternative splicing; Cytoplasm; DNA-binding; Methylation;
KW Nucleus; Phosphoprotein; Reference proteome; Repressor; RNA-binding;
KW Transcription; Transcription regulation.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250|UniProtKB:P16989"
FT CHAIN 2..361
FT /note="Y-box-binding protein 3"
FT /id="PRO_0000100215"
FT DOMAIN 82..152
FT /note="CSD"
FT REGION 1..74
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 173..361
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..15
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 22..38
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0000250|UniProtKB:P16989"
FT MOD_RES 2
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P16989"
FT MOD_RES 33
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT MOD_RES 52
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT MOD_RES 126
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P16989"
FT MOD_RES 193
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P16989"
FT MOD_RES 195
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT MOD_RES 196
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P16989"
FT MOD_RES 243
FT /note="Omega-N-methylarginine"
FT /evidence="ECO:0000250|UniProtKB:P16989"
FT MOD_RES 313
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P16989"
FT MOD_RES 315
FT /note="Omega-N-methylarginine"
FT /evidence="ECO:0007744|PubMed:24129315"
FT MOD_RES 335
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q62764"
FT MOD_RES 358
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q62764"
FT MOD_RES 359
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q62764"
FT VAR_SEQ 184..252
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:10956549,
FT ECO:0000303|PubMed:15489334"
FT /id="VSP_013051"
FT CONFLICT 237
FT /note="T -> N (in Ref. 2; AAG14418)"
FT /evidence="ECO:0000305"
FT CONFLICT 306
FT /note="A -> G (in Ref. 1; AAF61741)"
FT /evidence="ECO:0000305"
FT CONFLICT 349
FT /note="E -> A (in Ref. 1; AAF61741)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 361 AA; 38814 MW; 5BAF6A144A127CEC CRC64;
MSEAGEATTG GTTLPQAAAD APAAAPPDPA PKSPAASGAP QAPAPAALLA GSPGGDAAPG
PAPASSAPAG GEDAEKKVLA TKVLGTVKWF NVRNGYGFIN RNDTKEDVFV HQTAIKKNNP
RKYLRSVGDG ETVEFDVVEG EKGAEAANVT GPDGVPVEGS RYAADRRRYR RGYYGRRRGP
PRNYAGEEEE EGSGSSEGFE PPAADGQFSG ARNQLRRPQY RPPYRQRRFP PYHVGQTFDR
RSRVFPHPNR MQAGEIGEMK DGVPEGTQLQ AHRNPTYRPR FRRGPARPRP APAIGEAEDK
ENQQAANGPN QPSARRGFRR PYNYRRRSRP LNAVSQDGKE TKAGEAPTEN PAPATEQSSA
E
