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   27-MAR-2024, entry version 168.
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,
RC   Spleen, 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; 14.
DR   DIP; DIP-42746N; -.
DR   IntAct; Q9JKB3; 9.
DR   MINT; Q9JKB3; -.
DR   STRING; 10090.ENSMUSP00000032309; -.
DR   GlyGen; Q9JKB3; 1 site, 1 O-linked glycan (1 site).
DR   iPTMnet; Q9JKB3; -.
DR   PhosphoSitePlus; Q9JKB3; -.
DR   SwissPalm; Q9JKB3; -.
DR   EPD; Q9JKB3; -.
DR   jPOST; Q9JKB3; -.
DR   MaxQB; Q9JKB3; -.
DR   PaxDb; 10090-ENSMUSP00000032309; -.
DR   PeptideAtlas; Q9JKB3; -.
DR   ProteomicsDB; 299609; -. [Q9JKB3-1]
DR   ProteomicsDB; 299610; -. [Q9JKB3-2]
DR   Pumba; Q9JKB3; -.
DR   Antibodypedia; 11792; 262 antibodies from 23 providers.
DR   DNASU; 56449; -.
DR   Ensembl; ENSMUST00000032309.13; ENSMUSP00000032309.7; ENSMUSG00000030189.16. [Q9JKB3-1]
DR   Ensembl; ENSMUST00000087865.4; ENSMUSP00000085172.3; ENSMUSG00000030189.16. [Q9JKB3-2]
DR   GeneID; 56449; -.
DR   KEGG; mmu:56449; -.
DR   UCSC; uc009eis.1; mouse. [Q9JKB3-1]
DR   UCSC; uc009eit.1; mouse. [Q9JKB3-2]
DR   AGR; MGI:2137670; -.
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; FYPQFRQ; -.
DR   OrthoDB; 5487692at2759; -.
DR   PhylomeDB; Q9JKB3; -.
DR   TreeFam; TF317306; -.
DR   BioGRID-ORCS; 56449; 0 hits in 79 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 267 other cell types or tissues.
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:0045202; C:synapse; IDA:SynGO.
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; Nucleic acid-binding proteins; 1.
DR   InterPro; IPR011129; CSD.
DR   InterPro; IPR019844; CSD_1.
DR   InterPro; IPR002059; CSP_DNA-bd.
DR   InterPro; IPR012340; NA-bd_OB-fold.
DR   PANTHER; PTHR11544; COLD SHOCK DOMAIN CONTAINING PROTEINS; 1.
DR   PANTHER; PTHR11544:SF14; Y-BOX-BINDING PROTEIN 3; 1.
DR   Pfam; PF00313; CSD; 1.
DR   PRINTS; PR00050; COLDSHOCK.
DR   SMART; SM00357; CSP; 1.
DR   SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR   PROSITE; PS00352; CSD_1; 1.
DR   PROSITE; PS51857; CSD_2; 1.
DR   Genevisible; Q9JKB3; MM.
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
//