LOCUS       NM_003651               1931 bp    mRNA    linear   PRI 19-SEP-2024
DEFINITION  Homo sapiens Y-box binding protein 3 (YBX3), transcript variant 1,
            mRNA.
ACCESSION   NM_003651
VERSION     NM_003651.5
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 1931)
  AUTHORS   Awad,S., Skipper,W., Vostrejs,W., Ozorowski,K., Min,K., Pfuhler,L.,
            Mehta,D. and Cooke,A.
  TITLE     The YBX3 RNA-binding protein posttranscriptionally controls SLC1A5
            mRNA in proliferating and differentiating skeletal muscle cells
  JOURNAL   J Biol Chem 300 (2), 105602 (2024)
   PUBMED   38159852
  REMARK    GeneRIF: The YBX3 RNA-binding protein posttranscriptionally
            controls SLC1A5 mRNA in proliferating and differentiating skeletal
            muscle cells.
REFERENCE   2  (bases 1 to 1931)
  AUTHORS   Peng,W., Zeng,C., Xu,J., Zhao,H., Zhu,Q., Xu,H., Chen,H., Huang,H.,
            Zhou,Y. and Zhao,C.
  TITLE     Regulation of epithelial cell differentiation by the Ubiquitous
            expressed transcript isoform 1 in ulcerative colitis
  JOURNAL   J Gastroenterol Hepatol 38 (11), 2006-2017 (2023)
   PUBMED   37608570
REFERENCE   3  (bases 1 to 1931)
  AUTHORS   Xie,J., Zhang,H., Wang,K., Ni,J., Ma,X., Khoury,C.J., Prifti,V.,
            Hoard,B., Cerenzia,E.G., Yin,L., Zhang,H., Wang,R., Zhuo,D., Mao,W.
            and Peng,B.
  TITLE     M6A-mediated-upregulation of lncRNA BLACAT3 promotes bladder cancer
            angiogenesis and hematogenous metastasis through YBX3 nuclear
            shuttling and enhancing NCF2 transcription
  JOURNAL   Oncogene 42 (40), 2956-2970 (2023)
   PUBMED   37612524
  REMARK    GeneRIF: M6A-mediated-upregulation of lncRNA BLACAT3 promotes
            bladder cancer angiogenesis and hematogenous metastasis through
            YBX3 nuclear shuttling and enhancing NCF2 transcription.
REFERENCE   4  (bases 1 to 1931)
  AUTHORS   Wang,C., You,Z., He,Y. and Chen,X.
  TITLE     Identification of RNA-binding protein YBX3 as an oncogene in clear
            cell renal cell carcinoma
  JOURNAL   Funct Integr Genomics 23 (3), 225 (2023)
   PUBMED   37418046
  REMARK    GeneRIF: Identification of RNA-binding protein YBX3 as an oncogene
            in clear cell renal cell carcinoma.
            Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1931)
  AUTHORS   Hayashi,J., Kajino,K., Umeda,T., Takano,S., Arakawa,Y., Kudo,M. and
            Hino,O.
  TITLE     Somatic mutation and SNP in the promoter of dbpA and human
            hepatocarcinogenesis
  JOURNAL   Int J Oncol 21 (4), 847-850 (2002)
   PUBMED   12239625
  REMARK    GeneRIF: human dbpA has a role in accelerating hepatocarcinogenesis
REFERENCE   6  (bases 1 to 1931)
  AUTHORS   Argyrokastritis,A., Kontaraki,J., Kamakari,S., Pasparaki,A. and
            Moschonas,N.K.
  TITLE     Assignment of a human cold shock domain protein A intronless
            pseudogene (CSDAP1) to human chromosome 16 band p11.2 by in situ
            hybridization
  JOURNAL   Cytogenet Cell Genet 84 (1-2), 53-54 (1999)
   PUBMED   10343102
REFERENCE   7  (bases 1 to 1931)
  AUTHORS   Lloberas,J., Soler,C. and Celada,A.
  TITLE     Repression mechanisms of the I-A beta gene of the major
            histocompatibility complex
  JOURNAL   Immunobiology 198 (1-3), 249-263 (1997)
   PUBMED   9442396
  REMARK    Review article
REFERENCE   8  (bases 1 to 1931)
  AUTHORS   Coles,L.S., Diamond,P., Occhiodoro,F., Vadas,M.A. and Shannon,M.F.
  TITLE     Cold shock domain proteins repress transcription from the GM-CSF
            promoter
  JOURNAL   Nucleic Acids Res 24 (12), 2311-2317 (1996)
   PUBMED   8710501
REFERENCE   9  (bases 1 to 1931)
  AUTHORS   Kudo,S., Mattei,M.G. and Fukuda,M.
  TITLE     Characterization of the gene for dbpA, a family member of the
            nucleic-acid-binding proteins containing a cold-shock domain
  JOURNAL   Eur J Biochem 231 (1), 72-82 (1995)
   PUBMED   7628487
REFERENCE   10 (bases 1 to 1931)
  AUTHORS   Sakura,H., Maekawa,T., Imamoto,F., Yasuda,K. and Ishii,S.
  TITLE     Two human genes isolated by a novel method encode DNA-binding
            proteins containing a common region of homology
  JOURNAL   Gene 73 (2), 499-507 (1988)
   PUBMED   2977358
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC021049.12.
            
            On Nov 23, 2018 this sequence version replaced NM_003651.4.
            
            Transcript Variant: This variant (1) represents the longer
            transcript and encodes the longer isoform (a).
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC021926.1, SRR1163657.295287.1
                                           [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000228251.9/ ENSP00000228251.4
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-474               AC021049.12        26248-26721
            475-538             AC021049.12        30428-30491
            539-572             AC021049.12        31450-31483
            573-662             AC021049.12        33788-33877
            663-785             AC021049.12        36238-36360
            786-992             AC021049.12        39457-39663
            993-1090            AC021049.12        45423-45520
            1091-1265           AC021049.12        47437-47611
            1266-1365           AC021049.12        48218-48317
            1366-1931           AC021049.12        49917-50482
FEATURES             Location/Qualifiers
     source          1..1931
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="12"
                     /map="12p13.2"
     gene            1..1931
                     /gene="YBX3"
                     /gene_synonym="CSDA; CSDA1; DBPA; ZONAB"
                     /note="Y-box binding protein 3"
                     /db_xref="GeneID:8531"
                     /db_xref="HGNC:HGNC:2428"
                     /db_xref="MIM:603437"
     exon            1..474
                     /gene="YBX3"
                     /gene_synonym="CSDA; CSDA1; DBPA; ZONAB"
                     /inference="alignment:Splign:2.1.0"
     CDS             213..1331
                     /gene="YBX3"
                     /gene_synonym="CSDA; CSDA1; DBPA; ZONAB"
                     /note="isoform a is encoded by transcript variant 1;
                     cold-shock domain containing A1; DNA-binding protein A;
                     single-strand DNA-binding protein NF-GMB; ZO-1-associated
                     nucleic acid-binding protein; cold-shock domain protein A;
                     cold shock domain-containing protein A"
                     /codon_start=1
                     /product="Y-box-binding protein 3 isoform a"
                     /protein_id="NP_003642.3"
                     /db_xref="CCDS:CCDS8630.1"
                     /db_xref="GeneID:8531"
                     /db_xref="HGNC:HGNC:2428"
                     /db_xref="MIM:603437"
                     /translation="MSEAGEATTTTTTTLPQAPTEAAAAAPQDPAPKSPVGSGAPQAA
                     APAPAAHVAGNPGGDAAPAATGTAAAASLATAAGSEDAEKKVLATKVLGTVKWFNVRN
                     GYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGP
                     DGVPVEGSRYAADRRRYRRGYYGRRRGPPRNYAGEEEEEGSGSSEGFDPPATDRQFSG
                     ARNQLRRPQYRPQYRQRRFPPYHVGQTFDRRSRVLPHPNRIQAGEIGEMKDGVPEGAQ
                     LQGPVHRNPTYRPRYRSRGPPRPRPAPAVGEAEDKENQQATSGPNQPSVRRGYRRPYN
                     YRRRPRPPNAPSQDGKEAKAGEAPTENPAPPTQQSSAE"
     exon            475..538
                     /gene="YBX3"
                     /gene_synonym="CSDA; CSDA1; DBPA; ZONAB"
                     /inference="alignment:Splign:2.1.0"
     exon            539..572
                     /gene="YBX3"
                     /gene_synonym="CSDA; CSDA1; DBPA; ZONAB"
                     /inference="alignment:Splign:2.1.0"
     exon            573..662
                     /gene="YBX3"
                     /gene_synonym="CSDA; CSDA1; DBPA; ZONAB"
                     /inference="alignment:Splign:2.1.0"
     exon            663..785
                     /gene="YBX3"
                     /gene_synonym="CSDA; CSDA1; DBPA; ZONAB"
                     /inference="alignment:Splign:2.1.0"
     exon            786..992
                     /gene="YBX3"
                     /gene_synonym="CSDA; CSDA1; DBPA; ZONAB"
                     /inference="alignment:Splign:2.1.0"
     exon            993..1090
                     /gene="YBX3"
                     /gene_synonym="CSDA; CSDA1; DBPA; ZONAB"
                     /inference="alignment:Splign:2.1.0"
     exon            1091..1265
                     /gene="YBX3"
                     /gene_synonym="CSDA; CSDA1; DBPA; ZONAB"
                     /inference="alignment:Splign:2.1.0"
     exon            1266..1365
                     /gene="YBX3"
                     /gene_synonym="CSDA; CSDA1; DBPA; ZONAB"
                     /inference="alignment:Splign:2.1.0"
     exon            1366..1931
                     /gene="YBX3"
                     /gene_synonym="CSDA; CSDA1; DBPA; ZONAB"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1907..1912
                     /regulatory_class="polyA_signal_sequence"
                     /gene="YBX3"
                     /gene_synonym="CSDA; CSDA1; DBPA; ZONAB"
                     /note="hexamer: AATAAA"
     polyA_site      1931
                     /gene="YBX3"
                     /gene_synonym="CSDA; CSDA1; DBPA; ZONAB"
                     /note="major polyA site"
ORIGIN      
        1 agtaagatcg agcgaggagc ccaagagaga gcgcgcagca cgaagctcga gccgcctccg
       61 ccgcgcgacc ccacctcggc cgccgccgcc tgcgccgcga gatccgcccc ggcctccccg
      121 agagcgagcc ccggccgccg cgaccaccag ccgcgctaac cgccgaccaa ccgccaccga
      181 ggcgcctgag cgagagcaga ggaggaggag gcatgagtga ggcgggcgag gccaccacca
      241 ccaccaccac caccctcccg caggctccga cggaggcggc cgccgcggct ccccaggacc
      301 ccgcgcccaa gagcccggtg ggcagcggtg cgccccaggc cgcggccccg gcgcccgccg
      361 cccacgtcgc aggaaacccc ggtggggacg cggcccccgc agccacgggc accgcggccg
      421 ccgcctcttt agccaccgcc gccggcagcg aagacgcgga gaaaaaagtt ctcgccacca
      481 aagtccttgg cactgtcaaa tggttcaacg tcagaaatgg atatggattt ataaatcgaa
      541 atgacaccaa agaagatgta tttgtacatc agactgccat caagaagaat aacccacgga
      601 aatatctgcg cagtgtagga gatggagaaa ctgtagagtt tgatgtggtt gaaggagaga
      661 agggtgcaga agctgccaat gtgactggcc cggatggagt tcctgtggaa gggagtcgtt
      721 acgctgcaga tcggcgccgt tacagacgtg gctactatgg aaggcgccgt ggccctcccc
      781 ggaattacgc tggggaggag gaggaggaag ggagcggcag cagtgaagga tttgaccccc
      841 ctgccactga taggcagttc tctggggccc ggaatcagct gcgccgcccc cagtatcgcc
      901 ctcagtaccg gcagcggcgg ttcccgcctt accacgtggg acagaccttt gaccgtcgct
      961 cacgggtctt accccatccc aacagaatac aggctggtga gattggagag atgaaggatg
     1021 gagtcccaga gggagcacaa cttcagggac cggttcatcg aaatccaact taccgcccaa
     1081 ggtaccgtag caggggacct cctcgcccac gacctgcccc agcagttgga gaggctgaag
     1141 ataaagaaaa tcagcaagcc accagtggtc caaaccagcc gtctgttcgc cgtggatacc
     1201 ggcgtcccta caattaccgg cgtcgcccgc gtcctcctaa cgctccttca caagatggca
     1261 aagaggccaa ggcaggtgaa gcaccaactg agaaccctgc tccacccacc cagcagagca
     1321 gtgctgagta acaccaggct cctcaggcac cttcaccatc ggcaggtgac ctaaagaatt
     1381 aatgaccatt cagaaataaa gcaaaaagca ggccacaacc ttaaccaaca ccaaagaaac
     1441 atccaagcaa taaagtggaa gactaaccaa gatttggaca ttggaatgtt tactgttatt
     1501 ctttaagaaa caactacaaa aagaaaatgt caacaaattt ttccagcaag ctgagaacct
     1561 gggaattcct gcacggaaga caagagagta gcctctccag tttcagcaac cgctaggttt
     1621 ctattttttt tcctggtttt tactgttttg gtaatatata tattgaaaca agaaatatta
     1681 ataccacatg gggagaaccc caaccaaaga aatctgaaat atatagtaaa tgcttttttt
     1741 tccgtttttg ttcattttgg atgctggtgc taaacctcca agtgtcatga tttaaaaaaa
     1801 aaaaaaattt atgtccttct tatttatttc taggatgagg ggaggataac atttttgctt
     1861 tcttatgtga ctctctttga aaatgtgcag taagaaattc ctcaaaaata aaatttttac
     1921 ccttcagagg a
//
