LOCUS       NM_004559               2979 bp    mRNA    linear   PRI 24-OCT-2024
DEFINITION  Homo sapiens Y-box binding protein 1 (YBX1), transcript variant 1,
            mRNA.
ACCESSION   NM_004559
VERSION     NM_004559.5
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 2979)
  AUTHORS   Kwon,J.H. and Kim,S.H.
  TITLE     YBX1 promotes epithelial-mesenchymal transition in hepatocellular
            carcinoma via transcriptional regulation of PLRG1
  JOURNAL   Med Oncol 41 (11), 280 (2024)
   PUBMED   39400789
  REMARK    GeneRIF: YBX1 promotes epithelial-mesenchymal transition in
            hepatocellular carcinoma via transcriptional regulation of PLRG1.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2979)
  AUTHORS   Zhuo,H., Hou,J., Hong,Z., Yu,S., Peng,H., Zhang,L., Xie,W. and
            Hong,X.
  TITLE     TAGLN2 induces resistance signature ISGs by activating AKT-YBX1
            signal with dual pathways and mediates the IFN-related DNA damage
            resistance in gastric cancer
  JOURNAL   Cell Death Dis 15 (8), 608 (2024)
   PUBMED   39168971
  REMARK    GeneRIF: TAGLN2 induces resistance signature ISGs by activating
            AKT-YBX1 signal with dual pathways and mediates the IFN-related DNA
            damage resistance in gastric cancer.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2979)
  AUTHORS   Lyabin,D.N., Eliseeva,I.A. and Ovchinnikov,L.P.
  TITLE     YB-1 protein: functions and regulation
  JOURNAL   Wiley Interdiscip Rev RNA 5 (1), 95-110 (2014)
   PUBMED   24217978
  REMARK    GeneRIF: YB-1 participates in a wide variety of DNA/RNA-dependent
            events, including DNA reparation, pre-mRNA transcription and
            splicing, mRNA packaging, and regulation of mRNA stability and
            translation. [review]
            Review article
REFERENCE   4  (bases 1 to 2979)
  AUTHORS   Frye,B.C., Halfter,S., Djudjaj,S., Muehlenberg,P., Weber,S.,
            Raffetseder,U., En-Nia,A., Knott,H., Baron,J.M., Dooley,S.,
            Bernhagen,J. and Mertens,P.R.
  TITLE     Y-box protein-1 is actively secreted through a non-classical
            pathway and acts as an extracellular mitogen
  JOURNAL   EMBO Rep 10 (7), 783-789 (2009)
   PUBMED   19483673
  REMARK    GeneRIF: The secretion of YB-1 by mesangial and monocytic cells
            after inflammatory challenges, is reported.
REFERENCE   5  (bases 1 to 2979)
  AUTHORS   Toh,S., Nakamura,T., Ohga,T., Koike,K., Uchiumi,T., Wada,M.,
            Kuwano,M. and Kohno,K.
  TITLE     Genomic organization of the human Y-box protein (YB-1) gene
  JOURNAL   Gene 206 (1), 93-97 (1998)
   PUBMED   9461420
REFERENCE   6  (bases 1 to 2979)
  AUTHORS   Makino,Y., Ohga,T., Toh,S., Koike,K., Okumura,K., Wada,M.,
            Kuwano,M. and Kohno,K.
  TITLE     Structural and functional analysis of the human Y-box binding
            protein (YB-1) gene promoter
  JOURNAL   Nucleic Acids Res 24 (10), 1873-1878 (1996)
   PUBMED   8657568
REFERENCE   7  (bases 1 to 2979)
  AUTHORS   Horwitz,E.M., Maloney,K.A. and Ley,T.J.
  TITLE     A human protein containing a 'cold shock' domain binds specifically
            to H-DNA upstream from the human gamma-globin genes
  JOURNAL   J Biol Chem 269 (19), 14130-14139 (1994)
   PUBMED   8188694
REFERENCE   8  (bases 1 to 2979)
  AUTHORS   Kolluri,R., Torrey,T.A. and Kinniburgh,A.J.
  TITLE     A CT promoter element binding protein: definition of a
            double-strand and a novel single-strand DNA binding motif
  JOURNAL   Nucleic Acids Res 20 (1), 111-116 (1992)
   PUBMED   1738588
REFERENCE   9  (bases 1 to 2979)
  AUTHORS   Kolluri,R. and Kinniburgh,A.J.
  TITLE     Full length cDNA sequence encoding a nuclease-sensitive element DNA
            binding protein
  JOURNAL   Nucleic Acids Res 19 (17), 4771 (1991)
   PUBMED   1891370
REFERENCE   10 (bases 1 to 2979)
  AUTHORS   Didier,D.K., Schiffenbauer,J., Woulfe,S.L., Zacheis,M. and
            Schwartz,B.D.
  TITLE     Characterization of the cDNA encoding a protein binding to the
            major histocompatibility complex class II Y box
  JOURNAL   Proc Natl Acad Sci U S A 85 (19), 7322-7326 (1988)
   PUBMED   3174636
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from CN353145.1, BC090038.1 and
            AC098484.2.
            
            On Nov 22, 2018 this sequence version replaced NM_004559.4.
            
            Summary: This gene encodes a highly conserved cold shock domain
            protein that has broad nucleic acid binding properties. The encoded
            protein functions as both a DNA and RNA binding protein and has
            been implicated in numerous cellular processes including regulation
            of transcription and translation, pre-mRNA splicing, DNA reparation
            and mRNA packaging. This protein is also a component of messenger
            ribonucleoprotein (mRNP) complexes and may have a role in microRNA
            processing. This protein can be secreted through non-classical
            pathways and functions as an extracellular mitogen. Aberrant
            expression of the gene is associated with cancer proliferation in
            numerous tissues. This gene may be a prognostic marker for poor
            outcome and drug resistance in certain cancers. Alternate splicing
            results in multiple transcript variants. Pseudogenes of this gene
            are found on multiple chromosomes. [provided by RefSeq, Sep 2015].
            
            Transcript Variant: This variant (1) represents the longer
            transcript and encodes the functional protein.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            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 :: SRR3476690.43156.1,
                                           SRR3476690.829662.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000321358.12/ ENSP00000361626.3
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-25                CN353145.1         33-57
            26-1523             BC090038.1         1-1498
            1524-2979           AC098484.2         50328-51783
FEATURES             Location/Qualifiers
     source          1..2979
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="1"
                     /map="1p34.2"
     gene            1..2979
                     /gene="YBX1"
                     /gene_synonym="BP-8; CBF-A; CSDA2; CSDB; DBPB; EFI-A;
                     MDR-NF1; NSEP-1; NSEP1; YB-1; YB1"
                     /note="Y-box binding protein 1"
                     /db_xref="GeneID:4904"
                     /db_xref="HGNC:HGNC:8014"
                     /db_xref="MIM:154030"
     exon            1..314
                     /gene="YBX1"
                     /gene_synonym="BP-8; CBF-A; CSDA2; CSDB; DBPB; EFI-A;
                     MDR-NF1; NSEP-1; NSEP1; YB-1; YB1"
                     /inference="alignment:Splign:2.1.0"
     CDS             149..1123
                     /gene="YBX1"
                     /gene_synonym="BP-8; CBF-A; CSDA2; CSDB; DBPB; EFI-A;
                     MDR-NF1; NSEP-1; NSEP1; YB-1; YB1"
                     /note="DNA-binding protein B; nuclease-sensitive
                     element-binding protein 1; major histocompatibility
                     complex, class II, Y box-binding protein I; Y-box
                     transcription factor; enhancer factor I subunit A;
                     CCAAT-binding transcription factor I subunit A"
                     /codon_start=1
                     /product="Y-box-binding protein 1"
                     /protein_id="NP_004550.2"
                     /db_xref="CCDS:CCDS470.1"
                     /db_xref="GeneID:4904"
                     /db_xref="HGNC:HGNC:8014"
                     /db_xref="MIM:154030"
                     /translation="MSSEAETQQPPAAPPAAPALSAADTKPGTTGSGAGSGGPGGLTS
                     AAPAGGDKKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRS
                     VGDGETVEFDVVEGEKGAEAANVTGPGGVPVQGSKYAADRNHYRRYPRRRGPPRNYQQ
                     NYQNSESGEKNEGSESAPEGQAQQRRPYRRRRFPPYYMRRPYGRRPQYSNPPVQGEVM
                     EGADNQGAGEQGRPVRQNMYRGYRPRFRRGPPRQRQPREDGNEEDKENQGDETQGQQP
                     PQRRYRRNFNYRRRRPENPKPQDGKETKAADPPAENSSAPEAEQGGAE"
     exon            315..378
                     /gene="YBX1"
                     /gene_synonym="BP-8; CBF-A; CSDA2; CSDB; DBPB; EFI-A;
                     MDR-NF1; NSEP-1; NSEP1; YB-1; YB1"
                     /inference="alignment:Splign:2.1.0"
     exon            379..412
                     /gene="YBX1"
                     /gene_synonym="BP-8; CBF-A; CSDA2; CSDB; DBPB; EFI-A;
                     MDR-NF1; NSEP-1; NSEP1; YB-1; YB1"
                     /inference="alignment:Splign:2.1.0"
     exon            413..502
                     /gene="YBX1"
                     /gene_synonym="BP-8; CBF-A; CSDA2; CSDB; DBPB; EFI-A;
                     MDR-NF1; NSEP-1; NSEP1; YB-1; YB1"
                     /inference="alignment:Splign:2.1.0"
     exon            503..805
                     /gene="YBX1"
                     /gene_synonym="BP-8; CBF-A; CSDA2; CSDB; DBPB; EFI-A;
                     MDR-NF1; NSEP-1; NSEP1; YB-1; YB1"
                     /inference="alignment:Splign:2.1.0"
     exon            806..888
                     /gene="YBX1"
                     /gene_synonym="BP-8; CBF-A; CSDA2; CSDB; DBPB; EFI-A;
                     MDR-NF1; NSEP-1; NSEP1; YB-1; YB1"
                     /inference="alignment:Splign:2.1.0"
     exon            889..1154
                     /gene="YBX1"
                     /gene_synonym="BP-8; CBF-A; CSDA2; CSDB; DBPB; EFI-A;
                     MDR-NF1; NSEP-1; NSEP1; YB-1; YB1"
                     /inference="alignment:Splign:2.1.0"
     exon            1155..2979
                     /gene="YBX1"
                     /gene_synonym="BP-8; CBF-A; CSDA2; CSDB; DBPB; EFI-A;
                     MDR-NF1; NSEP-1; NSEP1; YB-1; YB1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1518..1523
                     /regulatory_class="polyA_signal_sequence"
                     /gene="YBX1"
                     /gene_synonym="BP-8; CBF-A; CSDA2; CSDB; DBPB; EFI-A;
                     MDR-NF1; NSEP-1; NSEP1; YB-1; YB1"
                     /note="hexamer: AATAAT"
     polyA_site      1537
                     /gene="YBX1"
                     /gene_synonym="BP-8; CBF-A; CSDA2; CSDB; DBPB; EFI-A;
                     MDR-NF1; NSEP-1; NSEP1; YB-1; YB1"
                     /note="major polyA site"
     regulatory      2958..2963
                     /regulatory_class="polyA_signal_sequence"
                     /gene="YBX1"
                     /gene_synonym="BP-8; CBF-A; CSDA2; CSDB; DBPB; EFI-A;
                     MDR-NF1; NSEP-1; NSEP1; YB-1; YB1"
                     /note="hexamer: ATTAAA"
     polyA_site      2979
                     /gene="YBX1"
                     /gene_synonym="BP-8; CBF-A; CSDA2; CSDB; DBPB; EFI-A;
                     MDR-NF1; NSEP-1; NSEP1; YB-1; YB1"
ORIGIN      
        1 attctcgcta gttcgatcgg tagcgggagc ggagagcgga ccccagagag ccctgagcag
       61 ccccaccgcc gccgccggcc tagttaccat cacaccccgg gaggagccgc agctgccgca
      121 gccggcccca gtcaccatca ccgcaaccat gagcagcgag gccgagaccc agcagccgcc
      181 cgccgccccc cccgccgccc ccgccctcag cgccgccgac accaagcccg gcactacggg
      241 cagcggcgca gggagcggtg gcccgggcgg cctcacatcg gcggcgcctg ccggcgggga
      301 caagaaggtc atcgcaacga aggttttggg aacagtaaaa tggttcaatg taaggaacgg
      361 atatggtttc atcaacagga atgacaccaa ggaagatgta tttgtacacc agactgccat
      421 aaagaagaat aaccccagga agtaccttcg cagtgtagga gatggagaga ctgtggagtt
      481 tgatgttgtt gaaggagaaa agggtgcgga ggcagcaaat gttacaggtc ctggtggtgt
      541 tccagttcaa ggcagtaaat atgcagcaga ccgtaaccat tatagacgct atccacgtcg
      601 taggggtcct ccacgcaatt accagcaaaa ttaccagaat agtgagagtg gggaaaagaa
      661 cgagggatcg gagagtgctc ccgaaggcca ggcccaacaa cgccggccct accgcaggcg
      721 aaggttccca ccttactaca tgcggagacc ctatgggcgt cgaccacagt attccaaccc
      781 tcctgtgcag ggagaagtga tggagggtgc tgacaaccag ggtgcaggag aacaaggtag
      841 accagtgagg cagaatatgt atcggggata tagaccacga ttccgcaggg gccctcctcg
      901 ccaaagacag cctagagagg acggcaatga agaagataaa gaaaatcaag gagatgagac
      961 ccaaggtcag cagccacctc aacgtcggta ccgccgcaac ttcaattacc gacgcagacg
     1021 cccagaaaac cctaaaccac aagatggcaa agagacaaaa gcagccgatc caccagctga
     1081 gaattcgtcc gctcccgagg ctgagcaggg cggggctgag taaatgccgg cttaccatct
     1141 ctaccatcat ccggtttagt catccaacaa gaagaaatat gaaattccag caataagaaa
     1201 tgaacaaaag attggagctg aagacctaaa gtgcttgctt tttgcccgtt gaccagataa
     1261 atagaactat ctgcattatc tatgcagcat ggggttttta ttatttttac ctaaagacgt
     1321 ctctttttgg taataacaaa cgtgtttttt aaaaaagcct ggtttttctc aatacgcctt
     1381 taaaggtttt taaattgttt catatctggt caagttgaga tttttaagaa cttcattttt
     1441 aatttgtaat aaaagtttac aacttgattt tttcaaaaaa gtcaacaaac tgcaagcacc
     1501 tgttaataaa ggtcttaaat aattgtcttt gtgtaaattt gtctagtttt gctttagttt
     1561 gtaagtattt agctatttat aggaccctta gcttgaccca gtctacaaat agatgatgct
     1621 cactggtaat tccctcaggt aaaatgtctc aaaatctcta atcctttaag tggcatgcct
     1681 gtgggcccat actaaaaatt agaaaataca tactctgata acctggccat ttttcattga
     1741 aggatttagc tcatttgtaa gaaagacttg agtgtagatt ttgggtgggt ccctttggct
     1801 gtgaggcatt gtttaaaagg gcattgctct agcctagacc gaccagactc tcatcctgct
     1861 ccacttagtt ttgtcacctt gggagaattt gtttcagtgt gtcaattgaa gatgccaatt
     1921 gaagtgttag gacaacctgt cacactgcct ggtgtggtca tcaaatattg gttcagctcc
     1981 ttatgtccta gagatggaaa caagtaatat aaaacccatg ggaaagctgc ttaggaacat
     2041 ggaggttggt gagcttgtaa ttatgtggtt ctcaacacct taaatcctaa gcctagtctg
     2101 gctgatcttt tctctttttg agacggagtc ttgttctgtc atcaggctgg agtacagtgg
     2161 cacaatcttg gctcactgca acctccacct ctaggtttaa gcgattctcc tgcctcggcc
     2221 accttagtag ctgggagtac aggtgcgtgc caccacaccc agctaatttt tgtattttta
     2281 atagagatgg ggttgcactg tgttagccag gatggtcttg atctcttgac cttgtgatcc
     2341 gcccgcctca gcctcccaaa gtgctgggat tacaggtgtg agccaccgca cctggcctct
     2401 ctggcttttg ttttctaatg ttttgttaga tgttctttgg cttgctttgt gaaatagtca
     2461 tgtagttgat agtgactgct gccccgaaac actccagatc atcctggcca gctatcaggg
     2521 cccaggggaa gcagacagta ggggtcggga gtaggccaga gtggcacatc aggaatcctg
     2581 cagtgctgtg gaagtcatct cctgcttggg actaactctt tgcagaggac ttgataagag
     2641 actactcaaa aaaaattttt ttaaccctac ttagtgtaaa tatctgtact gcagaagtga
     2701 gttagcctat ttcttgctgg tgttcatgaa aatactgtgt tggcaagagt gcagtggacc
     2761 tgaaacttca actgttggta gcatctaaac tgttacttac aactgcagac gcacacagtc
     2821 cctgacttaa acagtggttt gacttagggg cttttagtgg ggttacggtt tctactgaat
     2881 caacattgtt ttcatggcat cacagagttg aaaaatcata aatgaaacca ttgtaagttg
     2941 actgcagtgt tgccaacatt aaatgcagtt tcaacttaa
//
