LOCUS       NM_006615               2575 bp    mRNA    linear   PRI 04-APR-2024
DEFINITION  Homo sapiens calpain 9 (CAPN9), transcript variant 1, mRNA.
ACCESSION   NM_006615
VERSION     NM_006615.3
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 2575)
  AUTHORS   Kim,D.H., Beckett,J.D., Nagpal,V., Seman-Senderos,M.A., Gould,R.A.,
            Creamer,T.J., MacFarlane,E.G., Chen,Y., Bedja,D., Butcher,J.T.,
            Mitzner,W., Rouf,R., Hata,S., Warren,D.S. and Dietz,H.C.
  TITLE     Calpain 9 as a therapeutic target in TGFbeta-induced mesenchymal
            transition and fibrosis
  JOURNAL   Sci Transl Med 11 (501) (2019)
   PUBMED   31316008
  REMARK    GeneRIF: these data provide a strong signature for tolerance of
            therapeutic strategies for fibrosis aimed at CAPN9 antagonism.
REFERENCE   2  (bases 1 to 2575)
  AUTHORS   Peng,P., Wu,W., Zhao,J., Song,S., Wang,X., Jia,D., Shao,M.,
            Zhang,M., Li,L., Wang,L., Duan,F., Zhao,R., Yang,C., Wu,H.,
            Zhang,J., Shen,Z., Ruan,Y. and Gu,J.
  TITLE     Decreased expression of Calpain-9 predicts unfavorable prognosis in
            patients with gastric cancer
  JOURNAL   Sci Rep 6, 29604 (2016)
   PUBMED   27404891
  REMARK    GeneRIF: Study shows that calpain-9 is a tumor suppressor that can
            be regarded as a potential prognosis indicator for clinical
            outcomes in gastric cancer.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2575)
  AUTHORS   Davis,J., Martin,S.G., Patel,P.M., Green,A.R., Rakha,E.A.,
            Ellis,I.O. and Storr,S.J.
  TITLE     Low calpain-9 is associated with adverse disease-specific survival
            following endocrine therapy in breast cancer
  JOURNAL   BMC Cancer 14, 995 (2014)
   PUBMED   25539577
  REMARK    GeneRIF: calpain-9 may play a role in breast cancer and that low
            expression is associated with poorer patient clinical outcome
            following endocrine therapy.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2575)
  AUTHORS   Meng,W., Butterworth,J., Bradley,D.T., Hughes,A.E., Soler,V.,
            Calvas,P. and Malecaze,F.
  TITLE     A genome-wide association study provides evidence for association
            of chromosome 8p23 (MYP10) and 10q21.1 (MYP15) with high myopia in
            the French Population
  JOURNAL   Invest Ophthalmol Vis Sci 53 (13), 7983-7988 (2012)
   PUBMED   23049088
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 2575)
  AUTHORS   Liu,C.Y., Wu,M.C., Chen,F., Ter-Minassian,M., Asomaning,K.,
            Zhai,R., Wang,Z., Su,L., Heist,R.S., Kulke,M.H., Lin,X., Liu,G. and
            Christiani,D.C.
  TITLE     A Large-scale genetic association study of esophageal
            adenocarcinoma risk
  JOURNAL   Carcinogenesis 31 (7), 1259-1263 (2010)
   PUBMED   20453000
  REMARK    GeneRIF: Observational study of gene-disease association. (HuGE
            Navigator)
REFERENCE   6  (bases 1 to 2575)
  AUTHORS   Huang,Y. and Wang,K.K.
  TITLE     The calpain family and human disease
  JOURNAL   Trends Mol Med 7 (8), 355-362 (2001)
   PUBMED   11516996
  REMARK    Review article
REFERENCE   7  (bases 1 to 2575)
  AUTHORS   Yoshikawa,Y., Mukai,H., Hino,F., Asada,K. and Kato,I.
  TITLE     Isolation of two novel genes, down-regulated in gastric cancer
  JOURNAL   Jpn J Cancer Res 91 (5), 459-463 (2000)
   PUBMED   10835488
REFERENCE   8  (bases 1 to 2575)
  AUTHORS   Lee,H.J., Tomioka,S., Kinbara,K., Masumoto,H., Jeong,S.Y.,
            Sorimachi,H., Ishiura,S. and Suzuki,K.
  TITLE     Characterization of a human digestive tract-specific calpain,
            nCL-4, expressed in the baculovirus system
  JOURNAL   Arch Biochem Biophys 362 (1), 22-31 (1999)
   PUBMED   9917325
REFERENCE   9  (bases 1 to 2575)
  AUTHORS   Lee,H.J., Sorimachi,H., Jeong,S.Y., Ishiura,S. and Suzuki,K.
  TITLE     Molecular cloning and characterization of a novel tissue-specific
            calpain predominantly expressed in the digestive tract
  JOURNAL   Biol Chem 379 (2), 175-183 (1998)
   PUBMED   9524069
REFERENCE   10 (bases 1 to 2575)
  AUTHORS   Suzuki,K., Sorimachi,H., Yoshizawa,T., Kinbara,K. and Ishiura,S.
  TITLE     Calpain: novel family members, activation, and physiologic function
  JOURNAL   Biol Chem Hoppe Seyler 376 (9), 523-529 (1995)
   PUBMED   8561910
  REMARK    Review article
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AF022799.1, BC027993.1 and
            AL512328.16.
            
            On Nov 23, 2018 this sequence version replaced NM_006615.2.
            
            Summary: Calpains are ubiquitous, well-conserved family of
            calcium-dependent, cysteine proteases. The calpain proteins are
            heterodimers consisting of an invariant small subunit and variable
            large subunits. The large subunit possesses a cysteine protease
            domain, and both subunits possess calcium-binding domains. Calpains
            have been implicated in neurodegenerative processes, as their
            activation can be triggered by calcium influx and oxidative stress.
            The protein encoded by this gene is expressed predominantly in
            stomach and small intestine and may have specialized functions in
            the digestive tract. This gene is thought to be associated with
            gastric cancer. Multiple alternatively spliced transcript variants
            encoding different isoforms have been found for this gene.
            [provided by RefSeq, Jul 2008].
            
            Transcript Variant: This variant (1) represents the longest
            transcript and encodes the longest isoform (1).
            
            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 :: AF022799.1, AK313629.1 [ECO:0000332]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000271971.7/ ENSP00000271971.2
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-606               AF022799.1         5-610
            607-1072            BC027993.1         373-838
            1073-2348           AF022799.1         1077-2352
            2349-2358           BC027993.1         2115-2124
            2359-2575           AL512328.16        100141-100357
FEATURES             Location/Qualifiers
     source          1..2575
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="1"
                     /map="1q42.2"
     gene            1..2575
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /note="calpain 9"
                     /db_xref="GeneID:10753"
                     /db_xref="HGNC:HGNC:1486"
                     /db_xref="MIM:606401"
     exon            1..322
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /inference="alignment:Splign:2.1.0"
     CDS             110..2182
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /EC_number="3.4.22.-"
                     /note="isoform 1 is encoded by transcript variant 1; novel
                     calpain large subunit-4; new calpain 4; digestive
                     tract-specific calpain"
                     /codon_start=1
                     /product="calpain-9 isoform 1"
                     /protein_id="NP_006606.1"
                     /db_xref="CCDS:CCDS1586.1"
                     /db_xref="GeneID:10753"
                     /db_xref="HGNC:HGNC:1486"
                     /db_xref="MIM:606401"
                     /translation="MPYLYRAPGPQAHPVPKDARITHSSGQSFEQMRQECLQRGTLFE
                     DADFPASNSSLFYSERPQIPFVWKRPGEIVKNPEFILGGATRTDICQGELGDCWLLAA
                     IASLTLNQKALARVIPQDQSFGPGYAGIFHFQFWQHSEWLDVVIDDRLPTFRDRLVFL
                     HSADHNEFWSALLEKAYAKLNGSYEALKGGSAIEAMEDFTGGVAETFQTKEAPENFYE
                     ILEKALKRGSLLGCFIDTRSAAESEARTPFGLIKGHAYSVTGIDQVSFRGQRIELIRI
                     RNPWGQVEWNGSWSDSSPEWRSVGPAEQKRLCHTALDDGEFWMAFKDFKAHFDKVEIC
                     NLTPDALEEDAIHKWEVTVHQGSWVRGSTAGGCRNFLDTFWTNPQIKLSLTEKDEGQE
                     ECSFLVALMQKDRRKLKRFGANVLTIGYAIYECPDKDEHLNKDFFRYHASRARSKTFI
                     NLREVSDRFKLPPGEYILIPSTFEPHQEADFCLRIFSEKKAITRDMDGNVDIDLPEPP
                     KPTPPDQETEEEQRFRALFEQVAGEDMEVTAEELEYVLNAVLQKKKDIKFKKLSLISC
                     KNIISLMDTSGNGKLEFDEFKVFWDKLKQWINLFLRFDADKSGTMSTYELRTALKAAG
                     FQLSSHLLQLIVLRYADEELQLDFDDFLNCLVRLENASRVFQALSTKNKEFIHLNINE
                     FIHLTMNI"
     exon            323..392
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /inference="alignment:Splign:2.1.0"
     exon            393..511
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /inference="alignment:Splign:2.1.0"
     exon            512..645
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /inference="alignment:Splign:2.1.0"
     exon            646..814
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /inference="alignment:Splign:2.1.0"
     exon            815..898
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /inference="alignment:Splign:2.1.0"
     exon            899..984
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /inference="alignment:Splign:2.1.0"
     exon            985..1062
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /inference="alignment:Splign:2.1.0"
     exon            1063..1223
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /inference="alignment:Splign:2.1.0"
     exon            1224..1381
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /inference="alignment:Splign:2.1.0"
     exon            1382..1590
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /inference="alignment:Splign:2.1.0"
     exon            1591..1627
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /inference="alignment:Splign:2.1.0"
     exon            1628..1708
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /inference="alignment:Splign:2.1.0"
     exon            1709..1766
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /inference="alignment:Splign:2.1.0"
     exon            1767..1831
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /inference="alignment:Splign:2.1.0"
     exon            1832..1900
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /inference="alignment:Splign:2.1.0"
     exon            1901..1979
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /inference="alignment:Splign:2.1.0"
     exon            1980..2096
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /inference="alignment:Splign:2.1.0"
     exon            2097..2155
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /inference="alignment:Splign:2.1.0"
     exon            2156..2575
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2335..2340
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /note="hexamer: AATGAA"
     polyA_site      2350
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /note="major polyA site"
     regulatory      2555..2560
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
                     /note="hexamer: TATAAA"
     polyA_site      2575
                     /gene="CAPN9"
                     /gene_synonym="GC36; nCL-4"
ORIGIN      
        1 agcccagtgg ccctctgagc tgttccttct tgaccggcac acacagctcg cttcttcact
       61 ttcttttcca tccactgccg gacccaagcc agccttccag ggagcagcca tgccttacct
      121 ctaccgggcc ccagggcctc aggcacaccc ggttcccaag gacgcccgga tcacccactc
      181 ctcaggccag agctttgagc aaatgaggca ggagtgcctg cagagaggca ccctgtttga
      241 ggatgcagac ttcccagcca gcaattcctc cctgttctac agtgagaggc cgcagatccc
      301 ctttgtgtgg aaacgaccag gggaaatcgt gaaaaaccca gaattcattc ttggaggggc
      361 caccaggact gatatctgcc agggagagct gggagactgc tggctattag ccgccatcgc
      421 ctcccttacg cttaatcaaa aagcactggc cagagtcatc ccccaggacc aaagctttgg
      481 ccctggttat gccgggatat tccatttcca gttctggcag cacagtgagt ggctggacgt
      541 ggtgatcgat gaccgcctgc ccaccttcag ggaccgcttg gttttcctcc actctgccga
      601 ccacaacgag ttctggagcg ccttgctgga aaaagcctac gccaagctaa atgggagcta
      661 tgaagctctg aagggaggca gcgccatcga ggccatggaa gacttcactg ggggtgtggc
      721 agagaccttc caaactaaag aggcccccga gaacttctat gagattctag agaaggcttt
      781 gaagagaggc tccctgctgg gctgcttcat tgataccaga agtgctgcag aatctgaggc
      841 ccggacgccg tttggtctta ttaagggtca tgcctacagt gtaacgggaa ttgaccaggt
      901 aagcttccga ggccagagaa tcgagctcat ccgaatccgg aacccttggg gccaggttga
      961 gtggaacggg tcgtggagcg acagttctcc ggagtggcgt tctgttggtc cagctgagca
     1021 gaagcgtctg tgtcacactg ctctggatga tggggaattc tggatggcat ttaaggactt
     1081 caaggcccac tttgataaag tggagatctg caacctcact cccgatgccc tggaggaaga
     1141 cgcgatccac aaatgggagg tgacggtcca tcagggaagc tgggttcgcg gctccacggc
     1201 tgggggctgc cgcaatttcc tggatacctt ttggaccaat ccacaaataa aattgtctct
     1261 gactgagaaa gatgaggggc aggaggagtg tagtttcctt gtagccctga tgcagaaaga
     1321 tagaaggaaa ctcaagagat ttggtgccaa tgtgctgaca atcggctatg ccatttatga
     1381 gtgccctgac aaagacgaac acctgaacaa agacttcttc agataccacg cttctcgggc
     1441 cagaagcaag acgttcatca acctgagaga agtctccgac cggttcaagc tgccccctgg
     1501 ggagtacatc ctgattccca gcacttttga gccccaccag gaagctgatt tctgtctgag
     1561 aatcttttca gagaaaaaag ccattacccg ggatatggat ggaaatgtag acattgacct
     1621 tcctgagcct ccaaagccaa ctccacctga ccaggagaca gaggaggagc agcggtttcg
     1681 ggctctgttt gaacaagtcg ctggtgagga catggaggtg acagcagagg aacttgagta
     1741 tgttttaaat gctgtgctgc aaaagaaaaa ggacatcaaa ttcaagaagc taagcctgat
     1801 ctcctgtaaa aacatcattt ccctgatgga caccagcggc aatgggaagc tggagtttga
     1861 tgaattcaaa gtgttctggg acaagctgaa gcagtggatt aaccttttcc ttcggtttga
     1921 tgctgacaag tccggcacca tgtctaccta tgaactacgg actgcactga aagctgcagg
     1981 ctttcagctg agcagccacc tcctgcagct gattgtgctc aggtatgcgg atgaggagct
     2041 ccagctggac ttcgatgact tcctcaactg cctggtccgg ctggagaatg cgagccgggt
     2101 gttccaggct ctcagtacaa agaacaagga gttcattcat ctcaatataa atgagttcat
     2161 ccatttgaca atgaacatct gaggctgcct tgtagagatg cagcctgccc agctgaatct
     2221 tggcttctgg accttgacct tcagaacttc tcttggtgtg gaaccattac gcccagggtt
     2281 cactcccctc tcatcgtccg gccttctccc ttcatcttga tctgggaaga atgaaatgaa
     2341 ctcagctaca ctctctgatt ttgtgctact cctttgtaaa gtcactgcct taagggggct
     2401 gatggcgcca cctgtgcctt acatccaggt tcaggcatca ctagctttcc cacactctac
     2461 tttccttatt tccttccatt aagaattact cagagttcta acgcacagaa tcctgacttc
     2521 catgtagctc cagtcattgt gatcagacat cctttataaa acatgttttt ataaa
//
