LOCUS       NM_000070               3315 bp    mRNA    linear   PRI 09-OCT-2024
DEFINITION  Homo sapiens calpain 3 (CAPN3), transcript variant 1, mRNA.
ACCESSION   NM_000070
VERSION     NM_000070.3
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 3315)
  AUTHORS   Banerjee,S., Radotra,B.D., Luthra-Guptasarma,M. and Goyal,M.K.
  TITLE     Identification of novel pathogenic variants of Calpain-3 gene in
            limb girdle muscular dystrophy R1
  JOURNAL   Orphanet J Rare Dis 19 (1), 140 (2024)
   PUBMED   38561828
  REMARK    GeneRIF: Identification of novel pathogenic variants of Calpain-3
            gene in limb girdle muscular dystrophy R1.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3315)
  AUTHORS   Valls,A., Gutierrez-Gutierrez,G., Martinez,A., Ruiz-Roldan,C.,
            Camano,P., Lopez de Munain,A. and Saenz,A.
  TITLE     The CAPN3 p.Lys 254del variant is not always associated with
            dominant CAPN3-related muscular dystrophy
  JOURNAL   Muscle Nerve 69 (4), 472-476 (2024)
   PUBMED   38299438
  REMARK    GeneRIF: The CAPN3 p.Lys 254del variant is not always associated
            with dominant CAPN3-related muscular dystrophy.
REFERENCE   3  (bases 1 to 3315)
  AUTHORS   Zhang,L., Zhang,Y., Han,C., Jiang,J., Jiang,J., Cai,X., Yu,L.,
            Qi,H., Fang,Q. and Ding,D.
  TITLE     Two Novel Variants of the CAPN3 Gene in Chinese Patients with
            Limb-Girdle Muscular Dystrophy Recessive 1
  JOURNAL   Hum Hered 89 (1), 52-59 (2024)
   PUBMED   38830343
  REMARK    GeneRIF: Two Novel Variants of the CAPN3 Gene in Chinese Patients
            with Limb-Girdle Muscular Dystrophy Recessive 1.
REFERENCE   4  (bases 1 to 3315)
  AUTHORS   Tomforde,M., Steinbach,M., Haack,T.B. and Kuhlenbaumer,G.
  TITLE     Family and literature analysis demonstrates phenotypic effect of
            two variants in the calpain-3 gene
  JOURNAL   Neurogenetics 24 (4), 273-278 (2023)
   PUBMED   37589857
  REMARK    GeneRIF: Family and literature analysis demonstrates phenotypic
            effect of two variants in the calpain-3 gene.
REFERENCE   5  (bases 1 to 3315)
  AUTHORS   Sorimachi,H., Kinbara,K., Kimura,S., Takahashi,M., Ishiura,S.,
            Sasagawa,N., Sorimachi,N., Shimada,H., Tagawa,K., Maruyama,K. et
            al.
  TITLE     Muscle-specific calpain, p94, responsible for limb girdle muscular
            dystrophy type 2A, associates with connectin through IS2, a
            p94-specific sequence
  JOURNAL   J Biol Chem 270 (52), 31158-31162 (1995)
   PUBMED   8537379
REFERENCE   6  (bases 1 to 3315)
  AUTHORS   Richard,I., Broux,O., Allamand,V., Fougerousse,F.,
            Chiannilkulchai,N., Bourg,N., Brenguier,L., Devaud,C.,
            Pasturaud,P., Roudaut,C. et al.
  TITLE     Mutations in the proteolytic enzyme calpain 3 cause limb-girdle
            muscular dystrophy type 2A
  JOURNAL   Cell 81 (1), 27-40 (1995)
   PUBMED   7720071
REFERENCE   7  (bases 1 to 3315)
  AUTHORS   Pegoraro,E. and Hoffman,E.P.
  TITLE     Limb-Girdle Muscular Dystrophy Overview - RETIRED CHAPTER, FOR
            HISTORICAL REFERENCE ONLY
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301582
REFERENCE   8  (bases 1 to 3315)
  AUTHORS   Angelini,C.
  TITLE     Calpainopathy
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   20301490
REFERENCE   9  (bases 1 to 3315)
  AUTHORS   Ohno,S., Minoshima,S., Kudoh,J., Fukuyama,R., Shimizu,Y.,
            Ohmi-Imajoh,S., Shimizu,N. and Suzuki,K.
  TITLE     Four genes for the calpain family locate on four distinct human
            chromosomes
  JOURNAL   Cytogenet Cell Genet 53 (4), 225-229 (1990)
   PUBMED   2209092
REFERENCE   10 (bases 1 to 3315)
  AUTHORS   Sorimachi,H., Imajoh-Ohmi,S., Emori,Y., Kawasaki,H., Ohno,S.,
            Minami,Y. and Suzuki,K.
  TITLE     Molecular cloning of a novel mammalian calcium-dependent protease
            distinct from both m- and mu-types. Specific expression of the mRNA
            in skeletal muscle
  JOURNAL   J Biol Chem 264 (33), 20106-20111 (1989)
   PUBMED   2555341
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC012651.8.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 26, 2018 this sequence version replaced NM_000070.2.
            
            Summary: Calpain, a heterodimer consisting of a large and a small
            subunit, is a major intracellular protease, although its function
            has not been well established. This gene encodes a muscle-specific
            member of the calpain large subunit family that specifically binds
            to titin. Mutations in this gene are associated with limb-girdle
            muscular dystrophies type 2A. Alternate promoters and alternative
            splicing result in multiple transcript variants encoding different
            isoforms and some variants are ubiquitously expressed. [provided by
            RefSeq, Jul 2008].
            
            Transcript Variant: This variant (1) encodes the longest 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 :: SRR1803611.88161.1,
                                           SRR1803615.236543.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1966682, SAMEA1968189
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000397163.8/ ENSP00000380349.3
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-614               AC012651.8         39829-40442
            615-684             AC012651.8         64811-64880
            685-803             AC012651.8         66495-66613
            804-937             AC012651.8         68081-68214
            938-1106            AC012651.8         69256-69424
            1107-1250           AC012651.8         70281-70424
            1251-1334           AC012651.8         72967-73050
            1335-1420           AC012651.8         74584-74669
            1421-1498           AC012651.8         77128-77205
            1499-1659           AC012651.8         79820-79980
            1660-1829           AC012651.8         81969-82138
            1830-1841           AC012651.8         82452-82463
            1842-2050           AC012651.8         83122-83330
            2051-2087           AC012651.8         84069-84105
            2088-2105           AC012651.8         86254-86271
            2106-2219           AC012651.8         88539-88652
            2220-2297           AC012651.8         89631-89708
            2298-2355           AC012651.8         90115-90172
            2356-2420           AC012651.8         90259-90323
            2421-2489           AC012651.8         90756-90824
            2490-2568           AC012651.8         90916-90994
            2569-2685           AC012651.8         91212-91328
            2686-2744           AC012651.8         91615-91673
            2745-3315           AC012651.8         92075-92645
FEATURES             Location/Qualifiers
     source          1..3315
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="15"
                     /map="15q15.1"
     gene            1..3315
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /note="calpain 3"
                     /db_xref="GeneID:825"
                     /db_xref="HGNC:HGNC:1480"
                     /db_xref="MIM:114240"
     exon            1..614
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /inference="alignment:Splign:2.1.0"
     CDS             306..2771
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /EC_number="3.4.22.54"
                     /note="isoform a is encoded by transcript variant 1;
                     calpain, large polypeptide L3; calpain p94, large
                     [catalytic] subunit; muscle-specific calcium-activated
                     neutral protease 3 large subunit; new calpain 1"
                     /codon_start=1
                     /product="calpain-3 isoform a"
                     /protein_id="NP_000061.1"
                     /db_xref="CCDS:CCDS45245.1"
                     /db_xref="GeneID:825"
                     /db_xref="HGNC:HGNC:1480"
                     /db_xref="MIM:114240"
                     /translation="MPTVISASVAPRTAAEPRSPGPVPHPAQSKATEAGGGNPSGIYS
                     AIISRNFPIIGVKEKTFEQLHKKCLEKKVLYVDPEFPPDETSLFYSQKFPIQFVWKRP
                     PEICENPRFIIDGANRTDICQGELGDCWFLAAIACLTLNQHLLFRVIPHDQSFIENYA
                     GIFHFQFWRYGEWVDVVIDDCLPTYNNQLVFTKSNHRNEFWSALLEKAYAKLHGSYEA
                     LKGGNTTEAMEDFTGGVAEFFEIRDAPSDMYKIMKKAIERGSLMGCSIDDGTNMTYGT
                     SPSGLNMGELIARMVRNMDNSLLQDSDLDPRGSDERPTRTIIPVQYETRMACGLVRGH
                     AYSVTGLDEVPFKGEKVKLVRLRNPWGQVEWNGSWSDRWKDWSFVDKDEKARLQHQVT
                     EDGEFWMSYEDFIYHFTKLEICNLTADALQSDKLQTWTVSVNEGRWVRGCSAGGCRNF
                     PDTFWTNPQYRLKLLEEDDDPDDSEVICSFLVALMQKNRRKDRKLGASLFTIGFAIYE
                     VPKEMHGNKQHLQKDFFLYNASKARSKTYINMREVSQRFRLPPSEYVIVPSTYEPHQE
                     GEFILRVFSEKRNLSEEVENTISVDRPVKKKKTKPIIFVSDRANSNKELGVDQESEEG
                     KGKTSPDKQKQSPQPQPGSSDQESEEQQQFRNIFKQIAGDDMEICADELKKVLNTVVN
                     KHKDLKTHGFTLESCRSMIALMDTDGSGKLNLQEFHHLWNKIKAWQKIFKHYDTDQSG
                     TINSYEMRNAVNDAGFHLNNQLYDIITMRYADKHMNIDFDSFICCFVRLEGMFRAFHA
                     FDKDGDGIIKLNVLEWLQLTMYA"
     exon            615..684
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /inference="alignment:Splign:2.1.0"
     exon            685..803
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /inference="alignment:Splign:2.1.0"
     exon            804..937
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /inference="alignment:Splign:2.1.0"
     exon            938..1106
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /inference="alignment:Splign:2.1.0"
     exon            1107..1250
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /inference="alignment:Splign:2.1.0"
     exon            1251..1334
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /inference="alignment:Splign:2.1.0"
     exon            1335..1420
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /inference="alignment:Splign:2.1.0"
     exon            1421..1498
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /inference="alignment:Splign:2.1.0"
     exon            1499..1659
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /inference="alignment:Splign:2.1.0"
     exon            1660..1829
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /inference="alignment:Splign:2.1.0"
     exon            1830..1841
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /inference="alignment:Splign:2.1.0"
     exon            1842..2050
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /inference="alignment:Splign:2.1.0"
     exon            2051..2087
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /inference="alignment:Splign:2.1.0"
     exon            2088..2105
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /inference="alignment:Splign:2.1.0"
     exon            2106..2219
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /inference="alignment:Splign:2.1.0"
     exon            2220..2297
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /inference="alignment:Splign:2.1.0"
     exon            2298..2355
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /inference="alignment:Splign:2.1.0"
     exon            2356..2420
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /inference="alignment:Splign:2.1.0"
     exon            2421..2489
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /inference="alignment:Splign:2.1.0"
     exon            2490..2568
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /inference="alignment:Splign:2.1.0"
     exon            2569..2685
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /inference="alignment:Splign:2.1.0"
     exon            2686..2744
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /inference="alignment:Splign:2.1.0"
     exon            2745..3315
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3291..3296
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /note="hexamer: AATAAA"
     polyA_site      3315
                     /gene="CAPN3"
                     /gene_synonym="CANP3; CANPL3; LGMD2; LGMD2A; LGMDD4;
                     LGMDR1; nCL-1; p94"
                     /note="major polyA site"
ORIGIN      
        1 actctctttc tctctccctc tggcatgcat gctgctggta ggagaccccc aagtcaacat
       61 tgcttcagaa atcctttagc actcatttct caggagaact tatggcttca gaatcacagc
      121 tcggttttta agatggacat aacctgtacg accttctgat gggctttcaa ctttgaactg
      181 gatgtggaca cttttctctc agatgacaga attactccaa cttccccttt gcagttgctt
      241 cctttccttg aaggtagctg tatcttattt tctttaaaaa gctttttctt ccaaagccac
      301 ttgccatgcc gaccgtcatt agcgcatctg tggctccaag gacagcggct gagccccggt
      361 ccccagggcc agttcctcac ccggcccaga gcaaggccac tgaggctggg ggtggaaacc
      421 caagtggcat ctattcagcc atcatcagcc gcaattttcc tattatcgga gtgaaagaga
      481 agacattcga gcaacttcac aagaaatgtc tagaaaagaa agttctttat gtggaccctg
      541 agttcccacc ggatgagacc tctctctttt atagccagaa gttccccatc cagttcgtct
      601 ggaagagacc tccggaaatt tgcgagaatc cccgatttat cattgatgga gccaacagaa
      661 ctgacatctg tcaaggagag ctaggggact gctggtttct cgcagccatt gcctgcctga
      721 ccctgaacca gcaccttctt ttccgagtca taccccatga tcaaagtttc atcgaaaact
      781 acgcagggat cttccacttc cagttctggc gctatggaga gtgggtggac gtggttatag
      841 atgactgcct gccaacgtac aacaatcaac tggttttcac caagtccaac caccgcaatg
      901 agttctggag tgctctgctg gagaaggctt atgctaagct ccatggttcc tacgaagctc
      961 tgaaaggtgg gaacaccaca gaggccatgg aggacttcac aggaggggtg gcagagtttt
     1021 ttgagatcag ggatgctcct agtgacatgt acaagatcat gaagaaagcc atcgagagag
     1081 gctccctcat gggctgctcc attgatgatg gcacgaacat gacctatgga acctctcctt
     1141 ctggtctgaa catgggggag ttgattgcac ggatggtaag gaatatggat aactcactgc
     1201 tccaggactc agacctcgac cccagaggct cagatgaaag accgacccgg acaatcattc
     1261 cggttcagta tgagacaaga atggcctgcg ggctggtcag aggtcacgcc tactctgtca
     1321 cggggctgga tgaggtcccg ttcaaaggtg agaaagtgaa gctggtgcgg ctgcggaatc
     1381 cgtggggcca ggtggagtgg aacggttctt ggagtgatag atggaaggac tggagctttg
     1441 tggacaaaga tgagaaggcc cgtctgcagc accaggtcac tgaggatgga gagttctgga
     1501 tgtcctatga ggatttcatc taccatttca caaagttgga gatctgcaac ctcacggccg
     1561 atgctctgca gtctgacaag cttcagacct ggacagtgtc tgtgaacgag ggccgctggg
     1621 tacggggttg ctctgccgga ggctgccgca acttcccaga tactttctgg accaaccctc
     1681 agtaccgtct gaagctcctg gaggaggacg atgaccctga tgactcggag gtgatttgca
     1741 gcttcctggt ggccctgatg cagaagaacc ggcggaagga ccggaagcta ggggccagtc
     1801 tcttcaccat tggcttcgcc atctacgagg ttcccaaaga gatgcacggg aacaagcagc
     1861 acctgcagaa ggacttcttc ctgtacaacg cctccaaggc caggagcaaa acctacatca
     1921 acatgcggga ggtgtcccag cgcttccgcc tgcctcccag cgagtacgtc atcgtgccct
     1981 ccacctacga gccccaccag gagggggaat tcatcctccg ggtcttctct gaaaagagga
     2041 acctctctga ggaagttgaa aataccatct ccgtggatcg gccagtgaaa aagaaaaaaa
     2101 ccaagcccat catcttcgtt tcggacagag caaacagcaa caaggagctg ggtgtggacc
     2161 aggagtcaga ggagggcaaa ggcaaaacaa gccctgataa gcaaaagcag tccccacagc
     2221 cacagcctgg cagctctgat caggaaagtg aggaacagca acaattccgg aacattttca
     2281 agcagatagc aggagatgac atggagatct gtgcagatga gctcaagaag gtccttaaca
     2341 cagtcgtgaa caaacacaag gacctgaaga cacacgggtt cacactggag tcctgccgta
     2401 gcatgattgc gctcatggat acagatggct ctggaaagct caacctgcag gagttccacc
     2461 acctctggaa caagattaag gcctggcaga aaattttcaa acactatgac acagaccagt
     2521 ccggcaccat caacagctac gagatgcgaa atgcagtcaa cgacgcagga ttccacctca
     2581 acaaccagct ctatgacatc attaccatgc ggtacgcaga caaacacatg aacatcgact
     2641 ttgacagttt catctgctgc ttcgttaggc tggagggcat gttcagagct tttcatgcat
     2701 ttgacaagga tggagatggt atcatcaagc tcaacgttct ggagtggctg cagctcacca
     2761 tgtatgcctg aaccaggctg gcctcatcca aagccatgca ggatcactca ggatttcagt
     2821 ttcaccctct atttccaaag ccatttacct caaaggaccc agcagctaca cccctacagg
     2881 cttccaggca cctcatcagt catgctcctc ctccatttta ccccctaccc atccttgatc
     2941 ggtcatgcct agcctgaccc tttagtaaag caatgaggta ggaagaacaa acccttgtcc
     3001 ctttgccatg tggaggaaag tgcctgcctc tggtccgagc cgcctcggtt ctgaagcgag
     3061 tgctcctgct taccttgctc taggctgtct gcagaagcac ctgccggtgg cactcagcac
     3121 ctccttgtgc tagagccctc catcaccttc acgctgtccc accatgggcc aggaaccaaa
     3181 ccagcactgg gttctactgc tgtggggtaa actaactcag tggaataggg ctggttactt
     3241 tgggctgtcc aactcataag tttggctgca ttttgaaaaa agctgatcta aataaaggca
     3301 tgtgtatggc tggtc
//
