LOCUS       NM_015160               2086 bp    mRNA    linear   PRI 19-SEP-2024
DEFINITION  Homo sapiens peptidase, mitochondrial processing subunit alpha
            (PMPCA), transcript variant 1, mRNA; nuclear gene for mitochondrial
            product.
ACCESSION   NM_015160 XM_498426 XM_499555
VERSION     NM_015160.3
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 2086)
  AUTHORS   Charif,M., Chevrollier,A., Gueguen,N., Kane,S., Bris,C.,
            Goudenege,D., Desquiret-Dumas,V., Meunier,I., Mochel,F.,
            Jeanjean,L., Varenne,F., Procaccio,V., Reynier,P., Bonneau,D.,
            Amati-Bonneau,P. and Lenaers,G.
  TITLE     Next-Generation Sequencing Identifies Novel PMPCA Variants in
            Patients with Late-Onset Dominant Optic Atrophy
  JOURNAL   Genes (Basel) 13 (7), 1202 (2022)
   PUBMED   35885985
  REMARK    GeneRIF: Next-Generation Sequencing Identifies Novel PMPCA Variants
            in Patients with Late-Onset Dominant Optic Atrophy.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2086)
  AUTHORS   Morgenstern,M., Peikert,C.D., Lubbert,P., Suppanz,I., Klemm,C.,
            Alka,O., Steiert,C., Naumenko,N., Schendzielorz,A., Melchionda,L.,
            Muhlhauser,W.W.D., Knapp,B., Busch,J.D., Stiller,S.B.,
            Dannenmaier,S., Lindau,C., Licheva,M., Eickhorst,C., Galbusera,R.,
            Zerbes,R.M., Ryan,M.T., Kraft,C., Kozjak-Pavlovic,V., Drepper,F.,
            Dennerlein,S., Oeljeklaus,S., Pfanner,N., Wiedemann,N. and
            Warscheid,B.
  TITLE     Quantitative high-confidence human mitochondrial proteome and its
            dynamics in cellular context
  JOURNAL   Cell Metab 33 (12), 2464-2483 (2021)
   PUBMED   34800366
REFERENCE   3  (bases 1 to 2086)
  AUTHORS   Huttlin,E.L., Bruckner,R.J., Navarrete-Perea,J., Cannon,J.R.,
            Baltier,K., Gebreab,F., Gygi,M.P., Thornock,A., Zarraga,G., Tam,S.,
            Szpyt,J., Gassaway,B.M., Panov,A., Parzen,H., Fu,S., Golbazi,A.,
            Maenpaa,E., Stricker,K., Guha Thakurta,S., Zhang,T., Rad,R.,
            Pan,J., Nusinow,D.P., Paulo,J.A., Schweppe,D.K., Vaites,L.P.,
            Harper,J.W. and Gygi,S.P.
  TITLE     Dual proteome-scale networks reveal cell-specific remodeling of the
            human interactome
  JOURNAL   Cell 184 (11), 3022-3040 (2021)
   PUBMED   33961781
REFERENCE   4  (bases 1 to 2086)
  AUTHORS   Takahashi,Y., Kubota,M., Kosaki,R., Kosaki,K. and Ishiguro,A.
  TITLE     A severe form of autosomal recessive spinocerebellar ataxia
            associated with novel PMPCA variants
  JOURNAL   Brain Dev 43 (3), 464-469 (2021)
   PUBMED   33272776
  REMARK    GeneRIF: A severe form of autosomal recessive spinocerebellar
            ataxia associated with novel PMPCA variants.
REFERENCE   5  (bases 1 to 2086)
  AUTHORS   Kucukkose,C., Taskin,A.A., Marada,A., Brummer,T., Dennerlein,S. and
            Vogtle,F.N.
  TITLE     Functional coupling of presequence processing and degradation in
            human mitochondria
  JOURNAL   FEBS J 288 (2), 600-613 (2021)
   PUBMED   32491259
  REMARK    GeneRIF: Functional coupling of presequence processing and
            degradation in human mitochondria.
REFERENCE   6  (bases 1 to 2086)
  AUTHORS   Nagao,Y., Kitada,S., Kojima,K., Toh,H., Kuhara,S., Ogishima,T. and
            Ito,A.
  TITLE     Glycine-rich region of mitochondrial processing peptidase
            alpha-subunit is essential for binding and cleavage of the
            precursor proteins
  JOURNAL   J Biol Chem 275 (44), 34552-34556 (2000)
   PUBMED   10942759
REFERENCE   7  (bases 1 to 2086)
  AUTHORS   Megarbane,A., Delague,V., Salem,N. and Loiselet,J.
  TITLE     Autosomal recessive congenital cerebellar hypoplasia and short
            stature in a large inbred family
  JOURNAL   Am J Med Genet 87 (1), 88-90 (1999)
   PUBMED   10528257
REFERENCE   8  (bases 1 to 2086)
  AUTHORS   Luciano,P., Geoffroy,S., Brandt,A., Hernandez,J.F. and Geli,V.
  TITLE     Functional cooperation of the mitochondrial processing peptidase
            subunits
  JOURNAL   J Mol Biol 272 (2), 213-225 (1997)
   PUBMED   9299349
REFERENCE   9  (bases 1 to 2086)
  AUTHORS   Srinivasan,M., Kalousek,F. and Curthoys,N.P.
  TITLE     In vitro characterization of the mitochondrial processing and the
            potential function of the 68-kDa subunit of renal glutaminase
  JOURNAL   J Biol Chem 270 (3), 1185-1190 (1995)
   PUBMED   7836378
REFERENCE   10 (bases 1 to 2086)
  AUTHORS   Skre,H. and Berg,K.
  TITLE     Cerebellar ataxia and total albinism: a kindred suggesting
            pleitotropism or linkage
  JOURNAL   Clin Genet 5 (3), 196-204 (1974)
   PUBMED   4838888
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AL592301.14 and BC022949.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_015160.2.
            
            Summary: The protein encoded by this gene is found in the
            mitochondrion, where it represents the alpha subunit of a
            proteolytic heterodimer. This heterodimer is responsible for
            cleaving the transit peptide from nuclear-encoded mitochondrial
            proteins. Defects in this gene are a cause of spinocerebellar
            ataxia, autosomal recessive 2. [provided by RefSeq, Mar 2016].
            
            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 :: BC111399.1, SRR1803611.260433.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            gene product(s) localized to mito. :: reported by MitoCarta
            MANE Ensembl match                 :: ENST00000371717.8/
                                                  ENSP00000360782.3
            RefSeq Select criteria             :: based on conservation,
                                                  expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-23                AL592301.14        54282-54304
            24-1493             BC022949.1         1-1470
            1494-1494           AL592301.14        66793-66793
            1495-2086           BC022949.1         1472-2063
FEATURES             Location/Qualifiers
     source          1..2086
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="9"
                     /map="9q34.3"
     gene            1..2086
                     /gene="PMPCA"
                     /gene_synonym="Alpha-MPP; CLA1; CPD3; INPP5E; MAS2; P-55;
                     SCAR2"
                     /note="peptidase, mitochondrial processing subunit alpha"
                     /db_xref="GeneID:23203"
                     /db_xref="HGNC:HGNC:18667"
                     /db_xref="MIM:613036"
     exon            1..82
                     /gene="PMPCA"
                     /gene_synonym="Alpha-MPP; CLA1; CPD3; INPP5E; MAS2; P-55;
                     SCAR2"
                     /inference="alignment:Splign:2.1.0"
     CDS             12..1589
                     /gene="PMPCA"
                     /gene_synonym="Alpha-MPP; CLA1; CPD3; INPP5E; MAS2; P-55;
                     SCAR2"
                     /EC_number="3.4.24.64"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; inositol polyphosphate-5-phosphatase, 72 kD;
                     mitochondrial-processing peptidase subunit alpha;
                     mitochondrial matrix processing protease, alpha subunit;
                     Cerebellar ataxia-1; inactive zinc metalloprotease alpha;
                     cerebellar ataxia 1 (autosomal recessive); peptidase,
                     mitochondrial processing alpha subunit"
                     /codon_start=1
                     /product="mitochondrial-processing peptidase subunit alpha
                     isoform 1 precursor"
                     /protein_id="NP_055975.1"
                     /db_xref="CCDS:CCDS35180.1"
                     /db_xref="GeneID:23203"
                     /db_xref="HGNC:HGNC:18667"
                     /db_xref="MIM:613036"
                     /translation="MAAVVLAATRLLRGSGSWGCSRLRFGPPAYRRFSSGGAYPNIPL
                     SSPLPGVPKPVFATVDGQEKFETKVTTLDNGLRVASQNKFGQFCTVGILINSGSRYEA
                     KYLSGIAHFLEKLAFSSTARFDSKDEILLTLEKHGGICDCQTSRDTTMYAVSADSKGL
                     DTVVALLADVVLQPRLTDEEVEMTRMAVQFELEDLNLRPDPEPLLTEMIHEAAYRENT
                     VGLHRFCPTENVAKINREVLHSYLRNYYTPDRMVLAGVGVEHEHLVDCARKYLLGVQP
                     AWGSAEAVDIDRSVAQYTGGIAKLERDMSNVSLGPTPIPELTHIMVGLESCSFLEEDF
                     IPFAVLNMMMGGGGSFSAGGPGKGMFSRLYLNVLNRHHWMYNATSYHHSYEDTGLLCI
                     HASADPRQVREMVEIITKEFILMGGTVDTVELERAKTQLTSMLMMNLESRPVIFEDVG
                     RQVLATRSRKLPHELCTLIRNVKPEDVKRVASKMLRGKPAVAALGDLTDLPTYEHIQT
                     ALSSKDGRLPRTYRLFR"
     exon            83..285
                     /gene="PMPCA"
                     /gene_synonym="Alpha-MPP; CLA1; CPD3; INPP5E; MAS2; P-55;
                     SCAR2"
                     /inference="alignment:Splign:2.1.0"
     exon            286..365
                     /gene="PMPCA"
                     /gene_synonym="Alpha-MPP; CLA1; CPD3; INPP5E; MAS2; P-55;
                     SCAR2"
                     /inference="alignment:Splign:2.1.0"
     exon            366..448
                     /gene="PMPCA"
                     /gene_synonym="Alpha-MPP; CLA1; CPD3; INPP5E; MAS2; P-55;
                     SCAR2"
                     /inference="alignment:Splign:2.1.0"
     exon            449..543
                     /gene="PMPCA"
                     /gene_synonym="Alpha-MPP; CLA1; CPD3; INPP5E; MAS2; P-55;
                     SCAR2"
                     /inference="alignment:Splign:2.1.0"
     exon            544..644
                     /gene="PMPCA"
                     /gene_synonym="Alpha-MPP; CLA1; CPD3; INPP5E; MAS2; P-55;
                     SCAR2"
                     /inference="alignment:Splign:2.1.0"
     exon            645..908
                     /gene="PMPCA"
                     /gene_synonym="Alpha-MPP; CLA1; CPD3; INPP5E; MAS2; P-55;
                     SCAR2"
                     /inference="alignment:Splign:2.1.0"
     exon            909..1001
                     /gene="PMPCA"
                     /gene_synonym="Alpha-MPP; CLA1; CPD3; INPP5E; MAS2; P-55;
                     SCAR2"
                     /inference="alignment:Splign:2.1.0"
     exon            1002..1120
                     /gene="PMPCA"
                     /gene_synonym="Alpha-MPP; CLA1; CPD3; INPP5E; MAS2; P-55;
                     SCAR2"
                     /inference="alignment:Splign:2.1.0"
     exon            1121..1211
                     /gene="PMPCA"
                     /gene_synonym="Alpha-MPP; CLA1; CPD3; INPP5E; MAS2; P-55;
                     SCAR2"
                     /inference="alignment:Splign:2.1.0"
     exon            1212..1274
                     /gene="PMPCA"
                     /gene_synonym="Alpha-MPP; CLA1; CPD3; INPP5E; MAS2; P-55;
                     SCAR2"
                     /inference="alignment:Splign:2.1.0"
     exon            1275..1419
                     /gene="PMPCA"
                     /gene_synonym="Alpha-MPP; CLA1; CPD3; INPP5E; MAS2; P-55;
                     SCAR2"
                     /inference="alignment:Splign:2.1.0"
     exon            1420..2086
                     /gene="PMPCA"
                     /gene_synonym="Alpha-MPP; CLA1; CPD3; INPP5E; MAS2; P-55;
                     SCAR2"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2063..2068
                     /regulatory_class="polyA_signal_sequence"
                     /gene="PMPCA"
                     /gene_synonym="Alpha-MPP; CLA1; CPD3; INPP5E; MAS2; P-55;
                     SCAR2"
                     /note="hexamer: AATAAA"
     polyA_site      2086
                     /gene="PMPCA"
                     /gene_synonym="Alpha-MPP; CLA1; CPD3; INPP5E; MAS2; P-55;
                     SCAR2"
                     /note="major polyA site"
ORIGIN      
        1 ggagacgcaa gatggcggct gtggtgctgg cggcgacgcg gttgctgcgg ggctcgggtt
       61 cttggggctg ttcgcggctg aggtttggac ctcctgcgta cagacggttt agtagtggtg
      121 gtgcctatcc caacatcccc ctctcttctc ccttacctgg agtacccaag cctgtttttg
      181 ctacagttga tggacaggaa aagtttgaaa ccaaagtaac cacattggat aatgggcttc
      241 gcgtggcatc tcagaataag tttggacagt tttgtacagt aggaattctt atcaattcag
      301 gatcgagata tgaagcgaaa taccttagtg gaattgctca ctttttggaa aaattggcat
      361 tttcgtctac tgctcgattt gacagcaaag atgaaattct gcttacgttg gaaaagcatg
      421 ggggtatctg tgactgccag acatcaagag acaccaccat gtatgctgtg tctgctgata
      481 gcaaaggctt ggacacggtg gttgccttac tggctgatgt ggttctgcag ccccggctaa
      541 cagatgaaga agtcgagatg acgcggatgg cggtccagtt tgagctggag gacctgaacc
      601 tgcggcctga cccagagcca cttctcaccg agatgattca tgaagcggct tacagggaga
      661 acacagttgg cctccaccgt ttctgcccca cagaaaacgt agcaaagatc aaccgagagg
      721 tgctgcattc ctacctgagg aactactaca ctcccgaccg catggtgctg gccggcgtgg
      781 gcgtggagca cgagcatctg gtggactgtg cccggaagta cctcctgggg gtccagccgg
      841 cctgggggag cgcagaggcc gtggatattg acagatctgt ggcccagtac actgggggga
      901 ttgccaagct agaaagagac atgtccaatg tcagcctggg cccgaccccc atccccgagc
      961 tcacgcacat catggttgga ctggagagct gctccttcct ggaggaggac ttcatcccct
     1021 ttgcagtgtt gaacatgatg atgggcggag gtggctcctt ctcggctggt gggcccggca
     1081 agggcatgtt ctccaggctc tacctcaacg tgctcaacag gcaccactgg atgtataacg
     1141 cgacctccta ccaccacagc tacgaggaca ctggcctcct ttgcatccat gccagcgccg
     1201 acccaagaca ggttcgagaa atggtagaaa tcatcacaaa ggagtttatt ttaatgggcg
     1261 gaaccgtgga cacggtggag ctggaacgag ccaagacgca gctgacatca atgctcatga
     1321 tgaacctgga atccaggcct gtgatcttcg aggatgtggg gaggcaggtg ctggccactc
     1381 gctccagaaa gctgccgcac gagctgtgca cgctcatccg caacgtgaag ccggaagatg
     1441 tgaagagagt cgcttctaag atgctccgag ggaagccggc agtggccgcc ctgggtgacc
     1501 tgactgacct gcccacgtat gagcacatcc agaccgccct gtcgagtaag gacgggcgcc
     1561 tgcccaggac gtaccggctc ttccggtaga accgctcccc ggcctgacag acccagggag
     1621 ctgcagctgg agcccgttcc cgtgcgtgtt agtttggaca cgaatttagt ctaaaaagct
     1681 gtctggttgt ataaacggtg caaacaatgt cgccacagca cccacgcggt ttgcattctt
     1741 ttggaactca atgtgccgat cagtggagtc agtatcgagc ctgaccaccg caagccagga
     1801 agcaggtgaa gtgcccagcg ctggagtgca gcgtgccacg aggagggcgg tcggtgcttc
     1861 cctcctcggg ctgtgggcac atggggcccc gcaggttcct tggaggagcc ctgagctggg
     1921 aggcagcaaa ggctgaccta tcaaagcctc ccggaggcca ccgtgctggg taccaggact
     1981 cacctctgac aagcaggaga aggtaagggc ccggtcagct ccaaggagcg cgctccacgc
     2041 gcgtgcacac agcttccctg gtaataaaga gctggcatct ttctta
//
