LOCUS       NM_003060               3277 bp    mRNA    linear   PRI 12-DEC-2024
DEFINITION  Homo sapiens solute carrier family 22 member 5 (SLC22A5),
            transcript variant 2, mRNA.
ACCESSION   NM_003060
VERSION     NM_003060.4
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 3277)
  AUTHORS   Papierniak-Wygladala,A., Lamch,W., Jurewicz,E. and Nalecz,K.A.
  TITLE     The activity and surface presence of organic cation/carnitine
            transporter OCTN2 (SLC22A5) in breast cancer cells depends on AKT
            kinase
  JOURNAL   Arch Biochem Biophys 742, 109616 (2023)
   PUBMED   37187422
  REMARK    GeneRIF: The activity and surface presence of organic
            cation/carnitine transporter OCTN2 (SLC22A5) in breast cancer cells
            depends on AKT kinase.
REFERENCE   2  (bases 1 to 3277)
  AUTHORS   Dinarvand,N., Karimi,F., Azizi,R., Rastaghi,S., Sheikhi,A. and
            Pourfarzam,M.
  TITLE     Evaluation of the gene encoding carnitine transporter
            (OCTN2/SLC22A5) expression in human breast cancer and its
            association with clinicopathological characteristics
  JOURNAL   Mol Biol Rep 50 (3), 2061-2066 (2023)
   PUBMED   36539562
  REMARK    GeneRIF: Evaluation of the gene encoding carnitine transporter
            (OCTN2/SLC22A5) expression in human breast cancer and its
            association with clinicopathological characteristics.
REFERENCE   3  (bases 1 to 3277)
  AUTHORS   Koleske,M.L., McInnes,G., Brown,J.E.H., Thomas,N., Hutchinson,K.,
            Chin,M.Y., Koehl,A., Arkin,M.R., Schlessinger,A., Gallagher,R.C.,
            Song,Y.S., Altman,R.B. and Giacomini,K.M.
  TITLE     Functional genomics of OCTN2 variants informs protein-specific
            variant effect predictor for Carnitine Transporter Deficiency
  JOURNAL   Proc Natl Acad Sci U S A 119 (46), e2210247119 (2022)
   PUBMED   36343260
  REMARK    GeneRIF: Functional genomics of OCTN2 variants informs
            protein-specific variant effect predictor for Carnitine Transporter
            Deficiency.
REFERENCE   4  (bases 1 to 3277)
  AUTHORS   Maekawa,S., Mori,D., Nishiya,T., Takikawa,O., Horinouchi,T.,
            Nishimoto,A., Kajita,E. and Miwa,S.
  TITLE     OCTN2VT, a splice variant of OCTN2, does not transport carnitine
            because of the retention in the endoplasmic reticulum caused by
            insertion of 24 amino acids in the first extracellular loop of
            OCTN2
  JOURNAL   Biochim Biophys Acta 1773 (6), 1000-1006 (2007)
   PUBMED   17509700
REFERENCE   5  (bases 1 to 3277)
  AUTHORS   Nezu,J., Tamai,I., Oku,A., Ohashi,R., Yabuuchi,H., Hashimoto,N.,
            Nikaido,H., Sai,Y., Koizumi,A., Shoji,Y., Takada,G., Matsuishi,T.,
            Yoshino,M., Kato,H., Ohura,T., Tsujimoto,G., Hayakawa,J.,
            Shimane,M. and Tsuji,A.
  TITLE     Primary systemic carnitine deficiency is caused by mutations in a
            gene encoding sodium ion-dependent carnitine transporter
  JOURNAL   Nat Genet 21 (1), 91-94 (1999)
   PUBMED   9916797
REFERENCE   6  (bases 1 to 3277)
  AUTHORS   Tamai,I., Ohashi,R., Nezu,J., Yabuuchi,H., Oku,A., Shimane,M.,
            Sai,Y. and Tsuji,A.
  TITLE     Molecular and functional identification of sodium ion-dependent,
            high affinity human carnitine transporter OCTN2
  JOURNAL   J Biol Chem 273 (32), 20378-20382 (1998)
   PUBMED   9685390
REFERENCE   7  (bases 1 to 3277)
  AUTHORS   Shoji,Y., Koizumi,A., Kayo,T., Ohata,T., Takahashi,T., Harada,K.
            and Takada,G.
  TITLE     Evidence for linkage of human primary systemic carnitine deficiency
            with D5S436: a novel gene locus on chromosome 5q
  JOURNAL   Am J Hum Genet 63 (1), 101-108 (1998)
   PUBMED   9634512
REFERENCE   8  (bases 1 to 3277)
  AUTHORS   Wu,X., Prasad,P.D., Leibach,F.H. and Ganapathy,V.
  TITLE     cDNA sequence, transport function, and genomic organization of
            human OCTN2, a new member of the organic cation transporter family
  JOURNAL   Biochem Biophys Res Commun 246 (3), 589-595 (1998)
   PUBMED   9618255
REFERENCE   9  (bases 1 to 3277)
  AUTHORS   El-Hattab,A.W. and Almannai,M.
  TITLE     Primary Carnitine Deficiency
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   22420015
REFERENCE   10 (bases 1 to 3277)
  AUTHORS   Matsuishi,T., Hirata,K., Terasawa,K., Kato,H., Yoshino,M.,
            Ohtaki,E., Hirose,F., Nonaka,I., Sugiyama,N. and Ohta,K.
  TITLE     Successful carnitine treatment in two siblings having lipid storage
            myopathy with hypertrophic cardiomyopathy
  JOURNAL   Neuropediatrics 16 (1), 6-12 (1985)
   PUBMED   3974805
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from DA567722.1, AF057164.1,
            DA186237.1, BC012325.1 and AK128610.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Jun 2, 2019 this sequence version replaced NM_003060.3.
            
            Summary: Polyspecific organic cation transporters in the liver,
            kidney, intestine, and other organs are critical for elimination of
            many endogenous small organic cations as well as a wide array of
            drugs and environmental toxins. The encoded protein is a plasma
            integral membrane protein which functions both as an organic cation
            transporter and as a sodium-dependent high affinity carnitine
            transporter. The encoded protein is involved in the active cellular
            uptake of carnitine. Mutations in this gene are the cause of
            systemic primary carnitine deficiency (CDSP), an autosomal
            recessive disorder manifested early in life by hypoketotic
            hypoglycemia and acute metabolic decompensation, and later in life
            by skeletal myopathy or cardiomyopathy. Alternative splicing of
            this gene results in multiple transcript variants. [provided by
            RefSeq, Apr 2015].
            
            Transcript Variant: This variant (2) lacks an alternate in-frame
            exon in the 5' coding region, compared to variant 1, resulting in
            an isoform (b) that is shorter than 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 :: AF057164.1, SRR1660807.104115.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1966682, SAMEA1968540
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000245407.8/ ENSP00000245407.3
            RefSeq Select criteria :: based on manual assertion, conservation,
                                      expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-42                DA567722.1         2-43
            43-56               AF057164.1         1-14
            57-580              DA186237.1         30-553
            581-1069            AF057164.1         539-1027
            1070-2028           BC012325.1         978-1936
            2029-3277           AK128610.1         2444-3692
FEATURES             Location/Qualifiers
     source          1..3277
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="5"
                     /map="5q31.1"
     gene            1..3277
                     /gene="SLC22A5"
                     /gene_synonym="CDSP; OCTN2"
                     /note="solute carrier family 22 member 5"
                     /db_xref="GeneID:6584"
                     /db_xref="HGNC:HGNC:10969"
                     /db_xref="MIM:603377"
     exon            1..656
                     /gene="SLC22A5"
                     /gene_synonym="CDSP; OCTN2"
                     /inference="alignment:Splign:2.1.0"
     CDS             264..1937
                     /gene="SLC22A5"
                     /gene_synonym="CDSP; OCTN2"
                     /note="isoform b is encoded by transcript variant 2;
                     organic cation/carnitine transporter 2; high-affinity
                     sodium dependent carnitine cotransporter; systemic
                     carnitine deficiency"
                     /codon_start=1
                     /product="organic cation/carnitine transporter 2 isoform
                     b"
                     /protein_id="NP_003051.1"
                     /db_xref="CCDS:CCDS4154.1"
                     /db_xref="GeneID:6584"
                     /db_xref="HGNC:HGNC:10969"
                     /db_xref="MIM:603377"
                     /translation="MRDYDEVTAFLGEWGPFQRLIFFLLSASIIPNGFTGLSSVFLIA
                     TPEHRCRVPDAANLSSAWRNHTVPLRLRDGREVPHSCRRYRLATIANFSALGLEPGRD
                     VDLGQLEQESCLDGWEFSQDVYLSTIVTEWNLVCEDDWKAPLTISLFFVGVLLGSFIS
                     GQLSDRFGRKNVLFVTMGMQTGFSFLQIFSKNFEMFVVLFVLVGMGQISNYVAAFVLG
                     TEILGKSVRIIFSTLGVCIFYAFGYMVLPLFAYFIRDWRMLLVALTMPGVLCVALWWF
                     IPESPRWLISQGRFEEAEVIIRKAAKANGIVVPSTIFDPSELQDLSSKKQQSHNILDL
                     LRTWNIRMVTIMSIMLWMTISVGYFGLSLDTPNLHGDIFVNCFLSAMVEVPAYVLAWL
                     LLQYLPRRYSMATALFLGGSVLLFMQLVPPDLYYLATVLVMVGKFGVTAAFSMVYVYT
                     AELYPTVVRNMGVGVSSTASRLGSILSPYFVYLGAYDRFLPYILMGSLTILTAILTLF
                     LPESFGTPLPDTIDQMLRVKGMKHRKTPSHTRMLKDGQERPTILKSTAF"
     exon            657..760
                     /gene="SLC22A5"
                     /gene_synonym="CDSP; OCTN2"
                     /inference="alignment:Splign:2.1.0"
     exon            761..915
                     /gene="SLC22A5"
                     /gene_synonym="CDSP; OCTN2"
                     /inference="alignment:Splign:2.1.0"
     exon            916..1087
                     /gene="SLC22A5"
                     /gene_synonym="CDSP; OCTN2"
                     /inference="alignment:Splign:2.1.0"
     exon            1088..1214
                     /gene="SLC22A5"
                     /gene_synonym="CDSP; OCTN2"
                     /inference="alignment:Splign:2.1.0"
     exon            1215..1315
                     /gene="SLC22A5"
                     /gene_synonym="CDSP; OCTN2"
                     /inference="alignment:Splign:2.1.0"
     exon            1316..1530
                     /gene="SLC22A5"
                     /gene_synonym="CDSP; OCTN2"
                     /inference="alignment:Splign:2.1.0"
     exon            1531..1713
                     /gene="SLC22A5"
                     /gene_synonym="CDSP; OCTN2"
                     /inference="alignment:Splign:2.1.0"
     exon            1714..1849
                     /gene="SLC22A5"
                     /gene_synonym="CDSP; OCTN2"
                     /inference="alignment:Splign:2.1.0"
     exon            1850..3277
                     /gene="SLC22A5"
                     /gene_synonym="CDSP; OCTN2"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3256..3261
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SLC22A5"
                     /gene_synonym="CDSP; OCTN2"
                     /note="hexamer: AGTAAA"
     polyA_site      3277
                     /gene="SLC22A5"
                     /gene_synonym="CDSP; OCTN2"
                     /note="major polyA site"
ORIGIN      
        1 gccttcgccg gcgccgctct gcctgccagc ggggcgcgcc ttgcggccca ggcccgcaac
       61 cttccctggt cgtgcgccct atgtaaggcc agccgcggca ggaccaaggc ggcggtgtca
      121 gctcgcgagc ctaccctccg cggacggtct tgggtcgcct gctgcctggc ttgcctggtc
      181 ggcggcgggt gccccgcgcg cacgcgcaaa gcccgccgcg ttccccgacc ccaggccgcg
      241 ctctgtgggc ctctgagggc ggcatgcggg actacgacga ggtgaccgcc ttcctgggcg
      301 agtgggggcc cttccagcgc ctcatcttct tcctgctcag cgccagcatc atccccaatg
      361 gcttcaccgg cctgtcctcc gtgttcctga tagcgacccc ggagcaccgc tgccgggtgc
      421 cggacgccgc gaacctgagc agcgcctggc gcaaccacac tgtcccactg cggctgcggg
      481 acggccgcga ggtgccccac agctgccgcc gctaccggct cgccaccatc gccaacttct
      541 cggcgcttgg gctggagccg gggcgcgacg tggacctggg gcagctggag caggagagct
      601 gtctggatgg ctgggagttc agtcaggacg tctacctgtc caccattgtg accgagtgga
      661 acctggtgtg tgaggacgac tggaaggccc cactcacaat ctccttgttc ttcgtgggtg
      721 tgctgttggg ctccttcatt tcagggcagc tgtcagacag gtttggccgg aagaatgtgc
      781 tgttcgtgac catgggcatg cagacaggct tcagcttcct gcagatcttc tcgaagaatt
      841 ttgagatgtt tgtcgtgctg tttgtccttg taggcatggg ccagatctcc aactatgtgg
      901 cagcatttgt cctggggaca gaaattcttg gcaagtcagt tcgtataata ttctctacgt
      961 taggagtgtg catattttat gcatttggct acatggtgct gccactgttt gcttacttca
     1021 tccgagactg gcggatgctg ctggtggcgc tgacgatgcc gggggtgcta tgcgtggcac
     1081 tctggtggtt catccctgag tccccccgat ggctcatctc tcagggacga tttgaagagg
     1141 cagaggtgat catccgcaag gctgccaaag ccaatgggat tgttgtgcct tccactatct
     1201 ttgacccgag tgagttacaa gacctaagtt ccaagaagca gcagtcccac aacattctgg
     1261 atctgcttcg aacctggaat atccggatgg tcaccatcat gtccataatg ctgtggatga
     1321 ccatatcagt gggctatttt gggctttcgc ttgatactcc taacttgcat ggggacatct
     1381 ttgtgaactg cttcctttca gcgatggttg aagtcccagc atatgtgttg gcctggctgc
     1441 tgctgcaata tttgccccgg cgctattcca tggccactgc cctcttcctg ggtggcagtg
     1501 tccttctctt catgcagctg gtacccccag acttgtatta tttggctaca gtcctggtga
     1561 tggtgggcaa gtttggagtc acggctgcct tttccatggt ctacgtgtac acagccgagc
     1621 tgtatcccac agtggtgaga aacatgggtg tgggagtcag ctccacagca tcccgcctgg
     1681 gcagcatcct gtctccctac ttcgtttacc ttggtgccta cgaccgcttc ctgccctaca
     1741 ttctcatggg aagtctgacc atcctgacag ccatcctcac cttgtttctc ccagagagct
     1801 tcggtacccc actcccagac accattgacc agatgctaag agtcaaagga atgaaacaca
     1861 gaaaaactcc aagtcacaca aggatgttaa aagatggtca agaaaggccc acaatcctta
     1921 aaagcacagc cttctaacat cgcttccagt aagggagaaa ctgaagagga aagactgtct
     1981 tgccagaaat ggccagcttg tgcagactcc gagtccttca gtgacaaaag gcctttgctg
     2041 tttgtcctct tgacctgtgt ctgacttgct cctggatggg cacccacact cagaggctac
     2101 atatggccct agagcaccac cttcctctag ggacactggg gctacctaca gacaacttca
     2161 tctaagtcct aactattaca atgatggact cagcacctcc aaagcagtta atttttcact
     2221 agaaccagtg agatctggag gaatgtgaga agcatatgct aaatgtacat tttaatttta
     2281 gactacttga aaaggcccct aataaggcta gaggtctaag tcccccaccc ctttccccac
     2341 tcccctctag tggtgaactt tagaggaaaa ggaagtaatt gcacaaggag tttgattctt
     2401 accttttctc agttacagag gacattaact ggatcattgc ttccccaggg caggagagcg
     2461 cagagctagg gaaagtgaaa ggtaatgaag atggagcaga atgagcagat gcagatcacc
     2521 agcaaagtgc actgatgtgt gagctcttaa gaccactcag catgacgact gagtagactt
     2581 gtttacatct gatcaaagca ctgggcttgt ccaggctcat aataaatgct ccattgaatc
     2641 tactattctt gttttccact gctgtggaaa cctccttgct actatagcgt cttatgtatg
     2701 gtttaaagga aatttatcag gtgagagaga tgagcaacgt tgtcttttct ctcaaagctg
     2761 taatgtgggt tttgttttat tgtttatttg tttgttgttg tatccttttc tccttgttat
     2821 ttgcccttca gaatgcactt gggaaaggct ggttccttag cctcctggtt tgtgtctttt
     2881 tttttttttt tttaaaacag aatcactctg gcaattgtct gcagctgcca ctggtgcaag
     2941 gccttaccag ccctagcctc tagcacttct ctaagtgcca aaaacagtgt cattgtgtgt
     3001 gttcctttct tgatacttag tcatgggagg atattacaaa aaagaaattt aaattgtgtt
     3061 catagtcttt cagagtagct cactttagtc ctgtaacttt attgggtgat attttgtgtt
     3121 cagtgtaatt gtcttctctt tgctgattat gttaccatgg tactcctaaa gcatatgcct
     3181 cacctggtta aaaaagaaca aacatgtttt tgtgaaagct actgaagtgc cttgggaaat
     3241 gagaaagttt taataagtaa aatgattttt taaataa
//
