LOCUS       NM_000341               2969 bp    mRNA    linear   PRI 05-APR-2024
DEFINITION  Homo sapiens solute carrier family 3 member 1 (SLC3A1), mRNA.
ACCESSION   NM_000341
VERSION     NM_000341.4
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 2969)
  AUTHORS   Liu,D., Zhao,Y., Xue,X., Hou,X., Xu,H., Zhao,X., Tian,Y., Tang,W.,
            Guo,J. and Xu,C.
  TITLE     Novel compound heterozygous pathogenic variants in the SLC3A1 gene
            in a Chinese family with cystinuria
  JOURNAL   BMC Med Genomics 16 (1), 333 (2023)
   PUBMED   38114997
  REMARK    GeneRIF: Novel compound heterozygous pathogenic variants in the
            SLC3A1 gene in a Chinese family with cystinuria.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2969)
  AUTHORS   Wu,C.W., Badreddine,J., Chang,J., Huang,Y.M., Kim,F.J., Wild,T.,
            Tsai,A.C., Meeks,N., Donalisio Da Silva,R., Molina,W.R. and
            Schumacher,F.R.
  TITLE     Population genetics analysis of SLC3A1 and SLC7A9 revealed the
            etiology of cystine stone may be more than what our current genetic
            knowledge can explain
  JOURNAL   Urolithiasis 51 (1), 101 (2023)
   PUBMED   37561200
  REMARK    GeneRIF: Population genetics analysis of SLC3A1 and SLC7A9 revealed
            the etiology of cystine stone may be more than what our current
            genetic knowledge can explain.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 2969)
  AUTHORS   Lee,B., Lee,S.Y., Han,D.H. and Park,H.D.
  TITLE     Interpretation of SLC3A1 and SLC7A9 variants in cystinuria
            patients: The significance of the PM3 criterion and protein
            stability
  JOURNAL   Urolithiasis 51 (1), 94 (2023)
   PUBMED   37439839
  REMARK    GeneRIF: Interpretation of SLC3A1 and SLC7A9 variants in cystinuria
            patients: The significance of the PM3 criterion and protein
            stability.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2969)
  AUTHORS   Tkaczyk,M., Gadomska-Prokop,K., Zaluska-Lesniewska,I., Musial,K.,
            Zawadzki,J., Jobs,K., Porowski,T., Rogowska-Kalisz,A., Jander,A.,
            Kirolos,M., Halinski,A., Krzemien,A., Sobieszczanska-Drozdziel,A.,
            Zachwieja,K., Beck,B.B., Sikora,P. and Zaniew,M.
  TITLE     Clinical profile of a Polish cohort of children and young adults
            with cystinuria
  JOURNAL   Ren Fail 43 (1), 62-70 (2021)
   PUBMED   33349102
  REMARK    GeneRIF: Clinical profile of a Polish cohort of children and young
            adults with cystinuria.
REFERENCE   5  (bases 1 to 2969)
  AUTHORS   Wu,D., Grund,T.N., Welsch,S., Mills,D.J., Michel,M., Safarian,S.
            and Michel,H.
  TITLE     Structural basis for amino acid exchange by a human heteromeric
            amino acid transporter
  JOURNAL   Proc Natl Acad Sci U S A 117 (35), 21281-21287 (2020)
   PUBMED   32817565
  REMARK    GeneRIF: Structural basis for amino acid exchange by a human
            heteromeric amino acid transporter.
REFERENCE   6  (bases 1 to 2969)
  AUTHORS   Calonge,M.J., Volpini,V., Bisceglia,L., Rousaud,F., de Sanctis,L.,
            Beccia,E., Zelante,L., Testar,X., Zorzano,A., Estivill,X. et al.
  TITLE     Genetic heterogeneity in cystinuria: the SLC3A1 gene is linked to
            type I but not to type III cystinuria
  JOURNAL   Proc Natl Acad Sci U S A 92 (21), 9667-9671 (1995)
   PUBMED   7568194
REFERENCE   7  (bases 1 to 2969)
  AUTHORS   Gasparini,P., Calonge,M.J., Bisceglia,L., Purroy,J., Dianzani,I.,
            Notarangelo,A., Rousaud,F., Gallucci,M., Testar,X., Ponzone,A. et
            al.
  TITLE     Molecular genetics of cystinuria: identification of four new
            mutations and seven polymorphisms, and evidence for genetic
            heterogeneity
  JOURNAL   Am J Hum Genet 57 (4), 781-788 (1995)
   PUBMED   7573036
REFERENCE   8  (bases 1 to 2969)
  AUTHORS   Miyamoto,K., Katai,K., Tatsumi,S., Sone,K., Segawa,H., Yamamoto,H.,
            Taketani,Y., Takada,K., Morita,K., Kanayama,H. et al.
  TITLE     Mutations of the basic amino acid transporter gene associated with
            cystinuria
  JOURNAL   Biochem J 310 (Pt 3) (Pt 3), 951-955 (1995)
   PUBMED   7575432
REFERENCE   9  (bases 1 to 2969)
  AUTHORS   Pras,E., Raben,N., Golomb,E., Arber,N., Aksentijevich,I.,
            Schapiro,J.M., Harel,D., Katz,G., Liberman,U., Pras,M. et al.
  TITLE     Mutations in the SLC3A1 transporter gene in cystinuria
  JOURNAL   Am J Hum Genet 56 (6), 1297-1303 (1995)
   PUBMED   7539209
REFERENCE   10 (bases 1 to 2969)
  AUTHORS   Bertran,J., Werner,A., Chillaron,J., Nunes,V., Biber,J., Testar,X.,
            Zorzano,A., Estivill,X., Murer,H. and Palacin,M.
  TITLE     Expression cloning of a human renal cDNA that induces high affinity
            transport of L-cystine shared with dibasic amino acids in Xenopus
            oocytes
  JOURNAL   J Biol Chem 268 (20), 14842-14849 (1993)
   PUBMED   7686906
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC013717.8, BC093626.1 and
            AK223146.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On May 17, 2019 this sequence version replaced NM_000341.3.
            
            Summary: This gene encodes a type II membrane glycoprotein which is
            one of the components of the renal amino acid transporter which
            transports neutral and basic amino acids in the renal tubule and
            intestinal tract. Mutations and deletions in this gene are
            associated with cystinuria. Alternatively spliced transcript
            variants have been described, but their biological validity has not
            been determined. [provided by RefSeq, Jul 2008].
            
            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 :: AK289636.1, L11696.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968540, SAMEA1970526
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000260649.11/ ENSP00000260649.6
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-24                AC013717.8         82422-82445
            25-2163             BC093626.1         1-2139
            2164-2299           AK223146.1         2148-2283
            2300-2969           AC013717.8         127767-128436
FEATURES             Location/Qualifiers
     source          1..2969
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="2"
                     /map="2p21"
     gene            1..2969
                     /gene="SLC3A1"
                     /gene_synonym="ATR1; CSNU1; D2H; NBAT; RBAT"
                     /note="solute carrier family 3 member 1"
                     /db_xref="GeneID:6519"
                     /db_xref="HGNC:HGNC:11025"
                     /db_xref="MIM:104614"
     exon            1..486
                     /gene="SLC3A1"
                     /gene_synonym="ATR1; CSNU1; D2H; NBAT; RBAT"
                     /inference="alignment:Splign:2.1.0"
     CDS             57..2114
                     /gene="SLC3A1"
                     /gene_synonym="ATR1; CSNU1; D2H; NBAT; RBAT"
                     /note="amino acid transporter 1; solute carrier family 3
                     (cystine, dibasic and neutral amino acid transporters),
                     member 1; neutral and basic amino acid transport protein
                     rBAT; B(0,+)-type amino acid transport protein; solute
                     carrier family 3 (amino acid transporter heavy chain),
                     member 1; solute carrier family 3 (cystine, dibasic and
                     neutral amino acid transporters, activator of cystine,
                     dibasic and neutral amino acid transport), member 1;
                     b(0,+)-type amino acid transporter-related heavy chain"
                     /codon_start=1
                     /product="amino acid transporter heavy chain SLC3A1"
                     /protein_id="NP_000332.2"
                     /db_xref="CCDS:CCDS1819.1"
                     /db_xref="GeneID:6519"
                     /db_xref="HGNC:HGNC:11025"
                     /db_xref="MIM:104614"
                     /translation="MAEDKSKRDSIEMSMKGCQTNNGFVHNEDILEQTPDPGSSTDNL
                     KHSTRGILGSQEPDFKGVQPYAGMPKEVLFQFSGQARYRIPREILFWLTVASVLVLIA
                     ATIAIIALSPKCLDWWQEGPMYQIYPRSFKDSNKDGNGDLKGIQDKLDYITALNIKTV
                     WITSFYKSSLKDFRYGVEDFREVDPIFGTMEDFENLVAAIHDKGLKLIIDFIPNHTSD
                     KHIWFQLSRTRTGKYTDYYIWHDCTHENGKTIPPNNWLSVYGNSSWHFDEVRNQCYFH
                     QFMKEQPDLNFRNPDVQEEIKEILRFWLTKGVDGFSLDAVKFLLEAKHLRDEIQVNKT
                     QIPDTVTQYSELYHDFTTTQVGMHDIVRSFRQTMDQYSTEPGRYRFMGTEAYAESIDR
                     TVMYYGLPFIQEADFPFNNYLSMLDTVSGNSVYEVITSWMENMPEGKWPNWMIGGPDS
                     SRLTSRLGNQYVNVMNMLLFTLPGTPITYYGEEIGMGNIVAANLNESYDINTLRSKSP
                     MQWDNSSNAGFSEASNTWLPTNSDYHTVNVDVQKTQPRSALKLYQDLSLLHANELLLN
                     RGWFCHLRNDSHYVVYTRELDGIDRIFIVVLNFGESTLLNLHNMISGLPAKMRIRLST
                     NSADKGSKVDTSGIFLDKGEGLIFEHNTKNLLHRQTAFRDRCFVSNRACYSSVLNILY
                     TSC"
     exon            487..666
                     /gene="SLC3A1"
                     /gene_synonym="ATR1; CSNU1; D2H; NBAT; RBAT"
                     /inference="alignment:Splign:2.1.0"
     exon            667..821
                     /gene="SLC3A1"
                     /gene_synonym="ATR1; CSNU1; D2H; NBAT; RBAT"
                     /inference="alignment:Splign:2.1.0"
     exon            822..947
                     /gene="SLC3A1"
                     /gene_synonym="ATR1; CSNU1; D2H; NBAT; RBAT"
                     /inference="alignment:Splign:2.1.0"
     exon            948..1067
                     /gene="SLC3A1"
                     /gene_synonym="ATR1; CSNU1; D2H; NBAT; RBAT"
                     /inference="alignment:Splign:2.1.0"
     exon            1068..1192
                     /gene="SLC3A1"
                     /gene_synonym="ATR1; CSNU1; D2H; NBAT; RBAT"
                     /inference="alignment:Splign:2.1.0"
     exon            1193..1388
                     /gene="SLC3A1"
                     /gene_synonym="ATR1; CSNU1; D2H; NBAT; RBAT"
                     /inference="alignment:Splign:2.1.0"
     exon            1389..1556
                     /gene="SLC3A1"
                     /gene_synonym="ATR1; CSNU1; D2H; NBAT; RBAT"
                     /inference="alignment:Splign:2.1.0"
     exon            1557..1673
                     /gene="SLC3A1"
                     /gene_synonym="ATR1; CSNU1; D2H; NBAT; RBAT"
                     /inference="alignment:Splign:2.1.0"
     exon            1674..2969
                     /gene="SLC3A1"
                     /gene_synonym="ATR1; CSNU1; D2H; NBAT; RBAT"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2279..2284
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SLC3A1"
                     /gene_synonym="ATR1; CSNU1; D2H; NBAT; RBAT"
                     /note="hexamer: AATAAA"
     polyA_site      2299
                     /gene="SLC3A1"
                     /gene_synonym="ATR1; CSNU1; D2H; NBAT; RBAT"
                     /note="major polyA site"
     regulatory      2934..2939
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SLC3A1"
                     /gene_synonym="ATR1; CSNU1; D2H; NBAT; RBAT"
                     /note="hexamer: ATTAAA"
     polyA_site      2953
                     /gene="SLC3A1"
                     /gene_synonym="ATR1; CSNU1; D2H; NBAT; RBAT"
ORIGIN      
        1 actcttccac ctcccttact gcaggaaggc actccgaaga cataagtcgg tgagacatgg
       61 ctgaagataa aagcaagaga gactccatcg agatgagtat gaagggatgc cagacaaaca
      121 acgggtttgt ccataatgaa gacattctgg agcagacccc ggatccagga agctcaacag
      181 acaacctgaa gcacagcacc aggggcatcc ttggctccca ggagcccgac ttcaagggcg
      241 tccagcccta tgcggggatg cccaaggagg tgctgttcca gttctctggc caggcccgct
      301 accgcatacc tcgggagatc ctcttctggc tcacagtggc ttctgtgctg gtgctcatcg
      361 cggccaccat agccatcatt gccctctctc caaagtgcct agactggtgg caggaggggc
      421 ccatgtacca gatctaccca aggtctttca aggacagtaa caaggatggg aacggagatc
      481 tgaaaggtat tcaagataaa ctggactaca tcacagcttt aaatataaaa actgtttgga
      541 ttacttcatt ttataaatcg tcccttaaag atttcagata tggtgttgaa gatttccggg
      601 aagttgatcc catttttgga acgatggaag attttgagaa tctggttgca gccatacatg
      661 ataaaggttt aaaattaatc atcgatttca taccaaacca cacgagtgat aaacatattt
      721 ggtttcaatt gagtcggaca cggacaggaa aatatactga ttattatatc tggcatgact
      781 gtacccatga aaatggcaaa accattccac ccaacaactg gttaagtgtg tatggaaact
      841 ccagttggca ctttgacgaa gtgcgaaacc aatgttattt tcatcagttt atgaaagagc
      901 aacctgattt aaatttccgc aatcctgatg ttcaagaaga aataaaagaa attttacggt
      961 tctggctcac aaagggtgtt gatggtttta gtttggatgc tgttaaattc ctcctagaag
     1021 caaagcacct gagagatgag atccaagtaa ataagaccca aatcccggac acggtcacac
     1081 aatactcgga gctgtaccat gacttcacca ccacgcaggt gggaatgcac gacattgtcc
     1141 gcagcttccg gcagaccatg gaccaataca gcacggagcc cggcagatac aggttcatgg
     1201 ggactgaagc ctatgcagag agtattgaca ggaccgtgat gtactatgga ttgccattta
     1261 tccaagaagc tgattttccc ttcaacaatt acctcagcat gctagacact gtttctggga
     1321 acagcgtgta tgaggttatc acatcctgga tggaaaacat gccagaagga aaatggccta
     1381 actggatgat tggtggacca gacagttcac ggctgacttc gcgtttgggg aatcagtatg
     1441 tcaacgtgat gaacatgctt cttttcacac tccctggaac tcctataact tactatggag
     1501 aagaaattgg aatgggaaat attgtagccg caaatctcaa tgaaagctat gatattaata
     1561 cccttcgctc aaagtcacca atgcagtggg acaatagttc aaatgctggt ttttctgaag
     1621 ctagtaacac ctggttacct accaattcag attaccacac tgtgaatgtt gatgtccaaa
     1681 agactcagcc cagatcggct ttgaagttat atcaagattt aagtctactt catgccaatg
     1741 agctactcct caacaggggc tggttttgcc atttgaggaa tgacagccac tatgttgtgt
     1801 acacaagaga gctggatggc atcgacagaa tctttatcgt ggttctgaat tttggagaat
     1861 caacactgtt aaatctacat aatatgattt cgggccttcc cgctaaaatg agaataaggt
     1921 taagtaccaa ttctgccgac aaaggcagta aagttgatac aagtggcatt tttctggaca
     1981 agggagaggg actcatcttt gaacacaaca cgaagaatct ccttcatcgc caaacagctt
     2041 tcagagatag atgctttgtt tccaatcgag catgctattc cagtgtactg aacatactgt
     2101 atacctcgtg ttaggcacct ttatgaagag atgaagacac tggcatttca gtgggattgt
     2161 aagcatttgt aatagcttca tgtacagcat gctgcttggt gaacaatcat taattcttcg
     2221 atatttctgt agcttgaatg taactgcttt aagaaaggtt ctcaaatgtt ttgaaaaaaa
     2281 taaaatgttt aaaagtaaat tatggcttat aggagcttat aactttattc agatagcatc
     2341 aatcagggat gaccagaaca cattaggacc ccagattatt caaaaacttt aacgaatttt
     2401 aaggggaaga attttatctt ttcccttaaa atgcagtcat agaaattaga ggatgactca
     2461 ctgccacagt gtctaaaagc atttgctagc aaagaggcag gacactaatt tgtaaactgc
     2521 tcaactgttc tgactggaag ggaggcctgg agctctgcta tcaccaatcc ttcccttccc
     2581 tctactccac atccttctaa ggagcatgat ttgaaaatta ctttcctagg ttaatgggca
     2641 tgtgcatcaa tggagagaat agtataagca agtgagatgt agactaagca aaatttagat
     2701 ggagaagcac attttaaaaa attaataact taaaagtctc aagttattaa tttttttttt
     2761 gctaactcaa ttggaagtaa gactatgaaa tatttcagtg tgtttccaat tcccagttga
     2821 atgcagtgtt tcagaatttc aggtatttct taagatcctc gaaaacactg gtgctgtcaa
     2881 gtccaagttc ctcgtacagg aatttaattt gggctgtaat ctaaaagaaa cacattaaaa
     2941 aaattaaata gaaggccttt gtagtaaaa
//
