LOCUS       NM_016615               2188 bp    mRNA    linear   PRI 12-DEC-2024
DEFINITION  Homo sapiens solute carrier family 6 member 13 (SLC6A13),
            transcript variant 1, mRNA.
ACCESSION   NM_016615
VERSION     NM_016615.5
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 2188)
  AUTHORS   Zhang,H., Zong,R., Wu,H., Jiang,J., Liu,C. and Liu,S.
  TITLE     Transcription factor ASCL1 targets SLC6A13 to inhibit the
            progression of hepatocellular carcinoma via the
            glycine-inflammasome signaling
  JOURNAL   Biomol Biomed 24 (6), 1606-1619 (2024)
   PUBMED   38780447
  REMARK    GeneRIF: Transcription factor ASCL1 targets SLC6A13 to inhibit the
            progression of hepatocellular carcinoma via the
            glycine-inflammasome signaling.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2188)
  AUTHORS   Haenig,C., Atias,N., Taylor,A.K., Mazza,A., Schaefer,M.H., Russ,J.,
            Riechers,S.P., Jain,S., Coughlin,M., Fontaine,J.F., Freibaum,B.D.,
            Brusendorf,L., Zenkner,M., Porras,P., Stroedicke,M., Schnoegl,S.,
            Arnsburg,K., Boeddrich,A., Pigazzini,L., Heutink,P., Taylor,J.P.,
            Kirstein,J., Andrade-Navarro,M.A., Sharan,R. and Wanker,E.E.
  TITLE     Interactome Mapping Provides a Network of Neurodegenerative Disease
            Proteins and Uncovers Widespread Protein Aggregation in Affected
            Brains
  JOURNAL   Cell Rep 32 (7), 108050 (2020)
   PUBMED   32814053
REFERENCE   3  (bases 1 to 2188)
  AUTHORS   Sweeney,M.D., Zhao,Z., Montagne,A., Nelson,A.R. and Zlokovic,B.V.
  TITLE     Blood-Brain Barrier: From Physiology to Disease and Back
  JOURNAL   Physiol Rev 99 (1), 21-78 (2019)
   PUBMED   30280653
  REMARK    Review article
REFERENCE   4  (bases 1 to 2188)
  AUTHORS   Schlessinger,A., Wittwer,M.B., Dahlin,A., Khuri,N., Bonomi,M.,
            Fan,H., Giacomini,K.M. and Sali,A.
  TITLE     High selectivity of the gamma-aminobutyric acid transporter 2
            (GAT-2, SLC6A13) revealed by structure-based approach
  JOURNAL   J Biol Chem 287 (45), 37745-37756 (2012)
   PUBMED   22932902
  REMARK    GeneRIF: Results suggest that gamma-aminobutyric acid transporter 2
            GAT-2 is a high selectivity/low affinity transporter.
REFERENCE   5  (bases 1 to 2188)
  AUTHORS   Pallo,A., Simon,A., Bencsura,A., Heja,L. and Kardos,J.
  TITLE     Substrate-Na+ complex formation: coupling mechanism for
            gamma-aminobutyrate symporters
  JOURNAL   Biochem Biophys Res Commun 385 (2), 210-214 (2009)
   PUBMED   19450549
  REMARK    GeneRIF: homology models of hGAT-2 and hGAT-3 were built and
            searched for (i) substrate conformation, (ii) prediction of
            substrate (inhibitor) interaction, and (iii) distinguishable
            allosteric Zn2+ inhibition by combining docking and MD
            calculations.
REFERENCE   6  (bases 1 to 2188)
  AUTHORS   Gonzales,P.A., Pisitkun,T., Hoffert,J.D., Tchapyjnikov,D.,
            Star,R.A., Kleta,R., Wang,N.S. and Knepper,M.A.
  TITLE     Large-scale proteomics and phosphoproteomics of urinary exosomes
  JOURNAL   J Am Soc Nephrol 20 (2), 363-379 (2009)
   PUBMED   19056867
REFERENCE   7  (bases 1 to 2188)
  AUTHORS   Christiansen,B., Meinild,A.K., Jensen,A.A. and Brauner-Osborne,H.
  TITLE     Cloning and characterization of a functional human
            gamma-aminobutyric acid (GABA) transporter, human GAT-2
  JOURNAL   J Biol Chem 282 (27), 19331-19341 (2007)
   PUBMED   17502375
REFERENCE   8  (bases 1 to 2188)
  AUTHORS   Hoglund,P.J., Adzic,D., Scicluna,S.J., Lindblom,J. and
            Fredriksson,R.
  TITLE     The repertoire of solute carriers of family 6: identification of
            new human and rodent genes
  JOURNAL   Biochem Biophys Res Commun 336 (1), 175-189 (2005)
   PUBMED   16125675
REFERENCE   9  (bases 1 to 2188)
  AUTHORS   Gong,Y., Zhang,M., Cui,L. and Minuk,G.Y.
  TITLE     Sequence and chromosomal assignment of a human novel cDNA:
            similarity to gamma-aminobutyric acid transporter
  JOURNAL   Can J Physiol Pharmacol 79 (12), 977-984 (2001)
   PUBMED   11824941
REFERENCE   10 (bases 1 to 2188)
  AUTHORS   Borden,L.A., Smith,K.E., Hartig,P.R., Branchek,T.A. and
            Weinshank,R.L.
  TITLE     Molecular heterogeneity of the gamma-aminobutyric acid (GABA)
            transport system. Cloning of two novel high affinity GABA
            transporters from rat brain
  JOURNAL   J Biol Chem 267 (29), 21098-21104 (1992)
   PUBMED   1400419
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            DA374290.1, AK313511.1, BM662288.1 and DB540466.1.
            
            On Nov 22, 2018 this sequence version replaced NM_016615.4.
            
            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 :: BC022392.1, SRR1803616.100337.1
                                           [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1968189 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000343164.9/ ENSP00000339260.4
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-7                 DA374290.1         38-44
            8-1862              AK313511.1         1-1855
            1863-2177           BM662288.1         28-342              c
            2178-2188           DB540466.1         479-489
FEATURES             Location/Qualifiers
     source          1..2188
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="12"
                     /map="12p13.33"
     gene            1..2188
                     /gene="SLC6A13"
                     /gene_synonym="GAT-2; GAT2; GAT3"
                     /note="solute carrier family 6 member 13"
                     /db_xref="GeneID:6540"
                     /db_xref="HGNC:HGNC:11046"
                     /db_xref="MIM:615097"
     exon            1..48
                     /gene="SLC6A13"
                     /gene_synonym="GAT-2; GAT2; GAT3"
                     /inference="alignment:Splign:2.1.0"
     exon            49..255
                     /gene="SLC6A13"
                     /gene_synonym="GAT-2; GAT2; GAT3"
                     /inference="alignment:Splign:2.1.0"
     CDS             54..1862
                     /gene="SLC6A13"
                     /gene_synonym="GAT-2; GAT2; GAT3"
                     /note="isoform 1 is encoded by transcript variant 1; GABA
                     transport protein; sodium- and chloride-dependent GABA
                     transporter 2; solute carrier family 6 (neurotransmitter
                     transporter, GABA), member 13; solute carrier family 6
                     (neurotransmitter transporter), member 13"
                     /codon_start=1
                     /product="sodium- and chloride-dependent GABA transporter
                     2 isoform 1"
                     /protein_id="NP_057699.2"
                     /db_xref="CCDS:CCDS8502.1"
                     /db_xref="GeneID:6540"
                     /db_xref="HGNC:HGNC:11046"
                     /db_xref="MIM:615097"
                     /translation="MDSRVSGTTSNGETKPVYPVMEKKEEDGTLERGHWNNKMEFVLS
                     VAGEIIGLGNVWRFPYLCYKNGGGAFFIPYLVFLFTCGIPVFLLETALGQYTSQGGVT
                     AWRKICPIFEGIGYASQMIVILLNVYYIIVLAWALFYLFSSFTIDLPWGGCYHEWNTE
                     HCMEFQKTNGSLNGTSENATSPVIEFWERRVLKISDGIQHLGALRWELALCLLLAWVI
                     CYFCIWKGVKSTGKVVYFTATFPYLMLVVLLIRGVTLPGAAQGIQFYLYPNLTRLWDP
                     QVWMDAGTQIFFSFAICLGCLTALGSYNKYHNNCYRDCIALCFLNSGTSFVAGFAIFS
                     ILGFMSQEQGVPISEVAESGPGLAFIAYPRAVVMLPFSPLWACCFFFMVVLLGLDSQF
                     VCVESLVTALVDMYPHVFRKKNRREVLILGVSVVSFLVGLIMLTEGGMYVFQLFDYYA
                     ASGMCLLFVAIFESLCVAWVYGAKRFYDNIEDMIGYRPWPLIKYCWLFLTPAVCTATF
                     LFSLIKYTPLTYNKKYTYPWWGDALGWLLALSSMVCIPAWSLYRLGTLKGPFRERIRQ
                     LMCPAEDLPQRNPAGPSAPATPRTSLLRLTELESHC"
     exon            256..390
                     /gene="SLC6A13"
                     /gene_synonym="GAT-2; GAT2; GAT3"
                     /inference="alignment:Splign:2.1.0"
     exon            391..531
                     /gene="SLC6A13"
                     /gene_synonym="GAT-2; GAT2; GAT3"
                     /inference="alignment:Splign:2.1.0"
     exon            532..616
                     /gene="SLC6A13"
                     /gene_synonym="GAT-2; GAT2; GAT3"
                     /inference="alignment:Splign:2.1.0"
     exon            617..749
                     /gene="SLC6A13"
                     /gene_synonym="GAT-2; GAT2; GAT3"
                     /inference="alignment:Splign:2.1.0"
     exon            750..884
                     /gene="SLC6A13"
                     /gene_synonym="GAT-2; GAT2; GAT3"
                     /inference="alignment:Splign:2.1.0"
     exon            885..988
                     /gene="SLC6A13"
                     /gene_synonym="GAT-2; GAT2; GAT3"
                     /inference="alignment:Splign:2.1.0"
     exon            989..1113
                     /gene="SLC6A13"
                     /gene_synonym="GAT-2; GAT2; GAT3"
                     /inference="alignment:Splign:2.1.0"
     exon            1114..1226
                     /gene="SLC6A13"
                     /gene_synonym="GAT-2; GAT2; GAT3"
                     /inference="alignment:Splign:2.1.0"
     exon            1227..1364
                     /gene="SLC6A13"
                     /gene_synonym="GAT-2; GAT2; GAT3"
                     /inference="alignment:Splign:2.1.0"
     exon            1365..1467
                     /gene="SLC6A13"
                     /gene_synonym="GAT-2; GAT2; GAT3"
                     /inference="alignment:Splign:2.1.0"
     exon            1468..1568
                     /gene="SLC6A13"
                     /gene_synonym="GAT-2; GAT2; GAT3"
                     /inference="alignment:Splign:2.1.0"
     exon            1569..1739
                     /gene="SLC6A13"
                     /gene_synonym="GAT-2; GAT2; GAT3"
                     /inference="alignment:Splign:2.1.0"
     exon            1740..2188
                     /gene="SLC6A13"
                     /gene_synonym="GAT-2; GAT2; GAT3"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2164..2169
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SLC6A13"
                     /gene_synonym="GAT-2; GAT2; GAT3"
                     /note="hexamer: ATTAAA"
     polyA_site      2188
                     /gene="SLC6A13"
                     /gene_synonym="GAT-2; GAT2; GAT3"
                     /note="major polyA site"
ORIGIN      
        1 agataattct tctcccctga ctggacctct ggcagcagct tcactaaggt gggatggata
       61 gcagggtctc aggcacaacc agtaatggag agacaaaacc agtgtatcca gtcatggaaa
      121 agaaggagga agatggcacc ctggagcggg ggcactggaa caacaagatg gagtttgtgc
      181 tgtcagtggc tggggagatc attggcttag gcaacgtctg gaggtttccc tatctctgct
      241 acaaaaatgg gggaggtgcc ttcttcatcc cctacctcgt cttcctcttt acctgtggca
      301 ttcctgtctt ccttctggag acagcactag gccagtacac tagccaggga ggcgtcacag
      361 cctggaggaa gatctgcccc atctttgagg gcattggcta tgcctcccag atgatcgtca
      421 tcctcctcaa cgtctactac atcattgtgt tggcctgggc cctgttctac ctcttcagca
      481 gcttcaccat cgacctgccc tggggcggct gctaccatga gtggaacaca gaacactgta
      541 tggagttcca gaagaccaac ggctccctga atggtacctc tgagaatgcc acctctcctg
      601 tcatcgagtt ctgggagcgg cgggtcttga agatctctga tgggatccag cacctggggg
      661 ccctgcgctg ggagctggct ctgtgcctcc tgctggcctg ggtcatctgc tacttctgca
      721 tctggaaggg ggtgaagtcc acaggcaagg tggtgtactt cacggccaca tttccttacc
      781 tcatgctggt ggtcctgtta attcgagggg tgacgttgcc tggggcagcc caaggaattc
      841 agttttacct gtacccaaac ctcacgcgtc tgtgggatcc ccaggtgtgg atggatgcag
      901 gcacccagat attcttctcc ttcgccatct gtcttgggtg cctgacagcc ctgggcagct
      961 acaacaagta ccacaacaac tgctacaggg actgcatcgc cctctgcttc ctcaacagcg
     1021 gcaccagctt tgtggccggc tttgccatct tctccatcct gggcttcatg tctcaggagc
     1081 agggggtgcc catttctgag gtggccgagt caggccctgg cctggctttc atcgcttacc
     1141 cgcgggctgt ggtgatgctg cccttctctc ctctctgggc ctgctgtttc ttcttcatgg
     1201 tcgttctcct gggactggat agccagtttg tgtgtgtaga aagcctggtg acagcgctgg
     1261 tggacatgta ccctcacgtg ttccgcaaga agaaccggag ggaagtcctc atccttggag
     1321 tatctgtcgt ctccttcctt gtggggctga tcatgctcac agagggcgga atgtacgtgt
     1381 tccagctctt tgactactat gcggccagtg gcatgtgcct cctgttcgtg gccatcttcg
     1441 agtccctctg tgtggcttgg gtttacggag ccaagcgctt ctacgacaac atcgaagaca
     1501 tgattgggta caggccatgg cctcttatca aatactgttg gctcttcctc acaccagctg
     1561 tgtgcacagc cacctttctc ttctccctga taaagtacac tccgctgacc tacaacaaga
     1621 agtacacgta cccgtggtgg ggcgatgccc tgggctggct cctggctctg tcctccatgg
     1681 tctgcattcc tgcctggagc ctctacagac tcggaaccct caagggcccc ttcagagaga
     1741 gaatccgtca gctcatgtgc ccagccgagg acctgcccca gcggaaccca gcaggaccct
     1801 cggctcccgc cacccccagg acctcactgc tcagactcac agagctagag tctcactgct
     1861 agggggcagg cccttggatg gtgcctgtgt gcctggcctt ggggatggct gtggagggaa
     1921 cgtggcagaa gcagccccat gtgcttccct gcccccgacc tggagtggat aagacaagag
     1981 gggtattttg gagtccacct gctgagctgg aggcctccca ctgcaacttt tcagctcagg
     2041 ggttgttgaa cagatgtgaa aggccagtgc caagagtgtc cctctgagac ccttgggaag
     2101 ctgggtgggg gctggtaggt ggggcgagac ttgctggctt cgggccctct catccttcat
     2161 tccattaaat ccacattctt cccgctga
//
