LOCUS       NM_003042               4478 bp    mRNA    linear   PRI 08-OCT-2024
DEFINITION  Homo sapiens solute carrier family 6 member 1 (SLC6A1), transcript
            variant 1, mRNA.
ACCESSION   NM_003042
VERSION     NM_003042.4
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 4478)
  AUTHORS   Tao,H., Wu,Z., Liu,Y., Zhang,X., Li,K. and Zhou,X.
  TITLE     Abnormal Weakening of DNA Methylation around the SLC6A1 Gene
            Promoter in Temporal Lobe Epilepsy
  JOURNAL   J Integr Neurosci 23 (9), 181 (2024)
   PUBMED   39344240
  REMARK    GeneRIF: Abnormal Weakening of DNA Methylation around the SLC6A1
            Gene Promoter in Temporal Lobe Epilepsy.
REFERENCE   2  (bases 1 to 4478)
  AUTHORS   Dahshi,H., Kalvakuntla,S., Lee,M. and Goodspeed,K.
  TITLE     Beyond the Diagnosis: Evaluation of Quality-of-Life Measures and
            Family Functioning in SLC6A1-Related Neurodevelopmental Disorder
  JOURNAL   Pediatr Neurol 155, 160-166 (2024)
   PUBMED   38663152
  REMARK    GeneRIF: Beyond the Diagnosis: Evaluation of Quality-of-Life
            Measures and Family Functioning in SLC6A1-Related
            Neurodevelopmental Disorder.
REFERENCE   3  (bases 1 to 4478)
  AUTHORS   Stefanski,A., Perez-Palma,E., Brunger,T., Montanucci,L., Gati,C.,
            Klockner,C., Johannesen,K.M., Goodspeed,K., Macnee,M., Deng,A.T.,
            Aledo-Serrano,A., Borovikov,A., Kava,M., Bouman,A.M.,
            Hajianpour,M.J., Pal,D.K., Engelen,M., Hagebeuk,E.E.O., Shinawi,M.,
            Heidlebaugh,A.R., Oetjens,K., Hoffman,T.L., Striano,P., Freed,A.S.,
            Futtrup,L., Balslev,T., Abuli,A., Danvoye,L., Lederer,D., Balci,T.,
            Nouri,M.N., Butler,E., Drewes,S., van Engelen,K., Howell,K.B.,
            Khoury,J., May,P., Trinidad,M., Froelich,S., Lemke,J.R., Tiller,J.,
            Freed,A.N., Kang,J.Q., Wuster,A., Moller,R.S. and Lal,D.
  TITLE     SLC6A1 variant pathogenicity, molecular function and phenotype: a
            genetic and clinical analysis
  JOURNAL   Brain 146 (12), 5198-5208 (2023)
   PUBMED   37647852
  REMARK    GeneRIF: SLC6A1 variant pathogenicity, molecular function and
            phenotype: a genetic and clinical analysis.
REFERENCE   4  (bases 1 to 4478)
  AUTHORS   Lindquist,B.E., Voskobiynyk,Y., Goodspeed,K. and Paz,J.T.
  TITLE     Patient-derived SLC6A1 variant S295L results in an epileptic
            phenotype similar to haploinsufficient mice
  JOURNAL   Epilepsia 64 (10), e214-e221 (2023)
   PUBMED   37501613
  REMARK    GeneRIF: Patient-derived SLC6A1 variant S295L results in an
            epileptic phenotype similar to haploinsufficient mice.
REFERENCE   5  (bases 1 to 4478)
  AUTHORS   Kondratyev,N.V., Alfimova,M.V., Kaleda,V.G., Lezheiko,T.V.,
            Mikhailova,V.A., Karpov,D.S., Ublinsky,M.V., Ushakov,V.L.,
            Lebedeva,I.S. and Golimbet,V.E.
  TITLE     Assessing the impact of the de novo SLC6A1 mutation in
            schizophrenia through a comprehensive case study
  JOURNAL   Psychiatry Res 327, 115399 (2023)
   PUBMED   37540943
  REMARK    GeneRIF: Assessing the impact of the de novo SLC6A1 mutation in
            schizophrenia through a comprehensive case study.
REFERENCE   6  (bases 1 to 4478)
  AUTHORS   Bismuth,Y., Kavanaugh,M.P. and Kanner,B.I.
  TITLE     Tyrosine 140 of the gamma-aminobutyric acid transporter GAT-1 plays
            a critical role in neurotransmitter recognition
  JOURNAL   J Biol Chem 272 (26), 16096-16102 (1997)
   PUBMED   9195904
REFERENCE   7  (bases 1 to 4478)
  AUTHORS   Bennett,E.R. and Kanner,B.I.
  TITLE     The membrane topology of GAT-1, a (Na+ + Cl-)-coupled
            gamma-aminobutyric acid transporter from rat brain
  JOURNAL   J Biol Chem 272 (2), 1203-1210 (1997)
   PUBMED   8995422
REFERENCE   8  (bases 1 to 4478)
  AUTHORS   Huang,F., Shi,L.J., Heng,H.H., Fei,J. and Guo,L.H.
  TITLE     Assignment of the human GABA transporter gene (GABATHG) locus to
            chromosome 3p24-p25
  JOURNAL   Genomics 29 (1), 302-304 (1995)
   PUBMED   8530094
REFERENCE   9  (bases 1 to 4478)
  AUTHORS   Goodspeed,K., Demarest,S., Johannesen,K., Kang,J., Lal,D. and
            Angione,K.
  TITLE     SLC6A1-Related Neurodevelopmental Disorder
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   36780407
REFERENCE   10 (bases 1 to 4478)
  AUTHORS   Nelson,H., Mandiyan,S. and Nelson,N.
  TITLE     Cloning of the human brain GABA transporter
  JOURNAL   FEBS Lett 269 (1), 181-184 (1990)
   PUBMED   2387399
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC024910.5, BC033904.1,
            BC057291.1 and DA162953.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 22, 2018 this sequence version replaced NM_003042.3.
            
            Summary: The protein encoded by this gene is a gamma-aminobutyric
            acid (GABA) transporter that localizes to the plasma membrane. The
            encoded protein removes GABA from the synaptic cleft, restoring it
            to presynaptic terminals. [provided by RefSeq, Jan 2017].
            
            Transcript Variant: This variant (1) represents the longest
            transcript and encodes the longest isoform (a). Variants 1 and 2
            both encode the same isoform (a).
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            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 :: SRR1803617.45161.1, BC057291.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1968968, SAMEA2145122
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000287766.10/ ENSP00000287766.4
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-182               AC024910.5         88819-89000         c
            183-194             AC024910.5         66065-66076         c
            195-1443            BC033904.1         177-1425
            1444-1502           BC057291.1         1438-1496
            1503-1958           BC033904.1         1485-1940
            1959-2304           DA162953.1         231-576
            2305-4478           AC024910.5         42501-44674         c
FEATURES             Location/Qualifiers
     source          1..4478
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="3"
                     /map="3p25.3"
     gene            1..4478
                     /gene="SLC6A1"
                     /gene_synonym="GABATHG; GABATR; GAT1; hGAT-1; MAE"
                     /note="solute carrier family 6 member 1"
                     /db_xref="GeneID:6529"
                     /db_xref="HGNC:HGNC:11042"
                     /db_xref="MIM:137165"
     exon            1..182
                     /gene="SLC6A1"
                     /gene_synonym="GABATHG; GABATR; GAT1; hGAT-1; MAE"
                     /inference="alignment:Splign:2.1.0"
     exon            183..244
                     /gene="SLC6A1"
                     /gene_synonym="GABATHG; GABATR; GAT1; hGAT-1; MAE"
                     /inference="alignment:Splign:2.1.0"
     exon            245..635
                     /gene="SLC6A1"
                     /gene_synonym="GABATHG; GABATR; GAT1; hGAT-1; MAE"
                     /inference="alignment:Splign:2.1.0"
     CDS             398..2197
                     /gene="SLC6A1"
                     /gene_synonym="GABATHG; GABATR; GAT1; hGAT-1; MAE"
                     /note="isoform a is encoded by transcript variant 1;
                     sodium- and chloride-dependent GABA transporter 1; solute
                     carrier family 6 (neurotransmitter transporter, GABA),
                     member 1; solute carrier family 6 (neurotransmitter
                     transporter), member 1"
                     /codon_start=1
                     /product="sodium- and chloride-dependent GABA transporter
                     1 isoform a"
                     /protein_id="NP_003033.3"
                     /db_xref="CCDS:CCDS2603.1"
                     /db_xref="GeneID:6529"
                     /db_xref="HGNC:HGNC:11042"
                     /db_xref="MIM:137165"
                     /translation="MATNGSKVADGQISTEVSEAPVANDKPKTLVVKVQKKAADLPDR
                     DTWKGRFDFLMSCVGYAIGLGNVWRFPYLCGKNGGGAFLIPYFLTLIFAGVPLFLLEC
                     SLGQYTSIGGLGVWKLAPMFKGVGLAAAVLSFWLNIYYIVIISWAIYYLYNSFTTTLP
                     WKQCDNPWNTDRCFSNYSMVNTTNMTSAVVEFWERNMHQMTDGLDKPGQIRWPLAITL
                     AIAWILVYFCIWKGVGWTGKVVYFSATYPYIMLIILFFRGVTLPGAKEGILFYITPNF
                     RKLSDSEVWLDAATQIFFSYGLGLGSLIALGSYNSFHNNVYRDSIIVCCINSCTSMFA
                     GFVIFSIVGFMAHVTKRSIADVAASGPGLAFLAYPEAVTQLPISPLWAILFFSMLLML
                     GIDSQFCTVEGFITALVDEYPRLLRNRRELFIAAVCIISYLIGLSNITQGGIYVFKLF
                     DYYSASGMSLLFLVFFECVSISWFYGVNRFYDNIQEMVGSRPCIWWKLCWSFFTPIIV
                     AGVFIFSAVQMTPLTMGNYVFPKWGQGVGWLMALSSMVLIPGYMAYMFLTLKGSLKQR
                     IQVMVQPSEDIVRPENGPEQPQAGSSTSKEAYI"
     exon            636..767
                     /gene="SLC6A1"
                     /gene_synonym="GABATHG; GABATR; GAT1; hGAT-1; MAE"
                     /inference="alignment:Splign:2.1.0"
     exon            768..868
                     /gene="SLC6A1"
                     /gene_synonym="GABATHG; GABATR; GAT1; hGAT-1; MAE"
                     /inference="alignment:Splign:2.1.0"
     exon            869..978
                     /gene="SLC6A1"
                     /gene_synonym="GABATHG; GABATR; GAT1; hGAT-1; MAE"
                     /inference="alignment:Splign:2.1.0"
     exon            979..1111
                     /gene="SLC6A1"
                     /gene_synonym="GABATHG; GABATR; GAT1; hGAT-1; MAE"
                     /inference="alignment:Splign:2.1.0"
     exon            1112..1246
                     /gene="SLC6A1"
                     /gene_synonym="GABATHG; GABATR; GAT1; hGAT-1; MAE"
                     /inference="alignment:Splign:2.1.0"
     exon            1247..1350
                     /gene="SLC6A1"
                     /gene_synonym="GABATHG; GABATR; GAT1; hGAT-1; MAE"
                     /inference="alignment:Splign:2.1.0"
     exon            1351..1475
                     /gene="SLC6A1"
                     /gene_synonym="GABATHG; GABATR; GAT1; hGAT-1; MAE"
                     /inference="alignment:Splign:2.1.0"
     exon            1476..1588
                     /gene="SLC6A1"
                     /gene_synonym="GABATHG; GABATR; GAT1; hGAT-1; MAE"
                     /inference="alignment:Splign:2.1.0"
     exon            1589..1720
                     /gene="SLC6A1"
                     /gene_synonym="GABATHG; GABATR; GAT1; hGAT-1; MAE"
                     /inference="alignment:Splign:2.1.0"
     exon            1721..1823
                     /gene="SLC6A1"
                     /gene_synonym="GABATHG; GABATR; GAT1; hGAT-1; MAE"
                     /inference="alignment:Splign:2.1.0"
     exon            1824..1924
                     /gene="SLC6A1"
                     /gene_synonym="GABATHG; GABATR; GAT1; hGAT-1; MAE"
                     /inference="alignment:Splign:2.1.0"
     exon            1925..2092
                     /gene="SLC6A1"
                     /gene_synonym="GABATHG; GABATR; GAT1; hGAT-1; MAE"
                     /inference="alignment:Splign:2.1.0"
     exon            2093..4478
                     /gene="SLC6A1"
                     /gene_synonym="GABATHG; GABATR; GAT1; hGAT-1; MAE"
                     /inference="alignment:Splign:2.1.0"
     regulatory      4456..4461
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SLC6A1"
                     /gene_synonym="GABATHG; GABATR; GAT1; hGAT-1; MAE"
                     /note="hexamer: AATAAA"
     polyA_site      4478
                     /gene="SLC6A1"
                     /gene_synonym="GABATHG; GABATR; GAT1; hGAT-1; MAE"
                     /note="major polyA site"
ORIGIN      
        1 gccctcggaa gaccgagaca gcggagaggt tgcgggtgag ctgcgctgag cccaggagcc
       61 gaggagtcgg gagcgcagta gcgctgagcc cgagcccgag cggccccgcg tcccgagcgc
      121 atcggagcgg ccgagccgcc cggatgcagc gcctgtcccg ggcagcgcag ccccggccgc
      181 aggatctcac ccagggtggc agaaggaggc cttctggagc tgacccaccc ccgacgacca
      241 tcagggtgag gcaactccaa ggtcctactc tctttctgtg cctgttaccc accccgtcct
      301 cctagggtgc ccttgagccg caaaactgct gtccacgtgg accgggggtg acatcgcacg
      361 tccatctgcc aggacccctg cgtccaaatt ccgagacatg gcgaccaacg gcagcaaggt
      421 ggccgacggg cagatctcca ccgaggtcag cgaggcccct gtggccaatg acaagcccaa
      481 aaccttggtg gtcaaggtgc agaagaaggc ggcagacctc cccgaccggg acacgtggaa
      541 gggccgcttc gacttcctca tgtcctgtgt gggctatgcc atcggcctgg gcaacgtctg
      601 gaggttcccc tatctctgcg ggaaaaatgg tgggggagcc ttcctgatcc cctatttcct
      661 gacactcatc tttgcggggg tcccactctt cctgctggag tgctccctgg gccagtacac
      721 ctccatcggg gggctagggg tatggaagct ggctcctatg ttcaagggcg tgggccttgc
      781 ggctgctgtg ctatcattct ggctgaacat ctactacatc gtcatcatct cctgggccat
      841 ttactacctg tacaactcct tcaccacgac actgccgtgg aaacagtgcg acaacccctg
      901 gaacacagac cgctgcttct ccaactacag catggtcaac actaccaaca tgaccagcgc
      961 tgtggtggag ttctgggagc gcaacatgca tcagatgacg gacgggctgg ataagccagg
     1021 tcagatccgc tggccactgg ccatcacgct ggccatcgcc tggatccttg tgtatttctg
     1081 tatctggaag ggtgttggct ggactggaaa ggtggtctac ttttcagcca cataccccta
     1141 catcatgctg atcatcctgt tcttccgtgg agtgacgctg cccggggcca aggagggcat
     1201 cctcttctac atcacaccca acttccgcaa gctgtctgac tccgaggtgt ggctggatgc
     1261 ggcaacccag atcttcttct catacgggct gggcctgggg tccctgatcg ctctcgggag
     1321 ctacaactct ttccacaaca atgtctacag ggactccatc atcgtctgct gcatcaattc
     1381 gtgcaccagc atgttcgcag gattcgtcat cttctccatc gtgggcttca tggcccatgt
     1441 caccaagagg tccattgctg atgtggcggc ctcaggcccc gggctggcgt tcctggcata
     1501 cccagaggcg gtgacccagc tgcctatctc cccactctgg gccatcctct tcttctccat
     1561 gctgttgatg ctgggcattg acagccagtt ctgcactgtg gagggcttca tcacagccct
     1621 ggtggatgag taccccaggc tcctccgcaa ccgcagagag ctcttcattg ctgctgtctg
     1681 catcatctcc tacctgatcg gtctctctaa catcactcag gggggtattt atgtcttcaa
     1741 actctttgac tactactctg ccagtggcat gagcctgctg ttcctcgtgt tctttgaatg
     1801 tgtctctatt tcctggtttt acggtgtcaa ccgattctat gacaatatcc aagagatggt
     1861 tggatccagg ccctgcatct ggtggaaact ctgctggtct ttcttcacac caatcattgt
     1921 ggcgggcgtg ttcattttca gtgctgtgca gatgacgcca ctcaccatgg gaaactatgt
     1981 tttccccaag tggggccagg gtgtgggctg gctgatggct ctgtcttcca tggtcctcat
     2041 ccccgggtac atggcctaca tgttcctcac cttaaagggc tccctgaagc agcgcatcca
     2101 agtcatggtc cagcccagcg aagacatcgt tcgcccagag aatggtcctg agcagcccca
     2161 ggcgggcagc tccaccagca aggaggccta catctagggt gggggccact caccgacccg
     2221 acactctcac cccccgacct ggctgagtgc gaccaccact tgatgtctga ggataccttc
     2281 catctcaacc tacctcgagt ggcgagtcca gacaccatca ccacgcagag aggggaggtg
     2341 ggaggacagt tagacccctg ggtgggccct gccgtgggca aggatacccg gtggcttctg
     2401 gcacctggcg ggctggtgac ctttttaatc caggccccat cagcatccca cgatcggcct
     2461 tggtaaccgc cgcggtagat catttttatc ccgccaggga gtgtgatgca ggaagaccac
     2521 atgcgctcct ggcttttaaa cctgttcctg actgttctct tactgccgaa acccttgact
     2581 gttatctcgg actttgcagg agttcctttc cctccgaacg ctgctccatg cacaggaaaa
     2641 gggcattttg tacaatgggg acttcccggg aacgcttgct cttaagtacc agaagccggc
     2701 ggagctctgg ctttcgtgtt tttggttttc tccttcccaa ggcagctgga ttgaaaaaac
     2761 aaaacaaaac aaaaaaaccc aggggcgtca gtcgatattc ccagggccgc ttctcctgca
     2821 gtctgtggag cgtccttgtc cccgccgccg gaatgaatga gcattctgca gcccgatgtc
     2881 cctgtcccct cctcgccggg ccattctgat tggacctggc ccagtgcaat ctgtccagac
     2941 aagccctgct tgctggaaaa ctgccacaag cacaattgat ctctttttat cgccattcca
     3001 ggggcctcag gtcctactgg ggaaacttcc tataccggag ctccagtttc tcttaagctg
     3061 cccaatttca cagagtacaa aatagttgta ggggaaatca aggtgaagga tctgtccgac
     3121 agtcaagacg gatccacagt aatctttcgg tctccttaaa ctaccaccct cgctgccacc
     3181 caccccaagc tgctgccgcc tcaccttcct tgaaatttct cagcgggagt ctcctcactg
     3241 ccactaaaat ccacccagcc cactaactga ggagctagtg ttaatccaga gaaccccccg
     3301 caatgtgctt ccgagattca gactgcttca ttgggaagta tgatttgttc ctttctggaa
     3361 ttgggctccg tggtggcggc ggcacttcaa gcaaagacag tttcttgcaa gctccagtag
     3421 ctccgcgtgt ctcatttgcc aggaagatgg gttcccacgt agcaaatcgt acattgtgcc
     3481 ctgtagctcc ttagctagtt agctcacaag ccgtgtttta tgactaatcc ttaataacta
     3541 tggtaaataa ctgtgactgt ggggttttta atctcttgtc attctcatcc aaaagtgacc
     3601 agcataccag ttcttgcaat aagatattac cctcagaata ttaagcacat tattgtagag
     3661 aaaaaaaaat atgtgtacac atatgaacgc acaacatgca cattcatcct cacatgtggc
     3721 acgtaaggtc tcatttgata ttgtgtagga aatctgaagc cttttcctga ggtcatctgt
     3781 aaaatagtct cattgccaag gcatccccag tgccagctgg tgaatccatg atcaaaatgc
     3841 atacgtattg ttaaatgata aggtttagaa tgacaggaac ccatcactgt gtctcatggt
     3901 cccacttccc catctgtgtg tgaattcctt tagactaagg gcaggaagac ttccagcttt
     3961 ctctttgttc ttcaatgtga aactgagacc aagtctctct aagacaaatg cagtgtattt
     4021 aatgtttgta agcaattcta agtgagatgt ttggcaagaa atcccctaac tgatttccat
     4081 ccaaacctac cttatagagc acaatattaa gtgttgtaca attactgtga gaactgtgaa
     4141 tatgtgtaac ttttttttag tatttgcccg gggggaaaaa gatattgtat tatcatatat
     4201 gcttttttgc aataaggatt tattctcaga acaccaagta aatctatctc tatataaaaa
     4261 atatatgtaa tatatacata ttcaaagtat atacagagcc tgttttaaaa aatacagtat
     4321 tatttagtaa aattatctgt tctatggacc aaatgtaaaa tatttataaa tgaagatgca
     4381 ttttaaatgt ctataaatgg tgtcataact agagcacggg cgttatgtaa gtttctaaga
     4441 atttagagga taaataataa aggttctatg atatacaa
//
