LOCUS       NM_001024845            3206 bp    mRNA    linear   PRI 12-OCT-2024
DEFINITION  Homo sapiens solute carrier family 6 member 9 (SLC6A9), transcript
            variant 3, mRNA.
ACCESSION   NM_001024845
VERSION     NM_001024845.3
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 3206)
  AUTHORS   Wei,Y., Li,R., Meng,Y., Hu,T., Zhao,J., Gao,Y., Bai,Q., Li,N. and
            Zhao,Y.
  TITLE     Transport mechanism and pharmacology of the human GlyT1
  JOURNAL   Cell 187 (7), 1719-1732 (2024)
   PUBMED   38513663
  REMARK    GeneRIF: Transport mechanism and pharmacology of the human GlyT1.
REFERENCE   2  (bases 1 to 3206)
  AUTHORS   Piniella,D. and Zafra,F.
  TITLE     Functional crosstalk of the glycine transporter GlyT1 and NMDA
            receptors
  JOURNAL   Neuropharmacology 232, 109514 (2023)
   PUBMED   37003571
  REMARK    GeneRIF: Functional crosstalk of the glycine transporter GlyT1 and
            NMDA receptors.
            Review article
REFERENCE   3  (bases 1 to 3206)
  AUTHORS   Zhang,Y.W., Uchendu,S., Leone,V., Bradshaw,R.T., Sangwa,N.,
            Forrest,L.R. and Rudnick,G.
  TITLE     Chloride-dependent conformational changes in the GlyT1 glycine
            transporter
  JOURNAL   Proc Natl Acad Sci U S A 118 (10) (2021)
   PUBMED   33658361
  REMARK    GeneRIF: Chloride-dependent conformational changes in the GlyT1
            glycine transporter.
REFERENCE   4  (bases 1 to 3206)
  AUTHORS   Shahsavar,A., Stohler,P., Bourenkov,G., Zimmermann,I., Siegrist,M.,
            Guba,W., Pinard,E., Sinning,S., Seeger,M.A., Schneider,T.R.,
            Dawson,R.J.P. and Nissen,P.
  TITLE     Structural insights into the inhibition of glycine reuptake
  JOURNAL   Nature 591 (7851), 677-681 (2021)
   PUBMED   33658720
  REMARK    GeneRIF: Structural insights into the inhibition of glycine
            reuptake.
REFERENCE   5  (bases 1 to 3206)
  AUTHORS   Mademont-Soler,I., Casellas-Vidal,D., Trujillo,A.,
            Espuna-Capote,N., Maroto,A., Garcia-Gonzalez,M.D.M., Ruiz,M.D.,
            Diego-Alvarez,D., Queralt,X., Perapoch,J. and Obon,M.
  TITLE     GLYT1 encephalopathy: Further delineation of disease phenotype and
            discussion of pathophysiological mechanisms
  JOURNAL   Am J Med Genet A 185 (2), 476-485 (2021)
   PUBMED   33269555
  REMARK    GeneRIF: GLYT1 encephalopathy: Further delineation of disease
            phenotype and discussion of pathophysiological mechanisms.
REFERENCE   6  (bases 1 to 3206)
  AUTHORS   Olivares,L., Aragon,C., Gimenez,C. and Zafra,F.
  TITLE     The role of N-glycosylation in the targeting and activity of the
            GLYT1 glycine transporter
  JOURNAL   J Biol Chem 270 (16), 9437-9442 (1995)
   PUBMED   7721869
REFERENCE   7  (bases 1 to 3206)
  AUTHORS   Jones,E.M., Fernald,A., Bell,G.I. and Le Beau,M.M.
  TITLE     Assignment of SLC6A9 to human chromosome band 1p33 by in situ
            hybridization
  JOURNAL   Cytogenet Cell Genet 71 (3), 211 (1995)
   PUBMED   7587377
REFERENCE   8  (bases 1 to 3206)
  AUTHORS   Kim,K.M., Kingsmore,S.F., Han,H., Yang-Feng,T.L., Godinot,N.,
            Seldin,M.F., Caron,M.G. and Giros,B.
  TITLE     Cloning of the human glycine transporter type 1: molecular and
            pharmacological characterization of novel isoform variants and
            chromosomal localization of the gene in the human and mouse genomes
  JOURNAL   Mol Pharmacol 45 (4), 608-617 (1994)
   PUBMED   8183239
REFERENCE   9  (bases 1 to 3206)
  AUTHORS   Borowsky,B., Mezey,E. and Hoffman,B.J.
  TITLE     Two glycine transporter variants with distinct localization in the
            CNS and peripheral tissues are encoded by a common gene
  JOURNAL   Neuron 10 (5), 851-863 (1993)
   PUBMED   8494645
REFERENCE   10 (bases 1 to 3206)
  AUTHORS   Kurolap,A., Hershkovitz,T. and Baris,H.N.
  TITLE     GLYT1 Encephalopathy
  JOURNAL   (in) Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE and
            Amemiya A (Eds.);
            GENEREVIEWS(R);
            (1993)
   PUBMED   29190063
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from CN354684.1, S70609.1,
            AI884725.1 and AL139220.13.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Jun 2, 2019 this sequence version replaced NM_001024845.2.
            
            Summary: The amino acid glycine acts as an inhibitory
            neurotransmitter in the central nervous system. The protein encoded
            by this gene is one of two transporters that stop glycine signaling
            by removing it from the synaptic cleft. [provided by RefSeq, Jun
            2016].
            
            Transcript Variant: This variant (3) differs in the 5' UTR and
            coding region compared to variant 2. The resulting isoform (3) is
            shorter and has a distinct N-terminus compared to isoform 2.
            Variants 3 and 9 both encode the same isoform (3).
            
            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 :: SRR1660809.29189.1,
                                           SRR1803616.166028.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMEA1965299,
                                           SAMEA1966682 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000372310.8/ ENSP00000361384.4
            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
            1-360               CN354684.1         141-500
            361-1140            S70609.1           529-1308
            1141-1488           AI884725.1         14-361              c
            1489-2066           S70609.1           1657-2234
            2067-3206           AL139220.13        11774-12913         c
FEATURES             Location/Qualifiers
     source          1..3206
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="1"
                     /map="1p34.1"
     gene            1..3206
                     /gene="SLC6A9"
                     /gene_synonym="GCENSG; GLYT1"
                     /note="solute carrier family 6 member 9"
                     /db_xref="GeneID:6536"
                     /db_xref="HGNC:HGNC:11056"
                     /db_xref="MIM:601019"
     exon            1..157
                     /gene="SLC6A9"
                     /gene_synonym="GCENSG; GLYT1"
                     /inference="alignment:Splign:2.1.0"
     exon            158..272
                     /gene="SLC6A9"
                     /gene_synonym="GCENSG; GLYT1"
                     /inference="alignment:Splign:2.1.0"
     CDS             243..2144
                     /gene="SLC6A9"
                     /gene_synonym="GCENSG; GLYT1"
                     /note="isoform 3 is encoded by transcript variant 3;
                     sodium- and chloride-dependent glycine transporter 1;
                     glyT-1; solute carrier family 6 (neurotransmitter
                     transporter, glycine), member 9"
                     /codon_start=1
                     /product="sodium- and chloride-dependent glycine
                     transporter 1 isoform 3"
                     /protein_id="NP_001020016.1"
                     /db_xref="CCDS:CCDS30695.1"
                     /db_xref="GeneID:6536"
                     /db_xref="HGNC:HGNC:11056"
                     /db_xref="MIM:601019"
                     /translation="MVGKGAKGMLNGAVPSEATKRDQNLKRGNWGNQIEFVLTSVGYA
                     VGLGNVWRFPYLCYRNGGGAFMFPYFIMLIFCGIPLFFMELSFGQFASQGCLGVWRIS
                     PMFKGVGYGMMVVSTYIGIYYNVVICIAFYYFFSSMTHVLPWAYCNNPWNTHDCAGVL
                     DASNLTNGSRPAALPSNLSHLLNHSLQRTSPSEEYWRLYVLKLSDDIGNFGEVRLPLL
                     GCLGVSWLVVFLCLIRGVKSSGKVVYFTATFPYVVLTILFVRGVTLEGAFDGIMYYLT
                     PQWDKILEAKVWGDAASQIFYSLGCAWGGLITMASYNKFHNNCYRDSVIISITNCATS
                     VYAGFVIFSILGFMANHLGVDVSRVADHGPGLAFVAYPEALTLLPISPLWSLLFFFML
                     ILLGLGTQFCLLETLVTAIVDEVGNEWILQKKTYVTLGVAVAGFLLGIPLTSQAGIYW
                     LLLMDNYAASFSLVVISCIMCVAIMYIYGHRNYFQDIQMMLGFPPPLFFQICWRFVSP
                     AIIFFILVFTVIQYQPITYNHYQYPGWAVAIGFLMALSSVLCIPLYAMFRLCRTDGDT
                     LLQRLKNATKPSRDWGPALLEHRTGRYAPTIAPSPEDGFEVQPLHPDKAQIPIVGSNG
                     SSRLQDSRI"
     exon            273..429
                     /gene="SLC6A9"
                     /gene_synonym="GCENSG; GLYT1"
                     /inference="alignment:Splign:2.1.0"
     exon            430..561
                     /gene="SLC6A9"
                     /gene_synonym="GCENSG; GLYT1"
                     /inference="alignment:Splign:2.1.0"
     exon            562..832
                     /gene="SLC6A9"
                     /gene_synonym="GCENSG; GLYT1"
                     /inference="alignment:Splign:2.1.0"
     exon            833..965
                     /gene="SLC6A9"
                     /gene_synonym="GCENSG; GLYT1"
                     /inference="alignment:Splign:2.1.0"
     exon            966..1100
                     /gene="SLC6A9"
                     /gene_synonym="GCENSG; GLYT1"
                     /inference="alignment:Splign:2.1.0"
     exon            1101..1204
                     /gene="SLC6A9"
                     /gene_synonym="GCENSG; GLYT1"
                     /inference="alignment:Splign:2.1.0"
     exon            1205..1442
                     /gene="SLC6A9"
                     /gene_synonym="GCENSG; GLYT1"
                     /inference="alignment:Splign:2.1.0"
     exon            1443..1577
                     /gene="SLC6A9"
                     /gene_synonym="GCENSG; GLYT1"
                     /inference="alignment:Splign:2.1.0"
     exon            1578..1677
                     /gene="SLC6A9"
                     /gene_synonym="GCENSG; GLYT1"
                     /inference="alignment:Splign:2.1.0"
     exon            1678..1778
                     /gene="SLC6A9"
                     /gene_synonym="GCENSG; GLYT1"
                     /inference="alignment:Splign:2.1.0"
     exon            1779..1949
                     /gene="SLC6A9"
                     /gene_synonym="GCENSG; GLYT1"
                     /inference="alignment:Splign:2.1.0"
     exon            1950..3206
                     /gene="SLC6A9"
                     /gene_synonym="GCENSG; GLYT1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3181..3186
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SLC6A9"
                     /gene_synonym="GCENSG; GLYT1"
                     /note="hexamer: AATGAA"
     polyA_site      3206
                     /gene="SLC6A9"
                     /gene_synonym="GCENSG; GLYT1"
                     /note="major polyA site"
ORIGIN      
        1 acaacaggct gtggaagagc tgcgagcggc gcggcggggc gggcgaactc ggcgcggcac
       61 agagcctcgg gaggctgatg caactttccc tttaagaaag ccacctgggc gcaccgcggt
      121 gcggacccag cacgcctggg ccgggggctg cagcatgctc ttgagatctg tggcctgaaa
      181 ggcgctggaa gcagagcctg tgagtgtggt ccccgtcacc agagccccaa cccaccgccg
      241 ccatggtagg aaaaggtgcc aaagggatgc tgaatggtgc tgtgcccagc gaggccacca
      301 agagggacca gaacctcaaa cggggcaact ggggcaacca gatcgagttt gtactgacga
      361 gcgtgggcta tgccgtgggc ctgggcaatg tctggcgctt cccatacctc tgctatcgca
      421 acgggggagg cgccttcatg ttcccctact tcatcatgct catcttctgc gggatccccc
      481 tcttcttcat ggagctctcc ttcggccagt ttgcaagcca ggggtgcctg ggggtctgga
      541 ggatcagccc catgttcaaa ggagtgggct atggtatgat ggtggtgtcc acctacatcg
      601 gcatctacta caatgtggtc atctgcatcg ccttctacta cttcttctcg tccatgacgc
      661 acgtgctgcc ctgggcctac tgcaataacc cctggaacac gcatgactgc gccggtgtac
      721 tggacgcctc caacctcacc aatggctctc ggccagccgc cttgcccagc aacctctccc
      781 acctgctcaa ccacagcctc cagaggacca gccccagcga ggagtactgg aggctgtacg
      841 tgctgaagct gtcagatgac attgggaact ttggggaggt gcggctgccc ctccttggct
      901 gcctcggtgt ctcctggttg gtcgtcttcc tctgcctcat ccgaggggtc aagtcttcag
      961 ggaaagtggt gtacttcacg gccacgttcc cctacgtggt gctgaccatt ctgtttgtcc
     1021 gcggagtgac cctggaggga gcctttgacg gcatcatgta ctacctaacc ccgcagtggg
     1081 acaagatcct ggaggccaag gtgtggggtg atgctgcctc ccagatcttc tactcactgg
     1141 gctgcgcgtg gggaggcctc atcaccatgg cttcctacaa caagttccac aataactgtt
     1201 accgggacag tgtcatcatc agcatcacca actgtgccac cagcgtctat gctggcttcg
     1261 tcatcttctc catcctcggc ttcatggcca atcacctggg cgtggatgtg tcccgtgtgg
     1321 cagaccacgg ccctggcctg gccttcgtgg cttaccccga ggccctcaca ctacttccca
     1381 tctccccgct gtggtctctg ctcttcttct tcatgcttat cctgctgggg ctgggcactc
     1441 agttctgcct cctggagacg ctggtcacag ccattgtgga tgaggtgggg aatgagtgga
     1501 tcctgcagaa aaagacctat gtgaccttgg gcgtggctgt ggctggcttc ctgctgggca
     1561 tccccctcac cagccaggca ggcatctatt ggctgctgct gatggacaac tatgcggcca
     1621 gcttctcctt ggtggtcatc tcctgcatca tgtgtgtggc catcatgtac atctacgggc
     1681 accggaacta cttccaggac atccagatga tgctgggatt cccaccaccc ctcttctttc
     1741 agatctgctg gcgcttcgtc tctcccgcca tcatcttctt tattctagtt ttcactgtga
     1801 tccagtacca gccgatcacc tacaaccact accagtaccc aggctgggcc gtggccattg
     1861 gcttcctcat ggctctgtcc tccgtcctct gcatccccct ctacgccatg ttccggctct
     1921 gccgcacaga cggggacacc ctcctccagc gtttgaaaaa tgccacaaag ccaagcagag
     1981 actggggccc tgccctcctg gagcaccgga cagggcgcta cgcccccacc atagccccct
     2041 ctcctgagga cggcttcgag gtccagccac tgcacccgga caaggcgcag atccccattg
     2101 tgggcagtaa tggctccagc cgcctccagg actcccggat atgagcacag ctgccagggg
     2161 agtggcccca cccccacccc gtgctcccac cgcagagact ggtgaggcag aggccaggtg
     2221 tctctgcctg ccccctgcca cgccctggcc aggacggctg ctgtcacctt ggtcaccact
     2281 gctagtgcag tcattcatgc tcatgtcccc agtgtttaca tgtcctttgg atgccaagat
     2341 agcagctggg gggaggggtg ggagtggagg gttgctggga ggtccaaagc actttggagg
     2401 ggtctcgggc caggtcccca gcagcctgga tggctttacg tggcctccga tacccttata
     2461 ccctgccctg agctgaggtt ctgggtgggc ctccagcccc atgactagtg ctcctgccct
     2521 cagagccgac cccagcctct gccaggcaca tttggctatt cctccctagg ggcaggatga
     2581 agggctgggg gactgcccag tgttacttgt caggctgtgc tgcccagccc tgtttatctg
     2641 tgtaattatt tttgtaaaca ttgtattctc tgtggtcgcc acctcctcgc ccccagcctc
     2701 gggttcagtc tgtcttccag gcctgcttgc acctcactgg gctgctccgg ggtctctgcc
     2761 cctcattcca ggcctggctg tcaggcccag ccagcagggg cccgtgaccc agcagcctgc
     2821 ccaaagcatt tgtttctggg ggatggggtg ggggctgctc cacaggaggt ttgagcccag
     2881 caccctgggg aaggggaccc tgcacgacac ccccttgccc tccctccatg aggctaaagg
     2941 cccagtcttc ccaaatgtgc tgccctcgtt catgtgccaa atggccccag cccacatgcc
     3001 cctcccctct ctggagtggg agccccttct gaagtgtctg aatccctgaa gtgttcattt
     3061 gtccgtcctc tgtgcagtga cagccccggc caagccacct ctaatcctct gtagcaataa
     3121 cggtgcgccg cccatccctg cccattgtgc accactagga ttttaaagtc catagatttt
     3181 aatgaaattt ctattcctgt ctctga
//
