LOCUS       NM_003038               4563 bp    mRNA    linear   PRI 02-APR-2024
DEFINITION  Homo sapiens solute carrier family 1 member 4 (SLC1A4), transcript
            variant 1, mRNA.
ACCESSION   NM_003038
VERSION     NM_003038.5
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 4563)
  AUTHORS   Sarigecili,E., Bulut,F.D. and Anlas,O.
  TITLE     A rare cause of microcephaly, thin corpus callosum and refractory
            epilepsy due to a novel SLC1A4 gene mutation
  JOURNAL   Clin Neurol Neurosurg 218, 107283 (2022)
   PUBMED   35605507
  REMARK    GeneRIF: A rare cause of microcephaly, thin corpus callosum and
            refractory epilepsy due to a novel SLC1A4 gene mutation.
REFERENCE   2  (bases 1 to 4563)
  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   3  (bases 1 to 4563)
  AUTHORS   Foster,A.C., Rangel-Diaz,N., Staubli,U., Yang,J.Y., Penjwini,M.,
            Viswanath,V. and Li,Y.X.
  TITLE     Phenylglycine analogs are inhibitors of the neutral amino acid
            transporters ASCT1 and ASCT2 and enhance NMDA receptor-mediated LTP
            in rat visual cortex slices
  JOURNAL   Neuropharmacology 126, 70-83 (2017)
   PUBMED   28807674
  REMARK    GeneRIF: Results suggest that ASCT1/2 may play an important role in
            regulating extracellular d-serine and NMDA receptor-mediated
            physiological effects and that ASCT1/2 inhibitors have the
            potential for therapeutic benefit.
REFERENCE   4  (bases 1 to 4563)
  AUTHORS   Kvainickas,A., Orgaz,A.J., Nagele,H., Diedrich,B., Heesom,K.J.,
            Dengjel,J., Cullen,P.J. and Steinberg,F.
  TITLE     Retromer- and WASH-dependent sorting of nutrient transporters
            requires a multivalent interaction network with ANKRD50
  JOURNAL   J Cell Sci 130 (2), 382-395 (2017)
   PUBMED   27909246
  REMARK    GeneRIF: ANKRD50 simultaneously engages multiple parts of the
            SNX27-retromer-WASH complex machinery in a direct and co-operative
            interaction network that is needed to efficiently recycle the
            nutrient transporters
REFERENCE   5  (bases 1 to 4563)
  AUTHORS   Conroy,J., Allen,N.M., Gorman,K., O'Halloran,E., Shahwan,A.,
            Lynch,B., Lynch,S.A., Ennis,S. and King,M.D.
  TITLE     Novel European SLC1A4 variant: infantile spasms and population
            ancestry analysis
  JOURNAL   J Hum Genet 61 (8), 761-764 (2016)
   PUBMED   27193218
  REMARK    GeneRIF: SLC1A4 deficiency should not be considered a
            population-specific disorder, and all patients with unexplained
            severe neurodevelopmental delay and the features outlined should be
            investigated regardless of ethnicity, as there are no known
            metabolic markers of this potentially treatable condition.
REFERENCE   6  (bases 1 to 4563)
  AUTHORS   Zerangue,N. and Kavanaugh,M.P.
  TITLE     ASCT-1 is a neutral amino acid exchanger with chloride channel
            activity
  JOURNAL   J Biol Chem 271 (45), 27991-27994 (1996)
   PUBMED   8910405
REFERENCE   7  (bases 1 to 4563)
  AUTHORS   Tamarappoo,B.K., McDonald,K.K. and Kilberg,M.S.
  TITLE     Expressed human hippocampal ASCT1 amino acid transporter exhibits a
            pH-dependent change in substrate specificity
  JOURNAL   Biochim Biophys Acta 1279 (2), 131-136 (1996)
   PUBMED   8603078
REFERENCE   8  (bases 1 to 4563)
  AUTHORS   Hofmann,K., Duker,M., Fink,T., Lichter,P. and Stoffel,W.
  TITLE     Human neutral amino acid transporter ASCT1: structure of the gene
            (SLC1A4) and localization to chromosome 2p13-p15
  JOURNAL   Genomics 24 (1), 20-26 (1994)
   PUBMED   7896285
REFERENCE   9  (bases 1 to 4563)
  AUTHORS   Shafqat,S., Tamarappoo,B.K., Kilberg,M.S., Puranam,R.S.,
            McNamara,J.O., Guadano-Ferraz,A. and Fremeau,R.T. Jr.
  TITLE     Cloning and expression of a novel Na(+)-dependent neutral amino
            acid transporter structurally related to mammalian Na+/glutamate
            cotransporters
  JOURNAL   J Biol Chem 268 (21), 15351-15355 (1993)
   PUBMED   8340364
REFERENCE   10 (bases 1 to 4563)
  AUTHORS   Arriza,J.L., Kavanaugh,M.P., Fairman,W.A., Wu,Y.N., Murdoch,G.H.,
            North,R.A. and Amara,S.G.
  TITLE     Cloning and expression of a human neutral amino acid transporter
            with structural similarity to the glutamate transporter gene family
  JOURNAL   J Biol Chem 268 (21), 15329-15332 (1993)
   PUBMED   8101838
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from CR990382.1, L19444.1,
            BC026216.1 and BC072423.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_003038.4.
            
            Summary: The protein encoded by this gene is a sodium-dependent
            neutral amino acid transporter for alanine, serine, cysteine, and
            threonine. Defects in this gene have been associated with
            developmental delay, microcephaly, and intellectual disability.
            [provided by RefSeq, Jan 2017].
            
            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 :: BC026216.1, BC072423.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000234256.4/ ENSP00000234256.3
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-625               CR990382.1         2-626
            626-1844            L19444.1           543-1761
            1845-3266           BC026216.1         1784-3205
            3267-3272           BC072423.1         3265-3270
            3273-4048           BC026216.1         3230-4005
            4049-4563           BC026216.1         4008-4522
FEATURES             Location/Qualifiers
     source          1..4563
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="2"
                     /map="2p14"
     gene            1..4563
                     /gene="SLC1A4"
                     /gene_synonym="ASCT1; SATT; SPATCCM"
                     /note="solute carrier family 1 member 4"
                     /db_xref="GeneID:6509"
                     /db_xref="HGNC:HGNC:10942"
                     /db_xref="MIM:600229"
     exon            1..772
                     /gene="SLC1A4"
                     /gene_synonym="ASCT1; SATT; SPATCCM"
                     /inference="alignment:Splign:2.1.0"
     CDS             246..1844
                     /gene="SLC1A4"
                     /gene_synonym="ASCT1; SATT; SPATCCM"
                     /note="isoform 1 is encoded by transcript variant 1;
                     glutamate/neutral amino acid transporter; neutral amino
                     acid transporter A; alanine/serine/cysteine/threonine
                     transporter 1; solute carrier family 1 (glutamate/neutral
                     amino acid transporter), member 4"
                     /codon_start=1
                     /product="neutral amino acid transporter A isoform 1"
                     /protein_id="NP_003029.2"
                     /db_xref="CCDS:CCDS1879.1"
                     /db_xref="GeneID:6509"
                     /db_xref="HGNC:HGNC:10942"
                     /db_xref="MIM:600229"
                     /translation="MEKSNETNGYLDSAQAGPAAGPGAPGTAAGRARRCAGFLRRQAL
                     VLLTVSGVLAGAGLGAALRGLSLSRTQVTYLAFPGEMLLRMLRMIILPLVVCSLVSGA
                     ASLDASCLGRLGGIAVAYFGLTTLSASALAVALAFIIKPGSGAQTLQSSDLGLEDSGP
                     PPVPKETVDSFLDLARNLFPSNLVVAAFRTYATDYKVVTQNSSSGNVTHEKIPIGTEI
                     EGMNILGLVLFALVLGVALKKLGSEGEDLIRFFNSLNEATMVLVSWIMWYVPVGIMFL
                     VGSKIVEMKDIIVLVTSLGKYIFASILGHVIHGGIVLPLIYFVFTRKNPFRFLLGLLA
                     PFATAFATCSSSATLPSMMKCIEENNGVDKRISRFILPIGATVNMDGAAIFQCVAAVF
                     IAQLNNVELNAGQIFTILVTATASSVGAAGVPAGGVLTIAIILEAIGLPTHDLPLILA
                     VDWIVDRTTTVVNVEGDALGAGILHHLNQKATKKGEQELAEVKVEAIPNCKSEEETSP
                     LVTHQNPAGPVASAPELESKESVL"
     exon            773..815
                     /gene="SLC1A4"
                     /gene_synonym="ASCT1; SATT; SPATCCM"
                     /inference="alignment:Splign:2.1.0"
     exon            816..878
                     /gene="SLC1A4"
                     /gene_synonym="ASCT1; SATT; SPATCCM"
                     /inference="alignment:Splign:2.1.0"
     exon            879..1045
                     /gene="SLC1A4"
                     /gene_synonym="ASCT1; SATT; SPATCCM"
                     /inference="alignment:Splign:2.1.0"
     exon            1046..1279
                     /gene="SLC1A4"
                     /gene_synonym="ASCT1; SATT; SPATCCM"
                     /inference="alignment:Splign:2.1.0"
     exon            1280..1474
                     /gene="SLC1A4"
                     /gene_synonym="ASCT1; SATT; SPATCCM"
                     /inference="alignment:Splign:2.1.0"
     exon            1475..1609
                     /gene="SLC1A4"
                     /gene_synonym="ASCT1; SATT; SPATCCM"
                     /inference="alignment:Splign:2.1.0"
     exon            1610..4563
                     /gene="SLC1A4"
                     /gene_synonym="ASCT1; SATT; SPATCCM"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3514..3519
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SLC1A4"
                     /gene_synonym="ASCT1; SATT; SPATCCM"
                     /note="hexamer: ATTAAA"
     polyA_site      3544
                     /gene="SLC1A4"
                     /gene_synonym="ASCT1; SATT; SPATCCM"
                     /note="major polyA site"
     regulatory      4539..4544
                     /regulatory_class="polyA_signal_sequence"
                     /gene="SLC1A4"
                     /gene_synonym="ASCT1; SATT; SPATCCM"
                     /note="hexamer: AATGAA"
     polyA_site      4563
                     /gene="SLC1A4"
                     /gene_synonym="ASCT1; SATT; SPATCCM"
                     /note="major polyA site"
ORIGIN      
        1 atctccagcc ggcggctgct ccagggaggc tgggcgcgat cctctccgcc cgcggctcca
       61 acccgcactc tgcgcctctc ctcgcctttc tcgcacctgc tcctgcgcca ggcccggaga
      121 cccccggggc ggcttcccag aacctgcgga gcacaactgg ccgaccgacc cattcattgg
      181 gaaccccgtc ttttgccaga gcccacgtcc cctgccacct ctagctcgga gcggcgtgta
      241 gcgccatgga gaagagcaac gagaccaacg gctaccttga cagcgctcag gcggggcctg
      301 cggccgggcc cggagctccg gggaccgcgg cgggacgcgc acggcgttgc gcgggcttcc
      361 tgcggcgcca agcgctggtg ctgctcaccg tgtccggggt gctggcgggc gcgggcctgg
      421 gcgcggcgtt gcgcgggctc agcctgagcc gcacgcaggt cacctacctg gccttccccg
      481 gcgagatgct gctccgcatg ctgcgcatga tcatcctgcc gctggtggtc tgcagcctgg
      541 tgtcgggcgc cgcctcgctc gatgccagct gcctcgggcg tctgggcggc atcgctgtcg
      601 cctactttgg cctcaccaca ctgagtgcct cggcgctcgc cgtggccttg gcgttcatca
      661 tcaagccagg atccggtgcg cagacccttc agtccagcga cctggggctg gaggactcgg
      721 ggcctcctcc tgtccccaaa gagacggtgg actctttcct cgacctggcc agaaacctgt
      781 ttccctccaa tcttgtggtt gcagctttcc gtacgtatgc aaccgattat aaagtcgtga
      841 cccagaacag cagctctgga aatgtaaccc atgaaaagat ccccataggc actgagatag
      901 aagggatgaa cattttagga ttggtcctgt ttgctctggt gttaggagtg gccttaaaga
      961 aactaggctc cgaaggagaa gacctcatcc gtttcttcaa ttccctcaac gaggcgacga
     1021 tggtgctggt gtcctggatt atgtggtacg tacctgtggg catcatgttc cttgttggaa
     1081 gcaagatcgt ggaaatgaaa gacatcatcg tgctggtgac cagcctgggg aaatacatct
     1141 tcgcatctat attgggccat gttattcatg gaggaattgt tctgccactt atttattttg
     1201 ttttcacacg aaaaaaccca ttcagattcc tcctgggcct cctcgcccca tttgcgacag
     1261 catttgctac ctgctccagc tcagcgaccc ttccctctat gatgaagtgc attgaagaga
     1321 acaatggtgt ggacaagagg atcagcaggt ttattctccc catcggggcc accgtgaaca
     1381 tggacggagc agccatcttc cagtgtgtgg ccgcggtgtt cattgcgcaa ctcaacaacg
     1441 tagagctcaa cgcaggacag attttcacca ttctagtgac tgccacagcg tccagtgttg
     1501 gagcagcagg cgtgccagct ggaggggtcc tcaccattgc cattatcctg gaggccattg
     1561 ggctgcctac tcatgacctg cctctgatcc tggctgtgga ctggattgtg gaccggacca
     1621 ccacggtggt gaatgtggaa ggggatgccc tgggtgcagg cattctccac cacctgaatc
     1681 agaaggcaac aaagaaaggc gagcaggaac ttgctgaggt gaaagtggaa gccatcccca
     1741 actgcaagtc tgaggaggag acatcgcccc tggtgacaca ccagaacccc gctggccccg
     1801 tggccagtgc cccagaactg gaatccaagg agtcggttct gtgatggggc tgggctttgg
     1861 gcttgcctgc cagcagtgat gtcccaccct gttcacccag ccgccagtca tggacacagg
     1921 gcactgccct tgccaacttt taccctccca agcaatgctt tggcccagtc gctggcctga
     1981 ggcttacctc tcggcactgg cattgggctc cccagccgga actggttacc aaggacaagg
     2041 acactctgac attcggcttg atccatgtcc aggtgcaact gtgtgtacac cagggatctg
     2101 tttggaaaca accccttgag ctgccaggct caagaaatca tggactcaca gggtcctgtg
     2161 tggttacatc ttggaaaaaa tgcagatgta tttcactctc cccggtcagc tctgcatcag
     2221 gtgttttctg agcaaaccaa gggggtttat agtcatctgt cgcattgcct cgagttgcag
     2281 taattgaaaa aatgctcaaa ttcttagcca tggctggcct ttgctgagct gggactcagg
     2341 tgtttaaaga gtttgtgcta tagctaggtg tggatagctt ctgatccctg ggttctggga
     2401 gactgcaggt gccgcacatt gtcaagttag aaatactcca ggtgggtgtt agcactgtgg
     2461 tggtctctgg tccacagcct taggtaaaca acttagattc tgaggtcaaa gaaaaaagga
     2521 gagggaatgc agccttgtgg gggagaagcg gggcagaggg ttctctaatc taatcaggac
     2581 aggacaggtt tcacatacaa ttgtcccagt tcgcatccca gccctggggc acttttctgc
     2641 ttccttccag aggcctgggc ctctgataac actttggctt tttctccatt cacgctgatt
     2701 tggcaaaagg ccagagatgg gcctccttcc ctggggaggt gtgatgtagt tatcacattc
     2761 aggacccttg ttgatttatc atctattatt tgaattcaac tggacactct gtaaaatgct
     2821 gcactgcagc aaaaacaaaa ccaccaccac cccagagaaa accatgtact aattggagtg
     2881 gggtaccccc attcacaggt tcccaggtcc cctggctttg gctgatttca aaatatagag
     2941 ccctttcttg ccagtacatc caagtttaaa attatcagcg aaatggtcca tgtttttcca
     3001 attacctgct gacacggttc taagctaagt gaaggggaag atctgagagc gtgctgtttg
     3061 tggctgttga tgcatattcg tgatgtaaca ggtcctgggg cctcacttta ccccatttgt
     3121 aaaatggggc taatgtcacc tgcctcttac ctacctcaga gggatttggt gaagcaaact
     3181 gttaatcttc gaaaacgacc atttcacttc ttggatatca agtgctaacc cagtatgttc
     3241 ttctttttta tgtaagggac agctttctcc acagagtcct ttctgctggt gaggacagca
     3301 tttctgagca gggctttgtt ctctatgtgc attaggactt ttatcatgcc cttgttctgt
     3361 gtgtagttac ttgacagcat caaatgccgc ctcttcctaa tgtccttcaa gttttcatga
     3421 actagcaacc ccaccttcca ccatggttct gggcgcctga ttttgctgtg actcccagac
     3481 ccagccactg tttctgccac cctgtaacag gccattaaag ctccccagtg ttcagcctcc
     3541 ttcactccct tgttttccct gttgctatgt gtcacctggg ccctacagac aggggcacac
     3601 gcttatggat gtgtgtacca ttgagatgag aatgggtaga tggaacggag accatcaagc
     3661 cacaccccct tcttaaaact ggggacatga gcctgagcag aaagggtgaa gaagagccat
     3721 gggacacaga gttgacccag ccagggggaa agcccagctc tctttaaacc agctaagcca
     3781 ttccagtctc ctgtgaagcc aaaagggacc aggaaccgtg caaaggaaac tggaaacttt
     3841 tccccgctgg gtagagcatg ttgctgatac tcttctgttt tcaagggaaa caatcacatt
     3901 gtttgattcc aaatggtaaa tgaacactca ctattcttca ggcttcagta aatctttttt
     3961 tcttccttca tatatatata cacaacacac acacacatat gtatatctat acacacatgt
     4021 gtgttgtgta tatgcatgtg tgtgtgtgcg tgtgtgtata gttttagctc caagccaagc
     4081 aagtttgtgt ttggatagag gggaacttaa ctattaacta caagttgtat gtctgtggta
     4141 tcttgatttt cccatttcta aagatgaatt tcacaaagcc ataaagcgtg aaattagagc
     4201 tggacttaag actcattggc cgaccatcct gtgtcctggc ctggccctgc agtaagaagc
     4261 gtgtctgggt ctggagaagg gtgcttccga gagtgtgcag gtggcccttc cccttggagg
     4321 cgagaagaga gaatgtgctg tctatcttcc tggttttcag tccacagagt cggtagacca
     4381 ggggttacgt gactggggaa aatctcacat ctccttgtct gaaaacattt cccctgctgt
     4441 tctctttcta acatgttgtg gtaaatctgt tcagatactg ctcatctgac tgttttgtac
     4501 atgtgacaat tgccttaaaa cctagcacag tcctcagaaa tgaataccgt gtttccactg
     4561 gaa
//
