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    SLC38A6 solute carrier family 38 member 6 [ Homo sapiens (human) ]

    Gene ID: 145389, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SLC38A6provided by HGNC
    Official Full Name
    solute carrier family 38 member 6provided by HGNC
    Primary source
    HGNC:HGNC:19863
    See related
    Ensembl:ENSG00000139974 MIM:616518; AllianceGenome:HGNC:19863
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    NAT-1; SNAT6
    Summary
    Predicted to enable L-glutamate transmembrane transporter activity and L-glutamine transmembrane transporter activity. Predicted to be involved in amino acid transmembrane transport and glutamine transport. Predicted to be located in membrane and synapse. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 2.1), gall bladder (RPKM 1.9) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC38A6 in Genome Data Viewer
    Location:
    14q23.1
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (60981245..61083733)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (55187785..55290408)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (61447963..61550451)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene MNAT1 component of CDK activating kinase Neighboring gene Sharpr-MPRA regulatory region 12651 Neighboring gene Sharpr-MPRA regulatory region 14697 Neighboring gene Sharpr-MPRA regulatory region 5996 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8484 Neighboring gene SRM pseudogene 2 Neighboring gene RNA, U6 small nuclear 398, pseudogene Neighboring gene uncharacterized LOC101927756 Neighboring gene tRNA methyltransferase 5 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:61555743-61556244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8485 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:61567888-61568804 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:61570068-61571267 Neighboring gene Sharpr-MPRA regulatory region 14232 Neighboring gene NANOG hESC enhancer GRCh37_chr14:61641010-61641511 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:61644371-61644872 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr14:61644987-61646186 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8486 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr14:61721487-61722686 Neighboring gene protein kinase C eta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:61736629-61737128 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:61746518-61747481 Neighboring gene Sharpr-MPRA regulatory region 13098 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5817 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5818 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:61788641-61789185 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:61789186-61789729 Neighboring gene PRKCH antisense RNA 1 Neighboring gene transmembrane protein 30B

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. SLC38A6, regulated by EP300-mediated modifications of H3K27ac, promotes cell proliferation, glutamine metabolism and mitochondrial respiration in hepatocellular carcinoma. Huang L, et al. Carcinogenesis, 2022 Oct 22. PMID 35901507
    2. New Transcriptomic Biomarkers of 5-Fluorouracil Resistance. Fekete JT, et al. Int J Mol Sci, 2023 Jan 12. PMID 36675023, Free PMC Article
    3. Histological analysis of SLC38A6 (SNAT6) expression in mouse brain shows selective expression in excitatory neurons with high expression in the synapses. Bagchi S, et al. PLoS One, 2014. PMID 24752331, Free PMC Article
    4. Evolutionary origin of amino acid transporter families SLC32, SLC36 and SLC38 and physiological, pathological and therapeutic aspects. Schiöth HB, et al. Mol Aspects Med, 2013 Apr-Jun. PMID 23506890
    5. USP7 targets XIAP for cancer progression: Establishment of a p53-independent therapeutic avenue for glioma. Saha G, et al. Oncogene, 2022 Nov. PMID 36243803

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. New Transcriptomic Biomarkers of 5-Fluorouracil Resistance.
      Title: New Transcriptomic Biomarkers of 5-Fluorouracil Resistance.
    2. SLC38A6, regulated by EP300-mediated modifications of H3K27ac, promotes cell proliferation, glutamine metabolism and mitochondrial respiration in hepatocellular carcinoma.
      Title: SLC38A6, regulated by EP300-mediated modifications of H3K27ac, promotes cell proliferation, glutamine metabolism and mitochondrial respiration in hepatocellular carcinoma.
    3. SLC38A6 is primarily expressed in excitatory neurons and is not expressed in the astrocytes.
      Title: Histological analysis of SLC38A6 (SNAT6) expression in mouse brain shows selective expression in excitatory neurons with high expression in the synapses.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of solute carrier family 38, member 6 (SLC38A6) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC102697

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables L-glutamate transmembrane transporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables L-glutamine transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables L-glutamine transmembrane transporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in L-glutamate transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in amino acid transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in glutamine transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in synapse IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    solute carrier family 38 member 6
    Names
    N system amino acid transporter NAT-1
    N-system amino acid transporter 1
    Na(+)-coupled neutral amino acid transporter 6
    Sodium-coupled neutral amino acid transporter 6
    amino acid transporter SLC38A6
    probable sodium-coupled neutral amino acid transporter 6

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001172702.2 → NP_001166173.1  solute carrier family 38 member 6 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest coding transcript and encodes the longer isoform (1).
      Source sequence(s)
      BC050349, BX248072, DR002669
      Consensus CDS
      CCDS53900.1
      UniProtKB/TrEMBL
      A0A0C4DG39
      Related
      ENSP00000395851.1, ENST00000451406.5
      Conserved Domains (2) summary
      COG0814
      Location:50 → 434
      SdaC; Amino acid permease [Amino acid transport and metabolism]
      cl00456
      Location:46 → 429
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

    2. NM_153811.3 → NP_722518.2  solute carrier family 38 member 6 isoform 2

      See identical proteins and their annotated locations for NP_722518.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses a distinct splice pattern in the 3' coding region and 3' UTR, compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AL160234, BC110378, BX648332
      Consensus CDS
      CCDS9751.1
      UniProtKB/Swiss-Prot
      C9JWA6, Q86SY5, Q8IZM9
      UniProtKB/TrEMBL
      A0A0C4DG39
      Related
      ENSP00000267488.4, ENST00000267488.9
      Conserved Domains (2) summary
      COG0814
      Location:50 → 451
      SdaC; Amino acid permease [Amino acid transport and metabolism]
      cl00456
      Location:46 → 451
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

    RNA

    1. NR_033344.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in the 5' region, and uses an alternate splice acceptor site at the terminal exon. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK303839, AL160236, BC050349, BP352279, BX248072, DC394244
      Related
      ENST00000529345.6

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      60981245..61083733
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017021022.2 → XP_016876511.1  solute carrier family 38 member 6 isoform X4

      UniProtKB/TrEMBL
      B4E1H1

    2. XM_047431002.1 → XP_047286958.1  solute carrier family 38 member 6 isoform X1

    3. XM_017021020.2 → XP_016876509.1  solute carrier family 38 member 6 isoform X1

      UniProtKB/TrEMBL
      A0A0C4DG39

    4. XM_047431001.1 → XP_047286957.1  solute carrier family 38 member 6 isoform X1

    5. XM_017021021.2 → XP_016876510.1  solute carrier family 38 member 6 isoform X2

    6. XM_047431003.1 → XP_047286959.1  solute carrier family 38 member 6 isoform X2

    7. XM_017021023.2 → XP_016876512.1  solute carrier family 38 member 6 isoform X5

      UniProtKB/TrEMBL
      A0A0C4DG39

    8. XM_047431005.1 → XP_047286961.1  solute carrier family 38 member 6 isoform X6

    9. XM_047431006.1 → XP_047286962.1  solute carrier family 38 member 6 isoform X7

    10. XM_047431004.1 → XP_047286960.1  solute carrier family 38 member 6 isoform X3

    11. XM_047431008.1 → XP_047286964.1  solute carrier family 38 member 6 isoform X11

    12. XM_047431009.1 → XP_047286965.1  solute carrier family 38 member 6 isoform X12

    13. XM_047431010.1 → XP_047286966.1  solute carrier family 38 member 6 isoform X13

      Related
      ENSP00000515189.1, ENST00000703134.1

    14. XM_011536469.3 → XP_011534771.1  solute carrier family 38 member 6 isoform X9

      UniProtKB/TrEMBL
      A0A8V8TRG7
      Conserved Domains (1) summary
      cl00456
      Location:46 → 309
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

    15. XM_017021025.2 → XP_016876514.1  solute carrier family 38 member 6 isoform X8

    16. XM_047431007.1 → XP_047286963.1  solute carrier family 38 member 6 isoform X10

    17. XM_024449496.2 → XP_024305264.1  solute carrier family 38 member 6 isoform X14

      Conserved Domains (1) summary
      cl00456
      Location:3 → 228
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

    RNA

    1. XR_007063987.1 RNA Sequence

    2. XR_007063988.1 RNA Sequence

    3. XR_001750164.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      55187785..55290408
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054375442.1 → XP_054231417.1  solute carrier family 38 member 6 isoform X1

    2. XM_054375440.1 → XP_054231415.1  solute carrier family 38 member 6 isoform X1

    3. XM_054375441.1 → XP_054231416.1  solute carrier family 38 member 6 isoform X1

    4. XM_054375443.1 → XP_054231418.1  solute carrier family 38 member 6 isoform X2

    5. XM_054375444.1 → XP_054231419.1  solute carrier family 38 member 6 isoform X2

    6. XM_054375447.1 → XP_054231422.1  solute carrier family 38 member 6 isoform X5

    7. XM_054375445.1 → XP_054231420.1  solute carrier family 38 member 6 isoform X3

    8. XM_054375457.1 → XP_054231432.1  solute carrier family 38 member 6 isoform X11

    9. XM_054375458.1 → XP_054231433.1  solute carrier family 38 member 6 isoform X12

    10. XM_054375459.1 → XP_054231434.1  solute carrier family 38 member 6 isoform X13

    11. XM_054375455.1 → XP_054231430.1  solute carrier family 38 member 6 isoform X9

    12. XM_054375446.1 → XP_054231421.1  solute carrier family 38 member 6 isoform X4

    13. XM_054375448.1 → XP_054231423.1  solute carrier family 38 member 6 isoform X6

    14. XM_054375451.1 → XP_054231426.1  solute carrier family 38 member 6 isoform X8

    15. XM_054375449.1 → XP_054231424.1  solute carrier family 38 member 6 isoform X7

    16. XM_054375453.1 → XP_054231428.1  solute carrier family 38 member 6 isoform X16

    17. XM_054375450.1 → XP_054231425.1  solute carrier family 38 member 6 isoform X8

    18. XM_054375452.1 → XP_054231427.1  solute carrier family 38 member 6 isoform X15

    19. XM_054375454.1 → XP_054231429.1  solute carrier family 38 member 6 isoform X17

    20. XM_054375456.1 → XP_054231431.1  solute carrier family 38 member 6 isoform X10

    21. XM_054375460.1 → XP_054231435.1  solute carrier family 38 member 6 isoform X14

    RNA

    1. XR_008488823.1 RNA Sequence

    2. XR_008488824.1 RNA Sequence

    3. XR_008488825.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IZM9.2 GenPept UniProtKB/Swiss-Prot:Q8IZM9

    Gene LinkOut

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