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    SLC38A2 solute carrier family 38 member 2 [ Homo sapiens (human) ]

    Gene ID: 54407, updated on 11-Apr-2024

    Summary

    Official Symbol
    SLC38A2provided by HGNC
    Official Full Name
    solute carrier family 38 member 2provided by HGNC
    Primary source
    HGNC:HGNC:13448
    See related
    Ensembl:ENSG00000134294 MIM:605180; AllianceGenome:HGNC:13448
    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
    ATA2; SAT2; SNAT2; PRO1068
    Summary
    Enables neutral amino acid:sodium symporter activity. Involved in several processes, including amino acid transport; cellular response to arsenite(3-); and positive regulation of RNA splicing. Located in cytoplasm and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in skin (RPKM 105.3), liver (RPKM 101.3) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Location:
    12q13.11
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (46358188..46372773, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (46317747..46332332, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (46751971..46766556, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6238 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6239 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6240 Neighboring gene solute carrier family 38 member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4381 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:46660317-46661300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6242 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:46662284-46663266 Neighboring gene uncharacterized LOC105378248 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4383 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:46674619-46675430 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:46765735-46766438 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6245 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4385 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6248 Neighboring gene SLC38A2 antisense RNA 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:46776823-46777330 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4387 Neighboring gene NANOG hESC enhancer GRCh37_chr12:46780024-46780525 Neighboring gene SLC38A4 antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr12:46789058-46789559 Neighboring gene uncharacterized LOC124902923 Neighboring gene NANOG hESC enhancer GRCh37_chr12:46824129-46824630 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6249 Neighboring gene Sharpr-MPRA regulatory region 10724

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of SLC38A2 PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA1382

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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 L-serine transmembrane transporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables acidic amino acid transmembrane transporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables alanine:sodium symporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables amino acid transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables amino acid transmembrane transporter activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables amino acid transmembrane transporter activity TAS
    Traceable Author Statement
    more info
     
    enables amino acid:sodium symporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables neutral L-amino acid:sodium symporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables proline:sodium symporter 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-glutamine import across plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in L-proline import across plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in L-serine import across plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in L-serine transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in acidic amino acid transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in alanine transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in amino acid import ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in amino acid transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in amino acid transmembrane transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in amino acid transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in amino acid transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in amino acid transport TAS
    Traceable Author Statement
    more info
     
    involved_in cellular response to amino acid starvation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to arsenite(3-) IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cellular response to mechanical stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cerebral cortex development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in female pregnancy IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in glutamine transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in glutamine transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in glycine betaine transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neurotransmitter transport TAS
    Traceable Author Statement
    more info
     
    involved_in neutral amino acid transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of RNA splicing IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    involved_in positive regulation of gene expression IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    involved_in proline transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in regulation of cellular response to stress IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of glutamate secretion, neurotransmission ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in response to muscle activity IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in sodium ion transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in transport across blood-brain barrier NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in axon IEA
    Inferred from Electronic Annotation
    more info
     
    located_in brush border IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in dendrite IEA
    Inferred from Electronic Annotation
    more info
     
    located_in neuronal cell body IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    located_in sarcolemma IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    sodium-coupled neutral amino acid symporter 2
    Names
    amino acid transporter 2
    amino acid transporter A2
    protein 40-9-1
    sodium-coupled neutral amino acid transporter 2
    system A amino acid transporter 2
    system A transporter 1
    system N amino acid transporter 2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001307936.2NP_001294865.1  sodium-coupled neutral amino acid symporter 2 isoform 2

      See identical proteins and their annotated locations for NP_001294865.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an exon in its 5' coding region compared to variant 1. This variant represents translation initiation at an alternate start codon compared to variant 1; the 5'-most initiation codon, as used in variant 1, is associated with a truncated ORF that would render the transcript a candidate for nonsense-mediated decay (NMD). Leaky scanning may allow translation initiation at the alternate start codon to encode an isoform (2) that has a distinct and shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AK001700, BC029379, BC040342, DA725217
      Consensus CDS
      CCDS76551.1
      UniProtKB/Swiss-Prot
      Q96QD8
      UniProtKB/TrEMBL
      Q8NHT5
      Conserved Domains (1) summary
      cl00456
      Location:5395
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    2. NM_018976.5NP_061849.2  sodium-coupled neutral amino acid symporter 2 isoform 1

      See identical proteins and their annotated locations for NP_061849.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC025031, BC040342, DA725217
      Consensus CDS
      CCDS8749.1
      UniProtKB/Swiss-Prot
      Q6IA88, Q6ZMG2, Q96QD8, Q9HAV3, Q9NVA8, Q9P2G5
      UniProtKB/TrEMBL
      A8K6H9
      Related
      ENSP00000256689.5, ENST00000256689.10
      Conserved Domains (1) summary
      cl00456
      Location:69495
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      46358188..46372773 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047429019.1XP_047284975.1  sodium-coupled neutral amino acid symporter 2 isoform X1

      Related
      ENSP00000482873.1, ENST00000612232.1
    2. XM_047429020.1XP_047284976.1  sodium-coupled neutral amino acid symporter 2 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      46317747..46332332 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054372315.1XP_054228290.1  sodium-coupled neutral amino acid symporter 2 isoform X1

    2. XM_054372316.1XP_054228291.1  sodium-coupled neutral amino acid symporter 2 isoform X2