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    SLC38A4 solute carrier family 38 member 4 [ Homo sapiens (human) ]

    Gene ID: 55089, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SLC38A4provided by HGNC
    Official Full Name
    solute carrier family 38 member 4provided by HGNC
    Primary source
    HGNC:HGNC:14679
    See related
    Ensembl:ENSG00000139209 MIM:608065; AllianceGenome:HGNC:14679
    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
    ATA3; NAT3; PAAT; SNAT4
    Summary
    SLC38A4 is found predominantly in liver and transports both cationic and neutral amino acids. The transport of cationic amino acids by SLC38A4 is Na(+) and pH independent, while the transport of neutral amino acids is Na(+) and pH dependent (Hatanaka et al., 2001 [PubMed 11342143]).[supplied by OMIM, Mar 2008]
    Expression
    Restricted expression toward liver (RPKM 138.1) See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC38A4 in Genome Data Viewer
    Location:
    12q13.11
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (46764761..46832431, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (46724005..46791701, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (47158544..47219780, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene SLC38A4 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:46997992-46998511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:47011695-47012195 Neighboring gene olfactory receptor family 7 subfamily A member 19 pseudogene Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:47063431-47064104 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:47064118-47064618 Neighboring gene microtubule affinity regulating kinase 3 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:47219240-47219798 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:47219799-47220356 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:47225315-47226123 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:47232393-47232579 Neighboring gene uncharacterized LOC124902924 Neighboring gene uncharacterized LOC124902925

    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. The SNAT4 isoform of the system A amino acid transporter is functional in human placental microvillous plasma membrane. Desforges M, et al. J Physiol, 2009 Jan 15. PMID 19015196, Free PMC Article
    2. Evidence for the transport of neutral as well as cationic amino acids by ATA3, a novel and liver-specific subtype of amino acid transport system A. Hatanaka T, et al. Biochim Biophys Acta, 2001 Feb 9. PMID 11342143
    3. A novel human amino acid transporter, hNAT3: cDNA cloning, chromosomal mapping, genomic structure, expression, and functional characterization. Gu S, et al. Genomics, 2001 Jun 15. PMID 11414754
    4. Sodium-coupled neutral amino acid (System N/A) transporters of the SLC38 gene family. Mackenzie B, et al. Pflugers Arch, 2004 Feb. PMID 12845534
    5. SNAT4 isoform of system A amino acid transporter is expressed in human placenta. Desforges M, et al. Am J Physiol Cell Physiol, 2006 Jan. PMID 16148032

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Platelets Affect the Activity of Amino Acid Transporter SNAT4 in HuH-7 Human Hepatoma Cells.
      Title: Platelets Affect the Activity of Amino Acid Transporter SNAT4 in HuH-7 Human Hepatoma Cells.
    2. SLC38A4 Amino Acid Transporter Expression Is Significantly Lower in Early Preterm Intrauterine Growth Restriction Complicated Placentas.
      Title: SLC38A4 Amino Acid Transporter Expression Is Significantly Lower in Early Preterm Intrauterine Growth Restriction Complicated Placentas.
    3. SLC38A4 functions as a tumour suppressor in hepatocellular carcinoma through modulating Wnt/beta-catenin/MYC/HMGCS2 axis.
      Title: SLC38A4 functions as a tumour suppressor in hepatocellular carcinoma through modulating Wnt/β-catenin/MYC/HMGCS2 axis.
    4. three SNPs (corepressor interacting with RBPJ 1 (CIR1) rs13009079T>C, ribonucleotide reductase M1 (RRM1) rs1465952T>C and solute carrier family 38, member 4 (SLC38A4) rs2429467C>T), may play a role in the pathogenesis of lung cancer
      Title: Polymorphisms in cancer-related pathway genes and lung cancer.
    5. PAAT is a novel ATPase and a trans-regulator of mitochondrial ABC transporters that plays an important role in the maintenance of mitochondrial homeostasis
      Title: PAAT, a novel ATPase and trans-regulator of mitochondrial ABC transporters, is critically involved in the maintenance of mitochondrial homeostasis.
    6. Our results suggest that mutant allele A for SNP 1304 G>A of SLC38A4 gene is associated with hyperglycaemia.
      Title: Association of the polymorphisms 292 C>T and 1304 G>A in the SLC38A4 gene with hyperglycaemia.
    7. Membrane topological structure of neutral system N/A amino acid transporter 4 (SNAT4) protein
      Title: Membrane topological structure of neutral system N/A amino acid transporter 4 (SNAT4) protein.
    8. Report SNAT4 activity in fetal T lymphocytes in intrauterine growth restriction and with tumor necrosis factor-alpha treatment.
      Title: Amino acid transport systems beta and A in fetal T lymphocytes in intrauterine growth restriction and with tumor necrosis factor-alpha treatment.
    9. the contribution of SNAT4 to system A-mediated placental microvillous transport decreases between first trimester and term
      Title: The SNAT4 isoform of the system A amino acid transporter is functional in human placental microvillous plasma membrane.
    10. evidence of SNAT4 mRNA and protein expression in the human placenta, both at the first trimester and at full term
      Title: SNAT4 isoform of system A amino acid transporter is expressed in human placenta.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ10191, MGC126876

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables L-amino acid transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables L-arginine transmembrane transporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables alanine:sodium symporter activity IDA
    Inferred from Direct Assay
    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in L-alanine import across plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in L-arginine 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 amino acid transport TAS
    Traceable Author Statement
    more info
    		  
    involved_in neutral amino acid transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in sodium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in microvillus membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    sodium-coupled neutral amino acid transporter 4
    Names
    N amino acid transporter 3
    Na(+)-coupled neutral amino acid transporter 4
    amino acid transporter A3
    amino acid transporter system A3
    system A amino acid transporter 3
    system N amino acid transporter 3

    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_001143824.2 → NP_001137296.1  sodium-coupled neutral amino acid transporter 4

      See identical proteins and their annotated locations for NP_001137296.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      AC008014, AC080136, KF459548
      Consensus CDS
      CCDS8750.1
      UniProtKB/Swiss-Prot
      A8K553, Q969I6
      Related
      ENSP00000389843.1, ENST00000447411.5
      Conserved Domains (2) summary
      COG0814
      Location:71 → 534
      SdaC; Amino acid permease [Amino acid transport and metabolism]
      cl00456
      Location:73 → 535
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

    2. NM_018018.5 → NP_060488.2  sodium-coupled neutral amino acid transporter 4

      See identical proteins and their annotated locations for NP_060488.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 both encode the same protein.
      Source sequence(s)
      AC008014, AC080136, KF459548
      Consensus CDS
      CCDS8750.1
      UniProtKB/Swiss-Prot
      A8K553, Q969I6
      Related
      ENSP00000266579.4, ENST00000266579.9
      Conserved Domains (2) summary
      COG0814
      Location:71 → 534
      SdaC; Amino acid permease [Amino acid transport and metabolism]
      cl00456
      Location:73 → 535
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      46764761..46832431 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005268997.3 → XP_005269054.1  sodium-coupled neutral amino acid transporter 4 isoform X1

      See identical proteins and their annotated locations for XP_005269054.1

      UniProtKB/Swiss-Prot
      A8K553, Q969I6
      Conserved Domains (2) summary
      COG0814
      Location:71 → 534
      SdaC; Amino acid permease [Amino acid transport and metabolism]
      cl00456
      Location:73 → 535
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      46724005..46791701 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054372383.1 → XP_054228358.1  sodium-coupled neutral amino acid transporter 4 isoform X1

      UniProtKB/Swiss-Prot
      A8K553, Q969I6

    2. XM_054372385.1 → XP_054228360.1  sodium-coupled neutral amino acid transporter 4 isoform X1

      UniProtKB/Swiss-Prot
      A8K553, Q969I6

    3. XM_054372384.1 → XP_054228359.1  sodium-coupled neutral amino acid transporter 4 isoform X1

      UniProtKB/Swiss-Prot
      A8K553, Q969I6
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q969I6.1 GenPept UniProtKB/Swiss-Prot:Q969I6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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