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SLC38A1 solute carrier family 38 member 1 [ Homo sapiens (human) ]

Gene ID: 81539, updated on 21-Dec-2019

Summary

Official Symbol
SLC38A1provided by HGNC
Official Full Name
solute carrier family 38 member 1provided by HGNC
Primary source
HGNC:HGNC:13447
See related
Ensembl:ENSG00000111371 MIM:608490
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
ATA1; NAT2; SAT1; SNAT1
Summary
Amino acid transporters play essential roles in the uptake of nutrients, production of energy, chemical metabolism, detoxification, and neurotransmitter cycling. SLC38A1 is an important transporter of glutamine, an intermediate in the detoxification of ammonia and the production of urea. Glutamine serves as a precursor for the synaptic transmitter, glutamate (Gu et al., 2001 [PubMed 11325958]).[supplied by OMIM, Mar 2008]
Expression
Broad expression in lymph node (RPKM 24.7), thyroid (RPKM 21.1) and 23 other tissues See more
Orthologs

Genomic context

See SLC38A1 in Genome Data Viewer
Location:
12q13.11
Exon count:
22
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (46183063..46269149, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (46576838..46663208, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene SR-related CTD associated factor 11 Neighboring gene ribosomal protein L13a pseudogene 21 Neighboring gene uncharacterized LOC105378248 Neighboring gene uncharacterized LOC102723757 Neighboring gene solute carrier family 38 member 2

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 SLC38A1 PubMed

Protein interactions

Protein Gene Interaction Pubs
Vpu vpu HIV-1 Vpu degrades SLC38A1 (SNAT1) via the same pathway utilized for antgonism of BST2 (tetherin) but occurs independently of BST2 (tetherin) downregulation PubMed
vpu HIV-1 Vpu ubiquitinates endogeneous SLC38A1 (SNAT1) in HeLa cells PubMed
vpu HIV-1 Vpu binds endogeneous SLC38A1 (SNAT1) and is a beta-TrCP-dependent substrate PubMed
vpu HIV-1 Vpu depletes SLC38A1 (SNAT1) from activated primary human CD4+ T cells in the context of viral infection and as a single gene in transduced cells purified by antibody-free magnetic cell sorting (AFMACS) PubMed
vpu HIV-1 Vpu downregulates cell (CEMT4) surface expression of SLC38A1 (SNAT1) 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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
L-amino acid transmembrane transporter activity TAS
Traceable Author Statement
more info
 
amino acid transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
amino acid transmembrane transporter activity TAS
Traceable Author Statement
more info
 
amino acid:sodium symporter activity NAS
Non-traceable Author Statement
more info
PubMed 
neutral amino acid transmembrane transporter activity NAS
Non-traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
L-alpha-amino acid transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
amino acid transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
amino acid transport TAS
Traceable Author Statement
more info
 
neurotransmitter uptake TAS
Traceable Author Statement
more info
 
neutral amino acid transport NAS
Non-traceable Author Statement
more info
PubMed 
sodium ion transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
extracellular exosome HDA PubMed 
integral component of membrane NAS
Non-traceable Author Statement
more info
PubMed 
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
sodium-coupled neutral amino acid transporter 1
Names
N-system amino acid transporter 2
amino acid transporter A1
amino acid transporter system A1
system A amino acid transporter 1
system N amino acid transporter 1

NCBI Reference Sequences (RefSeq)

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_001077484.2NP_001070952.1  sodium-coupled neutral amino acid transporter 1 isoform 1

    See identical proteins and their annotated locations for NP_001070952.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 3. Variants 1, 2, 3, 4 and 5 encode the same isoform 1.
    Source sequence(s)
    AC016254, AK056670, BC010620, BX648495, DB229647
    Consensus CDS
    CCDS41774.1
    UniProtKB/Swiss-Prot
    Q9H2H9
    UniProtKB/TrEMBL
    A0A024R124
    Related
    ENSP00000447853.1, ENST00000546893.5
    Conserved Domains (1) summary
    cl00456
    Location:69474
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  2. NM_001278387.2NP_001265316.1  sodium-coupled neutral amino acid transporter 1 isoform 1

    See identical proteins and their annotated locations for NP_001265316.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) is the longest transcript and encodes the predominant isoform (1). Variants 1, 2, 3, 4 and 5 encode the same isoform 1.
    Source sequence(s)
    AC016254, AC025031, BQ019472, BX647547, BX648495, DB229647
    Consensus CDS
    CCDS41774.1
    UniProtKB/Swiss-Prot
    Q9H2H9
    UniProtKB/TrEMBL
    A0A024R124
    Related
    ENSP00000398142.1, ENST00000439706.5
    Conserved Domains (1) summary
    cl00456
    Location:69474
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  3. NM_001278388.2NP_001265317.1  sodium-coupled neutral amino acid transporter 1 isoform 1

    See identical proteins and their annotated locations for NP_001265317.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks two exons in the 5' UTR, compared to variant 3. Variants 1, 2, 3, 4 and 5 encode the same isoform 1.
    Source sequence(s)
    AC016254, BQ019472, BX648676, DB229647
    Consensus CDS
    CCDS41774.1
    UniProtKB/Swiss-Prot
    Q9H2H9
    UniProtKB/TrEMBL
    A0A024R124
    Related
    ENSP00000449607.1, ENST00000549049.5
    Conserved Domains (1) summary
    cl00456
    Location:69474
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  4. NM_001278389.2NP_001265318.1  sodium-coupled neutral amino acid transporter 1 isoform 1

    See identical proteins and their annotated locations for NP_001265318.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, compared to variant 3. Variants 1, 2, 3, 4 and 5 encode the same isoform 1.
    Source sequence(s)
    AC016254, AC025031, AK027825, BC010620, BQ019472
    Consensus CDS
    CCDS41774.1
    UniProtKB/Swiss-Prot
    Q9H2H9
    UniProtKB/TrEMBL
    A0A024R124
    Conserved Domains (1) summary
    cl00456
    Location:69474
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  5. NM_001278390.1NP_001265319.1  sodium-coupled neutral amino acid transporter 1 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and has an alternate 3' terminal exon, compared to variant 3. The resulting isoform (2) is longer and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AA740867, AA864710, AK309410
    Consensus CDS
    CCDS61106.1
    UniProtKB/TrEMBL
    F8VX04
    Related
    ENSP00000449756.1, ENST00000552197.5
    Conserved Domains (2) summary
    COG0814
    Location:68441
    SdaC; Amino acid permease [Amino acid transport and metabolism]
    cl00456
    Location:69480
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  6. NM_030674.4NP_109599.3  sodium-coupled neutral amino acid transporter 1 isoform 1

    See identical proteins and their annotated locations for NP_109599.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) lacks an exon in the 5' UTR, compared to variant 3. Variants 1, 2, 3, 4 and 5 encode the same isoform 1.
    Source sequence(s)
    AC016254, AK056670, BC010620, BX648495, DB229647
    Consensus CDS
    CCDS41774.1
    UniProtKB/Swiss-Prot
    Q9H2H9
    UniProtKB/TrEMBL
    A0A024R124
    Related
    ENSP00000381634.4, ENST00000398637.10
    Conserved Domains (1) summary
    cl00456
    Location:69474
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    46183063..46269149 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011538784.2XP_011537086.1  sodium-coupled neutral amino acid transporter 1 isoform X1

    See identical proteins and their annotated locations for XP_011537086.1

    Conserved Domains (2) summary
    COG0814
    Location:68441
    SdaC; Amino acid permease [Amino acid transport and metabolism]
    cl00456
    Location:69475
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  2. XM_011538786.2XP_011537088.1  sodium-coupled neutral amino acid transporter 1 isoform X2

    See identical proteins and their annotated locations for XP_011537088.1

    Conserved Domains (2) summary
    COG0814
    Location:68441
    SdaC; Amino acid permease [Amino acid transport and metabolism]
    cl00456
    Location:69454
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  3. XM_011538787.2XP_011537089.1  sodium-coupled neutral amino acid transporter 1 isoform X3

    See identical proteins and their annotated locations for XP_011537089.1

    Conserved Domains (1) summary
    cl00456
    Location:69456
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  4. XM_017019990.1XP_016875479.1  sodium-coupled neutral amino acid transporter 1 isoform X3

    Conserved Domains (1) summary
    cl00456
    Location:69456
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
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