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SLC38A9 solute carrier family 38 member 9 [ Homo sapiens (human) ]

Gene ID: 153129, updated on 17-Jun-2019

Summary

Official Symbol
SLC38A9provided by HGNC
Official Full Name
solute carrier family 38 member 9provided by HGNC
Primary source
HGNC:HGNC:26907
See related
Ensembl:ENSG00000177058 MIM:616203
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
URLC11
Expression
Broad expression in placenta (RPKM 15.1), testis (RPKM 7.5) and 22 other tissues See more
Orthologs

Genomic context

See SLC38A9 in Genome Data Viewer
Location:
5q11.2
Exon count:
21
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (55625845..55712343, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (54921673..55008163, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene adenylate kinase 4 pseudogene 2 Neighboring gene uncharacterized LOC105378975 Neighboring gene S-phase kinase-associated protein 1 pseudogene Neighboring gene DEAD-box helicase 4 Neighboring gene RNA, 5S ribosomal pseudogene 183

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 FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
NHGRI GWA Catalog

Pathways from BioSystems

  • mTOR signaling pathway, organism-specific biosystem (from KEGG)
    mTOR signaling pathway, organism-specific biosystemThe mammalian (mechanistic) target of rapamycin (mTOR) is a highly conserved serine/threonine protein kinase, which exists in two complexes termed mTOR complex 1 (mTORC1) and 2 (mTORC2). mTORC1 conta...
  • mTOR signaling pathway, conserved biosystem (from KEGG)
    mTOR signaling pathway, conserved biosystemThe mammalian (mechanistic) target of rapamycin (mTOR) is a highly conserved serine/threonine protein kinase, which exists in two complexes termed mTOR complex 1 (mTORC1) and 2 (mTORC2). mTORC1 conta...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ46104, FLJ90709, MGC120544

Gene Ontology Provided by GOA

Function Evidence Code Pubs
L-arginine transmembrane transporter activity IDA
Inferred from Direct Assay
more info
PubMed 
L-leucine transmembrane transporter activity IDA
Inferred from Direct Assay
more info
PubMed 
amino acid transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
amino acid transmembrane transporter activity IDA
Inferred from Direct Assay
more info
PubMed 
amino acid transmembrane transporter activity TAS
Traceable Author Statement
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
L-arginine 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 transmembrane transport IDA
Inferred from Direct Assay
more info
PubMed 
branched-chain amino acid transport IEA
Inferred from Electronic Annotation
more info
 
cell cycle arrest TAS
Traceable Author Statement
more info
 
cellular response to amino acid stimulus IDA
Inferred from Direct Assay
more info
PubMed 
neutral amino acid transport IEA
Inferred from Electronic Annotation
more info
 
positive regulation of TOR signaling IDA
Inferred from Direct Assay
more info
PubMed 
regulation of macroautophagy TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
colocalizes_with Ragulator complex IDA
Inferred from Direct Assay
more info
PubMed 
integral component of lysosomal membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
late endosome IDA
Inferred from Direct Assay
more info
PubMed 
lysosomal membrane TAS
Traceable Author Statement
more info
 
lysosome IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
sodium-coupled neutral amino acid transporter 9
Names
putative sodium-coupled neutral amino acid transporter 9
up-regulated in lung cancer 11

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_001258286.1NP_001245215.1  sodium-coupled neutral amino acid transporter 9 isoform 2

    See identical proteins and their annotated locations for NP_001245215.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus than isoform 1.
    Source sequence(s)
    AC008784, AI580489, BC036232
    Consensus CDS
    CCDS58947.1
    UniProtKB/Swiss-Prot
    Q8NBW4
    Related
    ENSP00000420934.1, ENST00000515629.5
    Conserved Domains (2) summary
    COG0814
    Location:52498
    SdaC; Amino acid permease [Amino acid transport and metabolism]
    cl00456
    Location:52493
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  2. NM_001258287.1NP_001245216.1  sodium-coupled neutral amino acid transporter 9 isoform 3

    See identical proteins and their annotated locations for NP_001245216.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) has multiple differences, including translation initiation at an alternate start codon, compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AI580489, AK127988, BC036232, BX641065
    Consensus CDS
    CCDS58948.1
    UniProtKB/Swiss-Prot
    Q8NBW4
    Related
    ENSP00000427335.1, ENST00000512595.5
    Conserved Domains (2) summary
    COG0814
    Location:88498
    SdaC; Amino acid permease [Amino acid transport and metabolism]
    cl00456
    Location:88493
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  3. NM_001282429.1NP_001269358.1  sodium-coupled neutral amino acid transporter 9 isoform 4

    See identical proteins and their annotated locations for NP_001269358.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses an alternate 5' exon structure and thus differs in the 5' UTR and 5' coding region compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (4) with a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AI580489, AK122957, DC371481
    Consensus CDS
    CCDS75243.1
    UniProtKB/TrEMBL
    B3KVK8
    Related
    ENSP00000397429.2, ENST00000416547.6
    Conserved Domains (2) summary
    COG0814
    Location:1437
    SdaC; Amino acid permease [Amino acid transport and metabolism]
    cl00456
    Location:4432
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  4. NM_001349382.1NP_001336311.1  sodium-coupled neutral amino acid transporter 9 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR compared to variant 1. Variants 1 6, 7 and 8 encode the same isoform (1).
    Source sequence(s)
    AC016632, AI580489, AK075190, BC066891, DB207931, DC371481
    Consensus CDS
    CCDS3968.1
    Conserved Domains (1) summary
    cl00456
    Location:115556
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  5. NM_001349383.1NP_001336312.1  sodium-coupled neutral amino acid transporter 9 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) differs in the 5' UTR compared to variant 1. Variants 1 6, 7 and 8 encode the same isoform (1).
    Source sequence(s)
    AC016632, AI580489, AK075190, BC066891, DB158005, DB207931, DC371481
    Consensus CDS
    CCDS3968.1
    Conserved Domains (1) summary
    cl00456
    Location:115556
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  6. NM_001349384.1NP_001336313.1  sodium-coupled neutral amino acid transporter 9 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (8) differs in the 5' UTR compared to variant 1. Variants 1 6, 7 and 8 encode the same isoform (1).
    Source sequence(s)
    AI580489, AK075190, BC066891, DC371481, DC398501
    Consensus CDS
    CCDS3968.1
    Conserved Domains (1) summary
    cl00456
    Location:115556
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  7. NM_001349385.1NP_001336314.1  sodium-coupled neutral amino acid transporter 9 isoform 5

    Status: VALIDATED

    Description
    Transcript Variant: This variant (9) lacks an alternate in-frame exon in the central coding region compared to variant 1. The encoded isoform (5) has the same N- and C-termiini, but is shorter than isoform 1.
    Source sequence(s)
    AI580489, AK075190, BC066891, DC371481
    Related
    ENSP00000423219.1, ENST00000511233.5
    Conserved Domains (1) summary
    cl00456
    Location:115491
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  8. NM_173514.4NP_775785.2  sodium-coupled neutral amino acid transporter 9 isoform 1

    See identical proteins and their annotated locations for NP_775785.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1). Variants 1 6, 7 and 8 encode the same isoform (1).
    Source sequence(s)
    AI580489, AK075190, BC066891, DC371481
    Consensus CDS
    CCDS3968.1
    UniProtKB/Swiss-Prot
    Q8NBW4
    UniProtKB/TrEMBL
    A0A024QZR9
    Related
    ENSP00000380074.2, ENST00000396865.7
    Conserved Domains (1) summary
    cl00456
    Location:115556
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

RNA

  1. NR_047649.1 RNA Sequence

    Status: VALIDATED

    Description
    This variant (5) uses an alternate 5' exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC008784, AI580489, BC036232, BC045589, BX641065
    Related
    ENST00000505708.5
  2. NR_146165.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (10) uses an alternate splice site at an internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI580489, AK075190, BC066891, DC371481
    Related
    ENST00000508124.5

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    55625845..55712343 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006714539.3XP_006714602.1  sodium-coupled neutral amino acid transporter 9 isoform X1

    See identical proteins and their annotated locations for XP_006714602.1

    UniProtKB/Swiss-Prot
    Q8NBW4
    UniProtKB/TrEMBL
    A0A024QZR9
    Conserved Domains (1) summary
    cl00456
    Location:115556
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  2. XM_017009080.1XP_016864569.1  sodium-coupled neutral amino acid transporter 9 isoform X5

    Conserved Domains (1) summary
    cl00456
    Location:115491
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  3. XM_011543184.1XP_011541486.1  sodium-coupled neutral amino acid transporter 9 isoform X10

    Conserved Domains (1) summary
    cl00456
    Location:199398
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  4. XM_011543183.1XP_011541485.1  sodium-coupled neutral amino acid transporter 9 isoform X9

    Conserved Domains (2) summary
    COG0814
    Location:115439
    SdaC; Amino acid permease [Amino acid transport and metabolism]
    cl00456
    Location:115434
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  5. XM_011543178.1XP_011541480.1  sodium-coupled neutral amino acid transporter 9 isoform X4

    Conserved Domains (2) summary
    COG0814
    Location:115504
    SdaC; Amino acid permease [Amino acid transport and metabolism]
    cl00456
    Location:115499
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  6. XM_011543180.1XP_011541482.1  sodium-coupled neutral amino acid transporter 9 isoform X7

    Conserved Domains (2) summary
    COG0814
    Location:115460
    SdaC; Amino acid permease [Amino acid transport and metabolism]
    cl00456
    Location:115455
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  7. XM_011543177.1XP_011541479.1  sodium-coupled neutral amino acid transporter 9 isoform X3

    Conserved Domains (1) summary
    cl00456
    Location:115520
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  8. XM_011543176.1XP_011541478.1  sodium-coupled neutral amino acid transporter 9 isoform X2

    Conserved Domains (1) summary
    cl00456
    Location:115526
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  9. XM_011543174.1XP_011541476.1  sodium-coupled neutral amino acid transporter 9 isoform X1

    See identical proteins and their annotated locations for XP_011541476.1

    UniProtKB/Swiss-Prot
    Q8NBW4
    UniProtKB/TrEMBL
    A0A024QZR9
    Conserved Domains (1) summary
    cl00456
    Location:115556
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  10. XM_017009082.1XP_016864571.1  sodium-coupled neutral amino acid transporter 9 isoform X7

    Conserved Domains (2) summary
    COG0814
    Location:115460
    SdaC; Amino acid permease [Amino acid transport and metabolism]
    cl00456
    Location:115455
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  11. XM_017009081.1XP_016864570.1  sodium-coupled neutral amino acid transporter 9 isoform X6

  12. XM_024454369.1XP_024310137.1  sodium-coupled neutral amino acid transporter 9 isoform X3

    Conserved Domains (1) summary
    cl00456
    Location:115520
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  13. XM_017009078.2XP_016864567.1  sodium-coupled neutral amino acid transporter 9 isoform X4

    Conserved Domains (2) summary
    COG0814
    Location:115504
    SdaC; Amino acid permease [Amino acid transport and metabolism]
    cl00456
    Location:115499
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  14. XM_017009077.1XP_016864566.1  sodium-coupled neutral amino acid transporter 9 isoform X2

    Conserved Domains (1) summary
    cl00456
    Location:115526
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
  15. XM_011543182.1XP_011541484.1  sodium-coupled neutral amino acid transporter 9 isoform X8

    See identical proteins and their annotated locations for XP_011541484.1

    Conserved Domains (1) summary
    cl00456
    Location:115415
    SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

RNA

  1. XR_001742002.1 RNA Sequence

  2. XR_948238.1 RNA Sequence

  3. XR_948237.2 RNA Sequence

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