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

    Gene ID: 153129, updated on 11-Apr-2024

    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; AllianceGenome:HGNC:26907
    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
    SNAT9; URLC11
    Summary
    Enables L-arginine transmembrane transporter activity and L-leucine transmembrane transporter activity. Involved in amino acid transmembrane transport; cellular response to amino acid stimulus; and positive regulation of TOR signaling. Located in late endosome and lysosomal membrane. Is integral component of lysosomal membrane. Colocalizes with Ragulator complex. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in placenta (RPKM 15.1), testis (RPKM 7.5) and 22 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Location:
    5q11.2
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (55625845..55712335, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (56453712..56540626, complement)
    105.20220307 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 H3K27ac hESC enhancer GRCh37_chr5:54870447-54871333 Neighboring gene adenylate kinase 4 pseudogene 2 Neighboring gene uncharacterized LOC124900980 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:54899656-54900855 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:54921170-54921984 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:54937991-54938490 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:54991046-54991576 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22556 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22557 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:55008415-55009058 Neighboring gene S-phase kinase-associated protein 1-like Neighboring gene DEAD-box helicase 4 Neighboring gene RNA, 5S ribosomal pseudogene 183

    Genomic regions, transcripts, and products

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ46104, FLJ90709, MGC120544

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    part_of FNIP-folliculin RagC/D GAP IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of Ragulator complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in late endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in late endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in lysosomal membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lysosomal membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in lysosomal membrane TAS
    Traceable Author Statement
    more info
     
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

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

    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_001258286.1NP_001245215.1  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  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/TrEMBL
      D6R9Q7
      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  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  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
      UniProtKB/Swiss-Prot
      A0A0A8K8P2, B3KXV1, B7Z7D0, Q0P5S0, Q6MZJ8, Q8NBW4
      UniProtKB/TrEMBL
      D6R9Q7
      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  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
      UniProtKB/Swiss-Prot
      A0A0A8K8P2, B3KXV1, B7Z7D0, Q0P5S0, Q6MZJ8, Q8NBW4
      UniProtKB/TrEMBL
      D6R9Q7
      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  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
      UniProtKB/Swiss-Prot
      A0A0A8K8P2, B3KXV1, B7Z7D0, Q0P5S0, Q6MZJ8, Q8NBW4
      UniProtKB/TrEMBL
      D6R9Q7
      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  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
      UniProtKB/TrEMBL
      D6R9Q7
      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  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
      A0A0A8K8P2, B3KXV1, B7Z7D0, Q0P5S0, Q6MZJ8, Q8NBW4
      UniProtKB/TrEMBL
      D6R9Q7
      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: 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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      55625845..55712335 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047416799.1XP_047272755.1  neutral amino acid transporter 9 isoform X12

    2. XM_047416796.1XP_047272752.1  neutral amino acid transporter 9 isoform X10

    3. XM_047416789.1XP_047272745.1  neutral amino acid transporter 9 isoform X6

    4. XM_017009078.3XP_016864567.1  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
    5. XM_017009082.2XP_016864571.1  neutral amino acid transporter 9 isoform X9

      UniProtKB/TrEMBL
      D6R9Q7
      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
    6. XM_017009081.2XP_016864570.1  neutral amino acid transporter 9 isoform X8

      UniProtKB/TrEMBL
      D6R9Q7
    7. XM_024454369.2XP_024310137.1  neutral amino acid transporter 9 isoform X3

      UniProtKB/TrEMBL
      D6R9Q7
      Conserved Domains (1) summary
      cl00456
      Location:115520
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    8. XM_017009077.2XP_016864566.1  neutral amino acid transporter 9 isoform X2

      UniProtKB/TrEMBL
      D6R9Q7
      Conserved Domains (1) summary
      cl00456
      Location:115526
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    9. XM_047416786.1XP_047272742.1  neutral amino acid transporter 9 isoform X4

    10. XM_047416783.1XP_047272739.1  neutral amino acid transporter 9 isoform X3

    11. XM_006714539.4XP_006714602.1  neutral amino acid transporter 9 isoform X1

      See identical proteins and their annotated locations for XP_006714602.1

      UniProtKB/Swiss-Prot
      A0A0A8K8P2, B3KXV1, B7Z7D0, Q0P5S0, Q6MZJ8, Q8NBW4
      UniProtKB/TrEMBL
      D6R9Q7
      Conserved Domains (1) summary
      cl00456
      Location:115556
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    12. XM_047416797.1XP_047272753.1  neutral amino acid transporter 9 isoform X10

    13. XM_047416791.1XP_047272747.1  neutral amino acid transporter 9 isoform X6

    14. XM_047416785.1XP_047272741.1  neutral amino acid transporter 9 isoform X4

    15. XM_047416794.1XP_047272750.1  neutral amino acid transporter 9 isoform X9

    16. XM_017009080.2XP_016864569.1  neutral amino acid transporter 9 isoform X5

      UniProtKB/TrEMBL
      D6R9Q7
      Conserved Domains (1) summary
      cl00456
      Location:115491
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    17. XM_047416782.1XP_047272738.1  neutral amino acid transporter 9 isoform X3

    18. XM_047416779.1XP_047272735.1  neutral amino acid transporter 9 isoform X2

    19. XM_047416790.1XP_047272746.1  neutral amino acid transporter 9 isoform X6

    20. XM_047416784.1XP_047272740.1  neutral amino acid transporter 9 isoform X4

    21. XM_047416795.1XP_047272751.1  neutral amino acid transporter 9 isoform X9

    22. XM_047416788.1XP_047272744.1  neutral amino acid transporter 9 isoform X5

    23. XM_047416781.1XP_047272737.1  neutral amino acid transporter 9 isoform X3

    24. XM_047416780.1XP_047272736.1  neutral amino acid transporter 9 isoform X2

    25. XM_011543183.2XP_011541485.1  neutral amino acid transporter 9 isoform X10

      UniProtKB/TrEMBL
      D6R9Q7
      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
    26. XM_047416792.1XP_047272748.1  neutral amino acid transporter 9 isoform X7

    27. XM_011543178.2XP_011541480.1  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
    28. XM_011543180.2XP_011541482.1  neutral amino acid transporter 9 isoform X9

      UniProtKB/TrEMBL
      D6R9Q7
      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
    29. XM_047416793.1XP_047272749.1  neutral amino acid transporter 9 isoform X8

    30. XM_047416787.1XP_047272743.1  neutral amino acid transporter 9 isoform X5

    31. XM_011543177.2XP_011541479.1  neutral amino acid transporter 9 isoform X3

      UniProtKB/TrEMBL
      D6R9Q7
      Conserved Domains (1) summary
      cl00456
      Location:115520
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    32. XM_011543176.2XP_011541478.1  neutral amino acid transporter 9 isoform X2

      UniProtKB/TrEMBL
      D6R9Q7
      Conserved Domains (1) summary
      cl00456
      Location:115526
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    33. XM_011543174.2XP_011541476.1  neutral amino acid transporter 9 isoform X1

      See identical proteins and their annotated locations for XP_011541476.1

      UniProtKB/Swiss-Prot
      A0A0A8K8P2, B3KXV1, B7Z7D0, Q0P5S0, Q6MZJ8, Q8NBW4
      UniProtKB/TrEMBL
      D6R9Q7
      Conserved Domains (1) summary
      cl00456
      Location:115556
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
    34. XM_047416778.1XP_047272734.1  neutral amino acid transporter 9 isoform X1

      UniProtKB/Swiss-Prot
      A0A0A8K8P2, B3KXV1, B7Z7D0, Q0P5S0, Q6MZJ8, Q8NBW4
    35. XM_047416798.1XP_047272754.1  neutral amino acid transporter 9 isoform X11

    RNA

    1. XR_007058583.1 RNA Sequence

    2. XR_007058582.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      56453712..56540626 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054351760.1XP_054207735.1  neutral amino acid transporter 9 isoform X12

    2. XM_054351757.1XP_054207732.1  neutral amino acid transporter 9 isoform X10

    3. XM_054351746.1XP_054207721.1  neutral amino acid transporter 9 isoform X6

    4. XM_054351738.1XP_054207713.1  neutral amino acid transporter 9 isoform X4

    5. XM_054351752.1XP_054207727.1  neutral amino acid transporter 9 isoform X9

    6. XM_054351750.1XP_054207725.1  neutral amino acid transporter 9 isoform X8

    7. XM_054351733.1XP_054207708.1  neutral amino acid transporter 9 isoform X3

    8. XM_054351729.1XP_054207704.1  neutral amino acid transporter 9 isoform X2

    9. XM_054351742.1XP_054207717.1  neutral amino acid transporter 9 isoform X4

    10. XM_054351737.1XP_054207712.1  neutral amino acid transporter 9 isoform X3

    11. XM_054351728.1XP_054207703.1  neutral amino acid transporter 9 isoform X1

    12. XM_054351758.1XP_054207733.1  neutral amino acid transporter 9 isoform X10

    13. XM_054351748.1XP_054207723.1  neutral amino acid transporter 9 isoform X6

    14. XM_054351741.1XP_054207716.1  neutral amino acid transporter 9 isoform X4

    15. XM_054351754.1XP_054207729.1  neutral amino acid transporter 9 isoform X9

    16. XM_054351744.1XP_054207719.1  neutral amino acid transporter 9 isoform X5

    17. XM_054351736.1XP_054207711.1  neutral amino acid transporter 9 isoform X3

    18. XM_054351730.1XP_054207705.1  neutral amino acid transporter 9 isoform X2

    19. XM_054351747.1XP_054207722.1  neutral amino acid transporter 9 isoform X6

    20. XM_054351739.1XP_054207714.1  neutral amino acid transporter 9 isoform X4

    21. XM_054351755.1XP_054207730.1  neutral amino acid transporter 9 isoform X9

    22. XM_054351745.1XP_054207720.1  neutral amino acid transporter 9 isoform X5

    23. XM_054351735.1XP_054207710.1  neutral amino acid transporter 9 isoform X3

    24. XM_054351731.1XP_054207706.1  neutral amino acid transporter 9 isoform X2

    25. XM_054351756.1XP_054207731.1  neutral amino acid transporter 9 isoform X10

    26. XM_054351749.1XP_054207724.1  neutral amino acid transporter 9 isoform X7

    27. XM_054351740.1XP_054207715.1  neutral amino acid transporter 9 isoform X4

    28. XM_054351753.1XP_054207728.1  neutral amino acid transporter 9 isoform X9

    29. XM_054351751.1XP_054207726.1  neutral amino acid transporter 9 isoform X8

    30. XM_054351743.1XP_054207718.1  neutral amino acid transporter 9 isoform X5

    31. XM_054351734.1XP_054207709.1  neutral amino acid transporter 9 isoform X3

    32. XM_054351732.1XP_054207707.1  neutral amino acid transporter 9 isoform X2

    33. XM_054351727.1XP_054207702.1  neutral amino acid transporter 9 isoform X1

    34. XM_054351726.1XP_054207701.1  neutral amino acid transporter 9 isoform X1

    35. XM_054351759.1XP_054207734.1  neutral amino acid transporter 9 isoform X11

    RNA

    1. XR_008487084.1 RNA Sequence

    2. XR_008487083.1 RNA Sequence