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    SLC6A20 solute carrier family 6 member 20 [ Homo sapiens (human) ]

    Gene ID: 54716, updated on 9-Dec-2024

    Summary

    Official Symbol
    SLC6A20provided by HGNC
    Official Full Name
    solute carrier family 6 member 20provided by HGNC
    Primary source
    HGNC:HGNC:30927
    See related
    Ensembl:ENSG00000163817 MIM:605616; AllianceGenome:HGNC:30927
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    XT3; SIT1; IMINO; Xtrp3
    Summary
    Transport of small hydrophilic substances across cell membranes is mediated by substrate-specific transporter proteins which have been classified into several families of related genes. The protein encoded by this gene belongs to the sodium:neurotransmitter symporter (SNF) family and functions as a proline transporter expressed in kidney and small intestine. Mutations in this gene are associated with Hyperglycinuria and Iminoglycinuria. [provided by RefSeq, Jul 2020]
    Annotation information
    Note: This gene has been reviewed for its involvement in coronavirus biology, and is locus in the vicinity of disease-associated variant(s).
    Expression
    Biased expression in duodenum (RPKM 11.0), small intestine (RPKM 8.2) and 4 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SLC6A20 in Genome Data Viewer
    Location:
    3p21.31
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (45755449..45796536, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (45771093..45812175, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (45796941..45838028, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19784 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19785 Neighboring gene tRNA-Arg (anticodon ACG) 2-1 Neighboring gene SAC1 like phosphatidylinositide phosphatase Neighboring gene ReSE screen-validated silencer GRCh37_chr3:45769094-45769290 Neighboring gene RNA, 7SL, cytoplasmic 145, pseudogene Neighboring gene uncharacterized LOC107986082 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:45859284-45860483 Neighboring gene leucine zipper transcription factor like 1 Neighboring gene uncharacterized LOC124909374 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:45921781-45921937 Neighboring gene succinate dehydrogenase complex subunit D pseudogene 4

    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

    Related articles in PubMed

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    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
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    EBI GWAS Catalog
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    EBI GWAS Catalog
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    Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients.
    EBI GWAS Catalog
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    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Vif vif HIV-1 Vif downregulates the expression of solute carrier family 6, member 20 (SLC6A20) in Vif-expression T cells 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

    • MGC161475

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables L-isoleucine transmembrane transporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    enables L-proline transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables L-proline transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables L-proline transmembrane transporter activity IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    enables amino acid transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables amino acid transmembrane transporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    enables amino acid transmembrane transporter activity TAS
    Traceable Author Statement
    more info
     
    enables amino-acid betaine transmembrane transporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables neutral L-amino acid transmembrane transporter activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables neutral L-amino acid transmembrane transporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables proline:sodium symporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables proline: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
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables solute:sodium symporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in L-isoleucine import across plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in L-proline import across plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in L-proline import across plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in L-proline import across plasma membrane IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in amino acid import across plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in amino acid transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in amino acid transport TAS
    Traceable Author Statement
    more info
     
    involved_in amino-acid betaine transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in glycine import across plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in glycine import across plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in glycine transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in proline import across plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in proline transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in sodium ion transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in transport across blood-brain barrier NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in apical plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in apical plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in apical plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    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

    Preferred Names
    sodium- and chloride-dependent transporter XTRP3
    Names
    X transporter protein 3
    neurotransmitter transporter RB21A
    orphan transporter XT3
    sodium-dependent imino acid transporter 1
    sodium/imino-acid transporter 1
    solute carrier family 6 (neurotransmitter transporter), member 20
    solute carrier family 6 (proline IMINO transporter), member 20
    transporter rB21A homolog

    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.

    Genomic

    1. NG_023204.1 RefSeqGene

      Range
      5008..46095
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001385683.1NP_001372612.1  sodium- and chloride-dependent transporter XTRP3 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC098476
      Consensus CDS
      CCDS93258.1
      UniProtKB/TrEMBL
      A0A8V8TQV4
      Related
      ENSP00000515266.1, ENST00000703343.1
      Conserved Domains (1) summary
      cd11518
      Location:2588
      SLC6sbd_SIT1; Na(+)- and Cl(-)-dependent imino acid transporter SIT1; solute-binding domain
    2. NM_001406066.1NP_001392995.1  sodium- and chloride-dependent transporter XTRP3 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC098476
      UniProtKB/TrEMBL
      B7ZLW4
    3. NM_001406067.1NP_001392996.1  sodium- and chloride-dependent transporter XTRP3 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC098476
    4. NM_001406069.1NP_001392998.1  sodium- and chloride-dependent transporter XTRP3 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC098476
    5. NM_020208.4NP_064593.1  sodium- and chloride-dependent transporter XTRP3 isoform 1

      See identical proteins and their annotated locations for NP_064593.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform 1.
      Source sequence(s)
      AC098476, AJ276207, DR006419, EL949345
      Consensus CDS
      CCDS43077.1
      UniProtKB/Swiss-Prot
      A1A4F2, O75590, Q8TF10, Q9NP91, Q9NPQ2, Q9NQ77
      Related
      ENSP00000346298.4, ENST00000358525.9
      Conserved Domains (1) summary
      cd11518
      Location:2577
      SLC6sbd_SIT1; Na(+)- and Cl(-)-dependent imino acid transporter SIT1; solute-binding domain
    6. NM_022405.4NP_071800.1  sodium- and chloride-dependent transporter XTRP3 isoform 2

      See identical proteins and their annotated locations for NP_071800.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1, resulting in a shorter protein (isoform 2) compared to isoform 1.
      Source sequence(s)
      AC098476, AJ276208, DR006419, EL949345
      Consensus CDS
      CCDS2730.1
      UniProtKB/Swiss-Prot
      Q9NP91
      Related
      ENSP00000296133.5, ENST00000353278.8
      Conserved Domains (1) summary
      cl00456
      Location:2540
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

    RNA

    1. NR_176011.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC098476
    2. NR_176012.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC098476

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      45755449..45796536 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011533847.3XP_011532149.1  sodium- and chloride-dependent transporter XTRP3 isoform X1

      Conserved Domains (1) summary
      cl00456
      Location:1478
      SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      45771093..45812175 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054346951.1XP_054202926.1  sodium- and chloride-dependent transporter XTRP3 isoform X1