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SLC22A5 solute carrier family 22 member 5 [ Homo sapiens (human) ]

Gene ID: 6584, updated on 17-Jun-2024

Summary

Official Symbol
SLC22A5provided by HGNC
Official Full Name
solute carrier family 22 member 5provided by HGNC
Primary source
HGNC:HGNC:10969
See related
Ensembl:ENSG00000197375 MIM:603377; AllianceGenome:HGNC:10969
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
CDSP; OCTN2
Summary
Polyspecific organic cation transporters in the liver, kidney, intestine, and other organs are critical for elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. The encoded protein is a plasma integral membrane protein which functions both as an organic cation transporter and as a sodium-dependent high affinity carnitine transporter. The encoded protein is involved in the active cellular uptake of carnitine. Mutations in this gene are the cause of systemic primary carnitine deficiency (CDSP), an autosomal recessive disorder manifested early in life by hypoketotic hypoglycemia and acute metabolic decompensation, and later in life by skeletal myopathy or cardiomyopathy. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2015]
Expression
Broad expression in kidney (RPKM 17.3), small intestine (RPKM 11.3) and 23 other tissues See more
Orthologs
NEW
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Try the new Transcript table

Genomic context

See SLC22A5 in Genome Data Viewer
Location:
5q31.1
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (132369710..132395612)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (132889604..132915514)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (131705402..131731304)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16315 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16316 Neighboring gene solute carrier family 22 member 4 Neighboring gene MIR3936 host gene Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:131656893-131657393 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131657550-131658068 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131658069-131658587 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:131681529-131681701 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:131690402-131691014 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23067 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16317 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131712295-131712796 Neighboring gene microRNA 3936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23068 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23069 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23070 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23071 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16318 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16319 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:131751322-131751510 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23073 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23074 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23075 Neighboring gene long intergenic non-protein coding RNA 2863 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131763030-131763616 Neighboring gene colitis associated IRF1 antisense regulator of intestinal homeostasis Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131763617-131764201 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:131780806-131781485 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:131786393-131787031 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:131791634-131791826 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131792105-131792775 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131792776-131793445 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131799668-131800632 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131800633-131801597 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:131801783-131802284 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16323 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23079 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23080 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:131821689-131822888 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16324 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:131825338-131825985 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16326 Neighboring gene interferon regulatory factor 1

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?

Phenotypes

Associated conditions

Description Tests
Renal carnitine transport defect Compare labs

EBI GWAS Catalog

Description
A large-scale, consortium-based genomewide association study of asthma.
EBI GWAS Catalog
An atlas of genetic influences on human blood metabolites.
EBI GWAS Catalog
Genome-wide association study of plasma N6 polyunsaturated fatty acids within the cohorts for heart and aging research in genomic epidemiology consortium.
EBI GWAS Catalog
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
EBI GWAS Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
EBI GWAS Catalog
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
EBI GWAS Catalog
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
EBI GWAS Catalog
Novel loci, including those related to Crohn disease, psoriasis, and inflammation, identified in a genome-wide association study of fibrinogen in 17 686 women: the Women's Genome Health Study.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ46769

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables (R)-carnitine transmembrane transporter activity IDA
Inferred from Direct Assay
more info
PubMed 
enables (R)-carnitine transmembrane transporter activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables (R)-carnitine transmembrane transporter activity ISS
Inferred from Sequence or Structural Similarity
more info
 
enables ATP binding IEA
Inferred from Electronic Annotation
more info
 
enables PDZ domain binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables amino-acid betaine transmembrane transporter activity IDA
Inferred from Direct Assay
more info
PubMed 
enables carnitine transmembrane transporter activity EXP
Inferred from Experiment
more info
PubMed 
enables carnitine transmembrane transporter activity IDA
Inferred from Direct Assay
more info
PubMed 
enables carnitine transmembrane transporter activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables carnitine transmembrane transporter activity TAS
Traceable Author Statement
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables quaternary ammonium group transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables quaternary ammonium group transmembrane transporter activity IDA
Inferred from Direct Assay
more info
PubMed 
enables quaternary ammonium group transmembrane transporter activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables symporter activity IEA
Inferred from Electronic Annotation
more info
 
enables xenobiotic transmembrane transporter activity IC
Inferred by Curator
more info
PubMed 
Process Evidence Code Pubs
involved_in (R)-carnitine transmembrane transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in (R)-carnitine transmembrane transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in (R)-carnitine transmembrane transport ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in (R)-carnitine transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in carnitine transmembrane transport TAS
Traceable Author Statement
more info
 
involved_in carnitine transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in carnitine transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of intestinal epithelial structure maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in quaternary ammonium group transport IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in quaternary ammonium group transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in quaternary ammonium group transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in response to symbiotic bacterium IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in response to tumor necrosis factor IDA
Inferred from Direct Assay
more info
PubMed 
involved_in response to type II interferon IDA
Inferred from Direct Assay
more info
PubMed 
involved_in sodium ion transport IEA
Inferred from Electronic Annotation
more info
 
involved_in sodium-dependent organic cation transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in transport across blood-brain barrier ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in transport across blood-brain barrier NAS
Non-traceable Author Statement
more info
PubMed 
involved_in xenobiotic detoxification by transmembrane export across the plasma membrane IC
Inferred by Curator
more info
PubMed 
Component Evidence Code Pubs
located_in apical plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in basal plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in brush border membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in brush border membrane ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in cytosol ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
 
located_in extracellular exosome HDA PubMed 
located_in plasma membrane IC
Inferred by Curator
more info
PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
organic cation/carnitine transporter 2
Names
high-affinity sodium dependent carnitine cotransporter
systemic carnitine deficiency

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_008982.2 RefSeqGene

    Range
    5007..30909
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001308122.2NP_001295051.1  organic cation/carnitine transporter 2 isoform a

    See identical proteins and their annotated locations for NP_001295051.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1, also known as OCTN2VT) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AB291606, AK128610, DA567722
    Consensus CDS
    CCDS78058.1
    UniProtKB/TrEMBL
    A0A8I5KTN6
    Related
    ENSP00000402760.2, ENST00000435065.7
    Conserved Domains (2) summary
    cd06174
    Location:162534
    MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
    TIGR00898
    Location:12544
    2A0119; cation transport protein
  2. NM_003060.4NP_003051.1  organic cation/carnitine transporter 2 isoform b

    See identical proteins and their annotated locations for NP_003051.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
    Source sequence(s)
    AF057164, AK128610, BC012325, DA186237, DA567722
    Consensus CDS
    CCDS4154.1
    UniProtKB/Swiss-Prot
    A2Q0V1, B2R844, D3DQ87, O76082, Q6ZQZ8, Q96EH6
    UniProtKB/TrEMBL
    A0A8I5KTN6
    Related
    ENSP00000245407.3, ENST00000245407.8
    Conserved Domains (2) summary
    cd06174
    Location:123510
    MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
    TIGR00898
    Location:12520
    2A0119; cation transport protein

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
    132369710..132395612
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017009778.3XP_016865267.1  organic cation/carnitine transporter 2 isoform X1

    UniProtKB/TrEMBL
    Q59FH6
  2. XM_047417595.1XP_047273551.1  organic cation/carnitine transporter 2 isoform X2

    UniProtKB/TrEMBL
    H7C1R8
    Related
    ENSP00000401860.2, ENST00000448810.6
  3. XM_047417597.1XP_047273553.1  organic cation/carnitine transporter 2 isoform X5

    UniProtKB/TrEMBL
    A0A8I5KXW0
    Related
    ENSP00000510721.1, ENST00000686757.1
  4. XM_047417598.1XP_047273554.1  organic cation/carnitine transporter 2 isoform X6

    UniProtKB/TrEMBL
    A0A8I5KXW0
  5. XM_047417596.1XP_047273552.1  organic cation/carnitine transporter 2 isoform X3

  6. XM_011543590.3XP_011541892.1  organic cation/carnitine transporter 2 isoform X4

    Conserved Domains (1) summary
    cd06174
    Location:132304
    MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    132889604..132915514
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054353250.1XP_054209225.1  organic cation/carnitine transporter 2 isoform X1

    UniProtKB/TrEMBL
    Q59FH6
  2. XM_054353251.1XP_054209226.1  organic cation/carnitine transporter 2 isoform X2

    UniProtKB/TrEMBL
    H7C1R8
  3. XM_054353254.1XP_054209229.1  organic cation/carnitine transporter 2 isoform X5

    UniProtKB/TrEMBL
    A0A8I5KXW0
  4. XM_054353255.1XP_054209230.1  organic cation/carnitine transporter 2 isoform X6

    UniProtKB/TrEMBL
    A0A8I5KXW0
  5. XM_054353252.1XP_054209227.1  organic cation/carnitine transporter 2 isoform X3

  6. XM_054353253.1XP_054209228.1  organic cation/carnitine transporter 2 isoform X4