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    SLC13A5 solute carrier family 13 member 5 [ Homo sapiens (human) ]

    Gene ID: 284111, updated on 8-Jul-2021

    Summary

    Official Symbol
    SLC13A5provided by HGNC
    Official Full Name
    solute carrier family 13 member 5provided by HGNC
    Primary source
    HGNC:HGNC:23089
    See related
    Ensembl:ENSG00000141485 MIM:608305
    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
    INDY; NACT; DEE25; mIndy; EIEE25
    Summary
    This gene encodes a protein belonging to the solute carrier family 13 group of proteins. This family member is a sodium-dependent citrate cotransporter that may regulate metabolic processes. Mutations in this gene cause early infantile epileptic encephalopathy 25. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2014]
    Expression
    Biased expression in liver (RPKM 61.1) and salivary gland (RPKM 7.3) See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SLC13A5 in Genome Data Viewer
    Location:
    17p13.1
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (6684719..6713400, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (6588038..6616688, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene microRNA 4520-1 Neighboring gene microRNA 4520-2 Neighboring gene arachidonate 15-lipoxygenase pseudogene 1 Neighboring gene Sharpr-MPRA regulatory regions 2431 and 6579 Neighboring gene ribosomal protein L23a pseudogene 73

    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
    An atlas of genetic influences on human blood metabolites.
    GeneReviews: Not available
    Epileptic encephalopathy, early infantile, 25
    MedGen: C4014621 OMIM: 615905 GeneReviews: Not available
    Compare labs
    The genetic architecture of economic and political preferences.
    GeneReviews: Not available

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ42326, MGC138356, DKFZp686E17257, DKFZp686K21244

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in alpha-ketoglutarate transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in anion transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in cellular response to lithium ion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in citrate transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in citrate transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in citrate transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in fumarate transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in oxaloacetate transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in sodium ion transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in succinate transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in succinate transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in tricarboxylic acid transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    is_active_in integral component of membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    solute carrier family 13 member 5
    Names
    Na(+)/citrate cotransporter
    Na+-coupled citrate transporter protein
    sodium-dependent dicarboxylate transporter
    solute carrier family 13 (sodium-dependent citrate transporter), member 5

    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_034220.1 RefSeqGene

      Range
      5001..33709
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1020

    mRNA and Protein(s)

    1. NM_001143838.3NP_001137310.1  solute carrier family 13 member 5 isoform b

      See identical proteins and their annotated locations for NP_001137310.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region compared to variant 1. This results in a shorter protein (isoform b), compared to isoform a.
      Source sequence(s)
      AK127797, BC143689, CR749584, H29568
      Consensus CDS
      CCDS45593.1
      UniProtKB/Swiss-Prot
      Q86YT5
      UniProtKB/TrEMBL
      Q68D44
      Related
      ENSP00000459372.1, ENST00000573648.5
      Conserved Domains (2) summary
      COG0471
      Location:31497
      CitT; Di- and tricarboxylate transporter [Carbohydrate transport and metabolism]
      cl21473
      Location:31482
      ArsB_NhaD_permease; Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices ...
    2. NM_001284509.2NP_001271438.1  solute carrier family 13 member 5 isoform c

      See identical proteins and their annotated locations for NP_001271438.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform c), compared to isoform a.
      Source sequence(s)
      AK127797, CR749584, H29568
      Consensus CDS
      CCDS67137.1
      UniProtKB/Swiss-Prot
      Q86YT5
      UniProtKB/TrEMBL
      Q68D44
      Related
      ENSP00000293800.6, ENST00000293800.10
      Conserved Domains (2) summary
      COG0471
      Location:31530
      CitT; Di- and tricarboxylate transporter [Carbohydrate transport and metabolism]
      cl21473
      Location:31535
      ArsB_NhaD_permease; Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices ...
    3. NM_001284510.2NP_001271439.1  solute carrier family 13 member 5 isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an alternate in-frame exon in the 5' coding region compared to variant 1. This results in a shorter protein (isoform d), compared to isoform a.
      Source sequence(s)
      AK127797, AK297612, CR749584, DA187094, H29568
      Consensus CDS
      CCDS67136.1
      UniProtKB/Swiss-Prot
      Q86YT5
      UniProtKB/TrEMBL
      Q68D44
      Related
      ENSP00000370464.4, ENST00000381074.8
      Conserved Domains (2) summary
      COG0471
      Location:45504
      CitT; Di- and tricarboxylate transporter [Carbohydrate transport and metabolism]
      cl21473
      Location:35509
      ArsB_NhaD_permease; Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices ...
    4. NM_177550.5NP_808218.1  solute carrier family 13 member 5 isoform a

      See identical proteins and their annotated locations for NP_808218.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AK127797, BC104795, CR749584, H29568
      Consensus CDS
      CCDS11079.1
      UniProtKB/Swiss-Prot
      Q86YT5
      UniProtKB/TrEMBL
      Q68D44
      Related
      ENSP00000406220.2, ENST00000433363.7
      Conserved Domains (1) summary
      cl21473
      Location:31552
      ArsB_NhaD_permease; Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices ...

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

      Range
      6684719..6713400 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011523795.3XP_011522097.1  solute carrier family 13 member 5 isoform X1

      Conserved Domains (2) summary
      COG0471
      Location:31478
      CitT; Di- and tricarboxylate transporter [Carbohydrate transport and metabolism]
      cl21473
      Location:31479
      ArsB_NhaD_permease; Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices ...
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