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    SLC13A3 solute carrier family 13 member 3 [ Homo sapiens (human) ]

    Gene ID: 64849, updated on 17-Jun-2024

    Summary

    Official Symbol
    SLC13A3provided by HGNC
    Official Full Name
    solute carrier family 13 member 3provided by HGNC
    Primary source
    HGNC:HGNC:14430
    See related
    Ensembl:ENSG00000158296 MIM:606411; AllianceGenome:HGNC:14430
    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
    NaC3; NADC3; SDCT2; ARLIAK
    Summary
    Mammalian sodium-dicarboxylate cotransporters transport succinate and other Krebs cycle intermediates. They fall into 2 categories based on their substrate affinity: low affinity and high affinity. Both the low- and high-affinity transporters play an important role in the handling of citrate by the kidneys. The protein encoded by this gene represents the high-affinity form. Alternatively spliced transcript variants encoding different isoforms have been found for this gene, although the full-length nature of some of them have not been characterized yet. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in kidney (RPKM 195.8) and placenta (RPKM 14.9) See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See SLC13A3 in Genome Data Viewer
    Location:
    20q13.12
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (46557828..46684485, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (48293974..48420764, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (45186467..45313124, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene zinc finger protein 334 Neighboring gene zinc finger protein 840, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr20:45142238-45142472 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:45173599-45174450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17976 Neighboring gene osteoclast stimulatory transmembrane protein Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:45197011-45197512 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr20:45211603-45212425 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr20:45212426-45213247 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17977 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:45250755-45251328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:45259736-45260484 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:45260485-45261231 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:45302100-45302256 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:45303169-45303683 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:45311939-45312450 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12976 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17978 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17979 Neighboring gene TP53RK divergent transcript Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:45331499-45332271 Neighboring gene TP53 regulating kinase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:45354240-45354740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:45354741-45355241 Neighboring gene solute carrier family 2 member 10

    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
    Leukoencephalopathy, acute reversible, with increased urinary alpha-ketoglutarate
    MedGen: C5193068 OMIM: 618384 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    An integrative study of the genetic, social and environmental determinants of chronic kidney disease characterized by tubulointerstitial damages in the North Central Region of Sri Lanka.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat Microarray analysis indicates HIV-1 Tat-induced upregulation of solute carrier family 13, member 3 (SLC13A3; sodium-dependent dicarboxylate transporter) in primary human brain microvascular endothelial 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

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in alpha-ketoglutarate transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in citrate transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in citrate transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in dicarboxylic acid transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in dicarboxylic acid transport TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in glutathione transmembrane transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in lipid transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in sodium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in succinate transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in succinate transmembrane transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in succinate transmembrane transport TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in transport across blood-brain barrier NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in basolateral plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular exosome HDA PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    Na(+)/dicarboxylate cotransporter 3
    Names
    Na(+)-coupled carboxylate transporter 3
    hNaDC3
    naDC-3
    sodium-dependent high affinity dicarboxylate transporter 3

    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_047182.1 RefSeqGene

      Range
      38027..131658
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001011554.3NP_001011554.1  Na(+)/dicarboxylate cotransporter 3 isoform b

      See identical proteins and their annotated locations for NP_001011554.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding region compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a.
      Source sequence(s)
      AL034424, AL442082, BM474324, CN310376, DA272524, DA503319
      Consensus CDS
      CCDS42886.1
      UniProtKB/TrEMBL
      B4DF27
      Related
      ENSP00000290317.5, ENST00000290317.9
      Conserved Domains (2) summary
      COG0471
      Location:1519
      CitT; Di- and tricarboxylate transporter [Carbohydrate transport and metabolism]
      cd01115
      Location:1511
      SLC13_permease; Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is ...
    2. NM_001193339.2NP_001180268.1  Na(+)/dicarboxylate cotransporter 3 isoform c

      See identical proteins and their annotated locations for NP_001180268.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate segment which changes the reading frame, and uses a different splice site, which restores the reading frame, compared to variant 1. The resulting protein (isoform c) is shorter and has an internal distinct sequence when it is compared to isoform a.
      Source sequence(s)
      AK293902, AK295748, AL034424, DA334816
      Consensus CDS
      CCDS54470.1
      UniProtKB/Swiss-Prot
      Q8WWT9
      UniProtKB/TrEMBL
      B4DF27
      Related
      ENSP00000415852.2, ENST00000413164.6
      Conserved Domains (2) summary
      COG0471
      Location:17516
      CitT; Di- and tricarboxylate transporter [Carbohydrate transport and metabolism]
      cd01115
      Location:42508
      SLC13_permease; Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is ...
    3. NM_001193340.2NP_001180269.1  Na(+)/dicarboxylate cotransporter 3 isoform d

      See identical proteins and their annotated locations for NP_001180269.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) has multiple differences in the 5' UTR and in the coding region which results in the use of a downstream start codon, compared to variant 1. The resulting protein (isoform d) is shorter when it is compared to isoform a.
      Source sequence(s)
      AK096658, AL034424, BP358260
      Consensus CDS
      CCDS54469.1
      UniProtKB/TrEMBL
      B4DF27
      Related
      ENSP00000420177.1, ENST00000472148.5
      Conserved Domains (2) summary
      COG0471
      Location:1484
      CitT; Di- and tricarboxylate transporter [Carbohydrate transport and metabolism]
      cd01115
      Location:1476
      SLC13_permease; Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is ...
    4. NM_001193342.2NP_001180271.1  Na(+)/dicarboxylate cotransporter 3 isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses a different splice site, which results in translation from a downstream, in-frame, start codon, compared to variant 1. The resulting isoform (e) is shorter at the N-terminus compared to isoform a.
      Source sequence(s)
      AK293902, AL034424, CB997336, DA636764
      UniProtKB/TrEMBL
      B4DF27
      Conserved Domains (2) summary
      COG0471
      Location:1468
      CitT; Di- and tricarboxylate transporter [Carbohydrate transport and metabolism]
      cd01115
      Location:2460
      SLC13_permease; Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is ...
    5. NM_022829.6NP_073740.2  Na(+)/dicarboxylate cotransporter 3 isoform a

      See identical proteins and their annotated locations for NP_073740.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (a).
      Source sequence(s)
      AL034424, AY072810, DA636764
      Consensus CDS
      CCDS13400.1
      UniProtKB/Swiss-Prot
      B4DIR8, E1P5U4, F6WI18, Q5JYC9, Q5JYD0, Q5JYD1, Q5TCQ2, Q8IVB1, Q8N8K4, Q8WWT9, Q96MM5, Q9BR25, Q9H1G1, Q9H3W4, Q9NQN5, Q9NS04
      UniProtKB/TrEMBL
      B4DF27
      Related
      ENSP00000279027.4, ENST00000279027.9
      Conserved Domains (2) summary
      COG0471
      Location:17566
      CitT; Di- and tricarboxylate transporter [Carbohydrate transport and metabolism]
      cd01115
      Location:42558
      SLC13_permease; Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is ...

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      46557828..46684485 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      48293974..48420764 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)