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

Gene ID: 64849, updated on 17-Jun-2019

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
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
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

Genomic context

See SLC13A3 in Genome Data Viewer
Location:
20q13.12
Exon count:
15
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 20 NC_000020.11 (46557828..46684485, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (45186462..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 osteoclast stimulatory transmembrane protein Neighboring gene TP53 regulating kinase Neighboring gene solute carrier family 2 member 10 Neighboring gene RN7SK pseudogene 33

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 FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI 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.
NHGRI GWA 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 BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
citrate transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
high-affinity sodium:dicarboxylate symporter activity TAS
Traceable Author Statement
more info
 
sodium:dicarboxylate symporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
succinate transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
citrate transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sodium ion transport IEA
Inferred from Electronic Annotation
more info
 
succinate transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
extracellular exosome HDA PubMed 
integral component of membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
solute carrier family 13 member 3
Names
Na(+)/dicarboxylate cotransporter 3
hNaDC3
naDC-3
sodium-dependent high affinity dicarboxylate transporter 3

NCBI Reference Sequences (RefSeq)

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
    5001..131663
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001011554.3NP_001011554.1  solute carrier family 13 member 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/Swiss-Prot
    Q8WWT9
    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  solute carrier family 13 member 3 isoform c precursor

    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  solute carrier family 13 member 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/Swiss-Prot
    Q8WWT9
    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  solute carrier family 13 member 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  solute carrier family 13 member 3 isoform a precursor

    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
    Q8WWT9
    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: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p13 Primary Assembly

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