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

Gene ID: 284111, updated on 23-Nov-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
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Genomic context

See SLC13A5 in Genome Data Viewer
Location:
17p13.1
Exon count:
12
Annotation release Status Assembly Chr Location
109.20211119 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
Developmental and epileptic encephalopathy, 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 109.20211119

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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