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SLC13A2 solute carrier family 13 member 2 [ Homo sapiens (human) ]

Gene ID: 9058, updated on 7-Apr-2024

Summary

Official Symbol
SLC13A2provided by HGNC
Official Full Name
solute carrier family 13 member 2provided by HGNC
Primary source
HGNC:HGNC:10917
See related
Ensembl:ENSG00000007216 MIM:604148; AllianceGenome:HGNC:10917
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
NaCT; NADC1; SDCT1; NaDC-1
Summary
The protein encoded by this gene is a sodium-coupled citrate transporter that is regulated by the chaperone activity of cyclophilin b. The encoded protein may play a role in the formation of kidney stones. [provided by RefSeq, Oct 2016]
Expression
Biased expression in duodenum (RPKM 49.7), small intestine (RPKM 41.0) and 4 other tissues See more
Orthologs
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Genomic context

See SLC13A2 in Genome Data Viewer
Location:
17q11.2
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (28473644..28497781)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (29416661..29440798)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (26800662..26824799)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene RAP1A, member of RAS oncogene family pseudogene Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr17:26782409-26783036 Neighboring gene ribosomal protein S7 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:26810033-26810546 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11927 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11928 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:26828166-26828362 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:26834617-26835569 Neighboring gene forkhead box N1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:26873952-26874789 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:26874790-26875626 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8341 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8342 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8343 Neighboring gene unc-119 lipid binding chaperone

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?

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 IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in alpha-ketoglutarate transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in cellular response to lithium ion IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in cellular response to lithium ion IDA
Inferred from Direct Assay
more info
PubMed 
involved_in fumarate transport IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in fumarate transport IDA
Inferred from Direct Assay
more info
PubMed 
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 
Component Evidence Code Pubs
located_in apical plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in extracellular exosome HDA PubMed 
located_in membrane TAS
Traceable Author Statement
more info
PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
solute carrier family 13 member 2
Names
Na(+)-coupled citrate transporter
Na(+)/dicarboxylate cotransporter 1
renal sodium/dicarboxylate cotransporter
solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2

NCBI Reference Sequences (RefSeq)

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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_051960.1 RefSeqGene

    Range
    4999..29136
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001145975.2NP_001139447.1  solute carrier family 13 member 2 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AC015917, AK298388, AK314684, AW024214, BC096277
    Consensus CDS
    CCDS54098.1
    UniProtKB/TrEMBL
    B4E1M6
    Related
    ENSP00000392411.3, ENST00000444914.7
    Conserved Domains (1) summary
    cl21473
    Location:6614
    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_001346683.2NP_001333612.1  solute carrier family 13 member 2 isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) includes an alternate internal exon and uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (d) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform a.
    Source sequence(s)
    AC015917
    Consensus CDS
    CCDS92282.1
    UniProtKB/TrEMBL
    B4E1M6, J3QL78
    Related
    ENSP00000463421.2, ENST00000579281.5
  3. NM_001346684.2NP_001333613.1  solute carrier family 13 member 2 isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) includes an alternate internal exon and lacks an alternate internal segment compared to variant 1. The resulting isoform (e) has a shorter and distinct N-terminus compared to isoform a.
    Source sequence(s)
    AC015917
    UniProtKB/TrEMBL
    B3KRN0
  4. NM_003984.4NP_003975.1  solute carrier family 13 member 2 isoform b

    See identical proteins and their annotated locations for NP_003975.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the internal coding region compared to variant 1. This results in a shorter isoform (b) compared to isoform a.
    Source sequence(s)
    AC015917, AW024214, DB320886, U26209
    Consensus CDS
    CCDS11231.1
    UniProtKB/Swiss-Prot
    B2RBI9, B4DPL1, E7ETH5, Q13183, Q4VAR7
    UniProtKB/TrEMBL
    B4E1M6
    Related
    ENSP00000316202.6, ENST00000314669.10
    Conserved Domains (1) summary
    pfam00939
    Location:6565
    Na_sulph_symp; Sodium:sulfate symporter transmembrane region

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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    28473644..28497781
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047437011.1XP_047292967.1  solute carrier family 13 member 2 isoform X2

  2. XM_011525450.4XP_011523752.1  solute carrier family 13 member 2 isoform X1

    UniProtKB/TrEMBL
    B4E1M6
    Conserved Domains (2) summary
    TIGR00785
    Location:33608
    dass; anion transporter
    cl21473
    Location:6615
    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. XM_011525453.3XP_011523755.1  solute carrier family 13 member 2 isoform X4

    UniProtKB/TrEMBL
    B4E1M6
    Conserved Domains (2) summary
    TIGR00785
    Location:33535
    dass; anion transporter
    cl21473
    Location:6542
    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. XM_011525452.2XP_011523754.1  solute carrier family 13 member 2 isoform X3

    UniProtKB/TrEMBL
    B4E1M6
    Conserved Domains (2) summary
    TIGR00785
    Location:33559
    dass; anion transporter
    pfam00939
    Location:6566
    Na_sulph_symp; Sodium:sulfate symporter transmembrane region
  5. XM_011525454.4XP_011523756.1  solute carrier family 13 member 2 isoform X5

    Conserved Domains (1) summary
    cl21473
    Location:6396
    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 ...

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    29416661..29440798
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054317707.1XP_054173682.1  solute carrier family 13 member 2 isoform X2

  2. XM_054317706.1XP_054173681.1  solute carrier family 13 member 2 isoform X1

  3. XM_054317709.1XP_054173684.1  solute carrier family 13 member 2 isoform X4

  4. XM_054317708.1XP_054173683.1  solute carrier family 13 member 2 isoform X3

  5. XM_054317710.1XP_054173685.1  solute carrier family 13 member 2 isoform X5

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001145976.1: Suppressed sequence

    Description
    NM_001145976.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.