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

    Gene ID: 9058, updated on 10-Dec-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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SLC13A2 in Genome Data Viewer
    Location:
    17q11.2
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (28473644..28497781)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (29416661..29440798)
    RS_2024_09 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)

    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_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_2024_08

    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

      UniProtKB/TrEMBL
      B4E1M6
    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

      UniProtKB/TrEMBL
      B4E1M6
    2. XM_054317706.1XP_054173681.1  solute carrier family 13 member 2 isoform X1

      UniProtKB/TrEMBL
      B4E1M6
    3. XM_054317709.1XP_054173684.1  solute carrier family 13 member 2 isoform X4

      UniProtKB/TrEMBL
      B4E1M6
    4. XM_054317708.1XP_054173683.1  solute carrier family 13 member 2 isoform X3

      UniProtKB/TrEMBL
      B4E1M6
    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.