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SLC24A1 solute carrier family 24 (sodium/potassium/calcium exchanger), member 1 [ Homo sapiens (human) ]

Gene ID: 9187, updated on 5-Apr-2015
Official Symbol
SLC24A1provided by HGNC
Official Full Name
solute carrier family 24 (sodium/potassium/calcium exchanger), member 1provided by HGNC
Primary source
HGNC:HGNC:10975
See related
Ensembl:ENSG00000074621; HPRD:04685; MIM:603617; Vega:OTTHUMG00000167960
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
NCKX; RODX; NCKX1; CSNB1D; HsT17412
Summary
This gene encodes a member of the potassium-dependent sodium/calcium exchanger protein family. The encoded protein plays an important role in sodium/calcium exchange in retinal rod and cone photoreceptors by mediating the extrusion of one calcium ion and one potassium ion in exchange for four sodium ions. Mutations in this gene may play a role in congenital stationary night blindness. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]
Orthologs
See SLC24A1 in MapViewer
Location:
15q22
Exon count:
16
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 15 NC_000015.10 (65611405..65661242)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (65903618..65953334)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene 3-hydroxyacyl-CoA dehydratase 3 Neighboring gene RNA, U6 small nuclear 19, pseudogene Neighboring gene von Willebrand factor A domain containing 9 Neighboring gene uncharacterized LOC102723464 Neighboring gene DENN/MADD domain containing 4A Neighboring gene microRNA 4511 Neighboring gene DnaJ (Hsp40) homolog, subfamily B, member 14 pseudogene

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Congenital stationary night blindness, type 1D
MedGen: C3151193 OMIM: 613830 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Genome-wide association study of hematological and biochemical traits in a Japanese population.
NHGRI GWA Catalog

Replication interactions

Interaction Pubs
Knockdown of solute carrier family 24 (sodium/potassium/calcium exchanger), member 1 (SLC24A1) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

Go to the HIV-1, Human Interaction Database

  • Activation of the phototransduction cascade, organism-specific biosystem (from REACTOME)
    Activation of the phototransduction cascade, organism-specific biosystemThe photoreceptor cascade starts with light isomerization of 11-cis-retinal (11cRAL) of rhodopsin (RHO) to all-trans-retinal (atRAL), inducing a conformational change in RHO to the active, metarhodop...
  • Phototransduction, organism-specific biosystem (from KEGG)
    Phototransduction, organism-specific biosystemPhototransduction is a biochemical process by which the photoreceptor cells generate electrical signals in response to captured photons. The vertebrate cascade starts with the absorption of photons b...
  • Phototransduction, conserved biosystem (from KEGG)
    Phototransduction, conserved biosystemPhototransduction is a biochemical process by which the photoreceptor cells generate electrical signals in response to captured photons. The vertebrate cascade starts with the absorption of photons b...
  • SLC-mediated transmembrane transport, organism-specific biosystem (from REACTOME)
    SLC-mediated transmembrane transport, organism-specific biosystemProteins with transporting functions can be roughly classified into 3 categories: ATP-powered pumps, ion channels, and transporters. Pumps utilize the energy released by ATP hydrolysis to power the m...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Sodium/Calcium exchangers, organism-specific biosystem (from REACTOME)
    Sodium/Calcium exchangers, organism-specific biosystemCalcium ions are used by cells as ubiquitous signalling molecules that control diverse physiological events. Three mammalian gene families control Ca2+ transport across plasma membranes and intracell...
  • The phototransduction cascade, organism-specific biosystem (from REACTOME)
    The phototransduction cascade, organism-specific biosystemThe visual pigment (rhodopsin in rods) consists of an 11-cis-retinal (11cRAL) chromophore covalently attached to a GPCR opsin family member via a Schiff base linkage. Upon photon absorption, 11cRAL i...
  • Transmembrane transport of small molecules, organism-specific biosystem (from REACTOME)
    Transmembrane transport of small molecules, organism-specific biosystem
    Transmembrane transport of small molecules
  • Transport of inorganic cations/anions and amino acids/oligopeptides, organism-specific biosystem (from REACTOME)
    Transport of inorganic cations/anions and amino acids/oligopeptides, organism-specific biosystemTeleologically, one might argue that inorganic cation and anion transport would be evolutionarily among the oldest transport functions. Eight families comprise the group that transports exclusively i...
  • Visual phototransduction, organism-specific biosystem (from REACTOME)
    Visual phototransduction, organism-specific biosystemVisual phototransduction is the process by which photon absorption by visual pigment molecules in photoreceptor cells is converted to an electrical cellular response. The events in this process are p...
  • Visual signal transduction: Rods, organism-specific biosystem (from Pathway Interaction Database)
    Visual signal transduction: Rods, organism-specific biosystem
    Visual signal transduction: Rods
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • KIAA0702

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium, potassium:sodium antiporter activity NAS
Non-traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
symporter activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
calcium ion transport NAS
Non-traceable Author Statement
more info
PubMed 
ion transport TAS
Traceable Author Statement
more info
 
phototransduction, visible light TAS
Traceable Author Statement
more info
 
response to light intensity NAS
Non-traceable Author Statement
more info
PubMed 
rhodopsin mediated signaling pathway TAS
Traceable Author Statement
more info
 
sodium ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
sodium ion transmembrane transport NAS
Non-traceable Author Statement
more info
PubMed 
transmembrane transport TAS
Traceable Author Statement
more info
 
transport TAS
Traceable Author Statement
more info
PubMed 
visual perception NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
membrane TAS
Traceable Author Statement
more info
PubMed 
outer membrane NAS
Non-traceable Author Statement
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
Preferred Names
sodium/potassium/calcium exchanger 1
Names
sodium/potassium/calcium exchanger 1
Na(+)/K(+)/Ca(2+)-exchange protein 1
retinal rod Na+/Ca+/K+ exchanger
solute carrier family 24 member 1

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_031968.1 RefSeqGene

    Range
    1943..39329
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001254740.1NP_001241669.1  sodium/potassium/calcium exchanger 1 isoform 2

    See proteins identical to NP_001241669.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) is shorter and has a distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AC011939, AK300633
    UniProtKB/TrEMBL
    B4DUG1
    Conserved Domains (1) summary
    pfam01699
    Location:274412
    Na_Ca_ex; Sodium/calcium exchanger protein
  2. NM_001301031.1NP_001287960.1  sodium/potassium/calcium exchanger 1 isoform 3

    See proteins identical to NP_001287960.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, and lacks an alternate in-frame exon in the 3' coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1.
    Source sequence(s)
    AI026072, AK304006, BC117263, BM129630, BM681488, EL947516, EL948740
    Consensus CDS
    CCDS73742.1
    UniProtKB/TrEMBL
    B4E1W0
    UniProtKB/Swiss-Prot
    O60721
    Related
    ENSP00000341837, ENST00000339868
    Conserved Domains (2) summary
    pfam01699
    Location:468600
    Na_Ca_ex; Sodium/calcium exchanger protein
    TIGR00927
    Location:11069
    retinal_rod; K+-dependent Na+/Ca+ exchanger
  3. NM_001301032.1NP_001287961.1  sodium/potassium/calcium exchanger 1 isoform 4

    See proteins identical to NP_001287961.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, and lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (4) that is shorter than isoform 1.
    Source sequence(s)
    AB014602, AF026132, AI026072, BM129630, BM681488, EL947516, EL948740
    Consensus CDS
    CCDS73743.1
    UniProtKB/Swiss-Prot
    O60721
    Conserved Domains (2) summary
    pfam01699
    Location:468600
    Na_Ca_ex; Sodium/calcium exchanger protein
    TIGR00927
    Location:11081
    retinal_rod; K+-dependent Na+/Ca+ exchanger
  4. NM_001301033.1NP_001287962.1  sodium/potassium/calcium exchanger 1 isoform 5

    See proteins identical to NP_001287962.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks an alternate in-frame exon in the central coding region, and contains alternate 3' exon structure and thus differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (5) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AB014602, AK304006
    Consensus CDS
    CCDS73744.1
    UniProtKB/TrEMBL
    B4E1W0
    UniProtKB/TrEMBL
    F5H127
    UniProtKB/Swiss-Prot
    O60721
    Related
    ENSP00000439693, OTTHUMP00000237476, ENST00000537259, OTTHUMT00000397303
    Conserved Domains (2) summary
    pfam01699
    Location:468600
    Na_Ca_ex; Sodium/calcium exchanger protein
    TIGR00927
    Location:11000
    retinal_rod; K+-dependent Na+/Ca+ exchanger
  5. NM_004727.2NP_004718.1  sodium/potassium/calcium exchanger 1 isoform 1

    See proteins identical to NP_004718.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC011939, AC027220, AF062922
    Consensus CDS
    CCDS45284.1
    UniProtKB/Swiss-Prot
    O60721
    Related
    ENSP00000261892, OTTHUMP00000237477, ENST00000261892, OTTHUMT00000397304
    Conserved Domains (2) summary
    pfam01699
    Location:468600
    Na_Ca_ex; Sodium/calcium exchanger protein
    TIGR00927
    Location:11099
    retinal_rod; K+-dependent Na+/Ca+ exchanger

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p2 Primary Assembly

    Range
    65611405..65661242
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006720764.2XP_006720827.1  

    See proteins identical to XP_006720827.1

    UniProtKB/Swiss-Prot
    O60721
    Conserved Domains (2) summary
    pfam01699
    Location:468600
    Na_Ca_ex; Sodium/calcium exchanger protein
    TIGR00927
    Location:11099
    retinal_rod; K+-dependent Na+/Ca+ exchanger
  2. XM_011522219.1XP_011520521.1  

    See proteins identical to XP_011520521.1

    Conserved Domains (2) summary
    pfam01699
    Location:468600
    Na_Ca_ex; Sodium/calcium exchanger protein
    TIGR00927
    Location:11099
    retinal_rod; K+-dependent Na+/Ca+ exchanger
  3. XM_006720767.2XP_006720830.1  

    See proteins identical to XP_006720830.1

    Conserved Domains (2) summary
    pfam01699
    Location:468600
    Na_Ca_ex; Sodium/calcium exchanger protein
    TIGR00927
    Location:11018
    retinal_rod; K+-dependent Na+/Ca+ exchanger
  4. XM_011522222.1XP_011520524.1  

    See proteins identical to XP_011520524.1

    Conserved Domains (2) summary
    pfam01699
    Location:468600
    Na_Ca_ex; Sodium/calcium exchanger protein
    TIGR00927
    Location:11018
    retinal_rod; K+-dependent Na+/Ca+ exchanger
  5. XM_006720769.2XP_006720832.1  

    See proteins identical to XP_006720832.1

    Conserved Domains (2) summary
    pfam01699
    Location:468600
    Na_Ca_ex; Sodium/calcium exchanger protein
    TIGR00927
    Location:1931
    retinal_rod; K+-dependent Na+/Ca+ exchanger
  6. XM_011522225.1XP_011520527.1  

    See proteins identical to XP_011520527.1

    Conserved Domains (2) summary
    pfam01699
    Location:468600
    Na_Ca_ex; Sodium/calcium exchanger protein
    TIGR00927
    Location:1931
    retinal_rod; K+-dependent Na+/Ca+ exchanger
  7. XM_011522223.1XP_011520525.1  

    See proteins identical to XP_011520525.1

    Conserved Domains (2) summary
    pfam01699
    Location:468600
    Na_Ca_ex; Sodium/calcium exchanger protein
    TIGR00927
    Location:11000
    retinal_rod; K+-dependent Na+/Ca+ exchanger
  8. XM_005254778.3XP_005254835.1  

    See proteins identical to XP_005254835.1

    UniProtKB/Swiss-Prot
    O60721
    Conserved Domains (2) summary
    pfam01699
    Location:468600
    Na_Ca_ex; Sodium/calcium exchanger protein
    TIGR00927
    Location:11099
    retinal_rod; K+-dependent Na+/Ca+ exchanger
  9. XM_011522221.1XP_011520523.1  

    See proteins identical to XP_011520523.1

    Conserved Domains (2) summary
    pfam01699
    Location:468600
    Na_Ca_ex; Sodium/calcium exchanger protein
    TIGR00927
    Location:11069
    retinal_rod; K+-dependent Na+/Ca+ exchanger
  10. XM_011522220.1XP_011520522.1  

    See proteins identical to XP_011520522.1

    Conserved Domains (2) summary
    pfam01699
    Location:468600
    Na_Ca_ex; Sodium/calcium exchanger protein
    TIGR00927
    Location:11081
    retinal_rod; K+-dependent Na+/Ca+ exchanger
  11. XM_006720768.2XP_006720831.1  

    UniProtKB/TrEMBL
    F5H483
    Conserved Domains (2) summary
    TIGR00927
    Location:1985
    2A1904; K+-dependent Na+/Ca+ exchanger
    pfam01699
    Location:468600
    Na_Ca_ex; Sodium/calcium exchanger protein
  12. XM_005254781.2XP_005254838.1  

    Conserved Domains (2) summary
    TIGR00927
    Location:1637
    2A1904; K+-dependent Na+/Ca+ exchanger
    pfam01699
    Location:468600
    Na_Ca_ex; Sodium/calcium exchanger protein
  13. XM_011522226.1XP_011520528.1  

    Conserved Domains (2) summary
    pfam01699
    Location:468600
    Na_Ca_ex; Sodium/calcium exchanger protein
    TIGR00927
    Location:1637
    retinal_rod; K+-dependent Na+/Ca+ exchanger

Alternate CHM1_1.1

Genomic

  1. NC_018926.2 Alternate CHM1_1.1

    Range
    66021450..66070976
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)