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SLC24A1 solute carrier family 24 member 1 [ Homo sapiens (human) ]

Gene ID: 9187, updated on 1-Aug-2020

Summary

Official Symbol
SLC24A1provided by HGNC
Official Full Name
solute carrier family 24 member 1provided by HGNC
Primary source
HGNC:HGNC:10975
See related
Ensembl:ENSG00000074621 MIM:603617
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]
Expression
Ubiquitous expression in thyroid (RPKM 3.0), testis (RPKM 2.7) and 25 other tissues See more
Orthologs

Genomic context

See SLC24A1 in Genome Data Viewer
Location:
15q22.31
Exon count:
17
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 15 NC_000015.10 (65611313..65661002)
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 integrator complex subunit 14 Neighboring gene uncharacterized LOC102723464 Neighboring gene DENN domain containing 4A Neighboring gene small nucleolar RNA, C/D box 13E Neighboring gene microRNA 4511

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

Phenotypes

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

HIV-1 interactions

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

Protein interactions

Protein Gene Interaction Pubs
capsid gag The interaction of HIV-1 CA with human cellular solute carrier family 24, member 1 protein (SLC24A1) is identified by yeast two-hybrid screen PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0702

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium channel activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
calcium, potassium:sodium antiporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
calcium, potassium:sodium antiporter activity IDA
Inferred from Direct Assay
more info
PubMed 
calcium, potassium:sodium antiporter activity ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
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
anion transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
calcium ion import across plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
calcium ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
calcium ion transmembrane transport IDA
Inferred from Direct Assay
more info
PubMed 
calcium ion transport NAS
Non-traceable Author Statement
more info
PubMed 
cellular calcium ion homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular calcium ion homeostasis IDA
Inferred from Direct Assay
more info
PubMed 
ion transport TAS
Traceable Author Statement
more info
 
long-term synaptic depression IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
long-term synaptic potentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
potassium ion transmembrane transport IDA
Inferred from Direct Assay
more info
PubMed 
response to light intensity NAS
Non-traceable Author Statement
more info
PubMed 
sodium ion transmembrane transport IDA
Inferred from Direct Assay
more info
PubMed 
visual perception NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
membrane TAS
Traceable Author Statement
more info
PubMed 
neuronal cell body ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
outer membrane NAS
Non-traceable Author Statement
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
spanning component of plasma membrane RCA
inferred from Reviewed Computational Analysis
more info
PubMed 

General protein information

Preferred Names
sodium/potassium/calcium exchanger 1
Names
Na(+)/K(+)/Ca(2+)-exchange protein 1
retinal rod Na+/Ca+/K+ exchanger
solute carrier family 24 (sodium/potassium/calcium exchanger), member 1

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_031968.2 RefSeqGene

    Range
    15534..49856
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    See identical proteins and their annotated locations for 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, AC027220, AK300633
    UniProtKB/TrEMBL
    B4DUG1
    Conserved Domains (1) summary
    pfam01699
    Location:263414
    Na_Ca_ex; Sodium/calcium exchanger protein
  2. NM_001301031.1NP_001287960.1  sodium/potassium/calcium exchanger 1 isoform 3

    See identical proteins and their annotated locations for 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/Swiss-Prot
    O60721
    UniProtKB/TrEMBL
    B4E1W0
    Related
    ENSP00000381991.4, ENST00000399033.8
    Conserved Domains (2) summary
    TIGR00927
    Location:11069
    2A1904; K+-dependent Na+/Ca+ exchanger
    pfam01699
    Location:458602
    Na_Ca_ex; Sodium/calcium exchanger protein
  3. NM_001301032.1NP_001287961.1  sodium/potassium/calcium exchanger 1 isoform 4

    See identical proteins and their annotated locations for 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
    Related
    ENSP00000439190.1, ENST00000546330.1
    Conserved Domains (2) summary
    TIGR00927
    Location:11081
    2A1904; K+-dependent Na+/Ca+ exchanger
    pfam01699
    Location:458602
    Na_Ca_ex; Sodium/calcium exchanger protein
  4. NM_001301033.2NP_001287962.1  sodium/potassium/calcium exchanger 1 isoform 5

    See identical proteins and their annotated locations for 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, AC011939, AC027220, AK304006
    Consensus CDS
    CCDS73744.1
    UniProtKB/Swiss-Prot
    O60721
    UniProtKB/TrEMBL
    B4E1W0, F5H127
    Related
    ENSP00000439693.1, ENST00000537259.5
    Conserved Domains (1) summary
    cl27511
    Location:11000
    Na_Ca_ex; Sodium/calcium exchanger protein
  5. NM_004727.3NP_004718.1  sodium/potassium/calcium exchanger 1 isoform 1

    See identical proteins and their annotated locations for 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
    ENSP00000261892.6, ENST00000261892.11
    Conserved Domains (1) summary
    TIGR00927
    Location:11099
    2A1904; K+-dependent Na+/Ca+ exchanger

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20200522

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p13 Primary Assembly

    Range
    65611313..65661002
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024450105.1XP_024305873.1  sodium/potassium/calcium exchanger 1 isoform X1

    Conserved Domains (1) summary
    TIGR00927
    Location:11099
    2A1904; K+-dependent Na+/Ca+ exchanger
  2. XM_024450104.1XP_024305872.1  sodium/potassium/calcium exchanger 1 isoform X1

    Conserved Domains (1) summary
    TIGR00927
    Location:11099
    2A1904; K+-dependent Na+/Ca+ exchanger
  3. XM_011522222.3XP_011520524.1  sodium/potassium/calcium exchanger 1 isoform X5

    See identical proteins and their annotated locations for XP_011520524.1

    Conserved Domains (2) summary
    TIGR00927
    Location:11018
    2A1904; K+-dependent Na+/Ca+ exchanger
    pfam01699
    Location:458602
    Na_Ca_ex; Sodium/calcium exchanger protein
  4. XM_024450106.1XP_024305874.1  sodium/potassium/calcium exchanger 1 isoform X6

    Conserved Domains (1) summary
    cl27511
    Location:11000
    Na_Ca_ex; Sodium/calcium exchanger protein
  5. XM_017022724.2XP_016878213.1  sodium/potassium/calcium exchanger 1 isoform X4

  6. XM_017022725.2XP_016878214.1  sodium/potassium/calcium exchanger 1 isoform X8

  7. XM_011522221.3XP_011520523.1  sodium/potassium/calcium exchanger 1 isoform X3

    See identical proteins and their annotated locations for XP_011520523.1

    UniProtKB/Swiss-Prot
    O60721
    Conserved Domains (2) summary
    TIGR00927
    Location:11069
    2A1904; K+-dependent Na+/Ca+ exchanger
    pfam01699
    Location:458602
    Na_Ca_ex; Sodium/calcium exchanger protein
  8. XM_011522220.3XP_011520522.1  sodium/potassium/calcium exchanger 1 isoform X2

    See identical proteins and their annotated locations for XP_011520522.1

    UniProtKB/Swiss-Prot
    O60721
    Conserved Domains (2) summary
    TIGR00927
    Location:11081
    2A1904; K+-dependent Na+/Ca+ exchanger
    pfam01699
    Location:458602
    Na_Ca_ex; Sodium/calcium exchanger protein
  9. XM_005254778.4XP_005254835.1  sodium/potassium/calcium exchanger 1 isoform X1

    See identical proteins and their annotated locations for XP_005254835.1

    UniProtKB/Swiss-Prot
    O60721
    Conserved Domains (1) summary
    TIGR00927
    Location:11099
    2A1904; K+-dependent Na+/Ca+ exchanger
  10. XM_024450103.1XP_024305871.1  sodium/potassium/calcium exchanger 1 isoform X1

    Conserved Domains (1) summary
    TIGR00927
    Location:11099
    2A1904; K+-dependent Na+/Ca+ exchanger
  11. XM_011522219.1XP_011520521.1  sodium/potassium/calcium exchanger 1 isoform X1

    See identical proteins and their annotated locations for XP_011520521.1

    UniProtKB/Swiss-Prot
    O60721
    Conserved Domains (1) summary
    TIGR00927
    Location:11099
    2A1904; K+-dependent Na+/Ca+ exchanger
  12. XM_006720768.4XP_006720831.1  sodium/potassium/calcium exchanger 1 isoform X7

    UniProtKB/TrEMBL
    F5H483
    Related
    ENSP00000445163.1, ENST00000544319.6
    Conserved Domains (2) summary
    TIGR00927
    Location:1985
    2A1904; K+-dependent Na+/Ca+ exchanger
    pfam01699
    Location:458602
    Na_Ca_ex; Sodium/calcium exchanger protein
  13. XM_005254781.4XP_005254838.1  sodium/potassium/calcium exchanger 1 isoform X9

    Conserved Domains (2) summary
    TIGR00927
    Location:1637
    2A1904; K+-dependent Na+/Ca+ exchanger
    pfam01699
    Location:458602
    Na_Ca_ex; Sodium/calcium exchanger protein
  14. XM_011522226.3XP_011520528.1  sodium/potassium/calcium exchanger 1 isoform X10

    Conserved Domains (2) summary
    TIGR00927
    Location:1637
    2A1904; K+-dependent Na+/Ca+ exchanger
    pfam01699
    Location:458602
    Na_Ca_ex; Sodium/calcium exchanger protein
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