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SLC24A5 solute carrier family 24 member 5 [ Homo sapiens (human) ]

Gene ID: 283652, updated on 17-Jun-2024

Summary

Official Symbol
SLC24A5provided by HGNC
Official Full Name
solute carrier family 24 member 5provided by HGNC
Primary source
HGNC:HGNC:20611
See related
Ensembl:ENSG00000188467 MIM:609802; AllianceGenome:HGNC:20611
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
JSX; OCA6; NCKX5; SHEP4
Summary
This gene is a member of the potassium-dependent sodium/calcium exchanger family and encodes an intracellular membrane protein with 2 large hydrophilic loops and 2 sets of multiple transmembrane-spanning segments. Sequence variation in this gene has been associated with differences in skin pigmentation. [provided by RefSeq, Jul 2008]
Expression
Broad expression in brain (RPKM 6.4), adrenal (RPKM 4.4) and 23 other tissues See more
Orthologs
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Genomic context

See SLC24A5 in Genome Data Viewer
Location:
15q21.1
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (48120990..48142672)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (45929094..45950765)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (48413187..48434869)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900354 Neighboring gene uncharacterized LOC107984792 Neighboring gene uncharacterized LOC105370805 Neighboring gene NANOG hESC enhancer GRCh37_chr15:48304383-48304897 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:48324991-48326190 Neighboring gene uncharacterized LOC124903485 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:48442018-48442582 Neighboring gene myelin expression factor 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6412 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6413 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:48470436-48471087 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:48483866-48484369 Neighboring gene CTXN2 antisense RNA 1 Neighboring gene cortexin 2 Neighboring gene uncharacterized LOC128966560 Neighboring gene solute carrier family 12 member 1

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

EBI GWAS Catalog

Description
A genomewide association study of skin pigmentation in a South Asian population.
EBI GWAS Catalog
Genome-wide association studies and heritability estimates of body mass index related phenotypes in bangladeshi adults.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium channel activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables calcium, potassium:sodium antiporter activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables calcium, potassium:sodium antiporter activity IDA
Inferred from Direct Assay
more info
PubMed 
enables calcium, potassium:sodium antiporter activity TAS
Traceable Author Statement
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables symporter activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in calcium ion import IDA
Inferred from Direct Assay
more info
PubMed 
involved_in calcium ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in intracellular calcium ion homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in melanin biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
involved_in melanocyte differentiation IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within monoatomic ion transmembrane transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in monoatomic ion transport TAS
Traceable Author Statement
more info
 
involved_in negative regulation of melanin biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
involved_in potassium ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
involved_in sodium ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in melanosome IEA
Inferred from Electronic Annotation
more info
 
is_active_in trans-Golgi network IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in trans-Golgi network IDA
Inferred from Direct Assay
more info
PubMed 
located_in trans-Golgi network membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
sodium/potassium/calcium exchanger 5
Names
Na(+)/K(+)/Ca(2+)-exchange protein 5
Na/Ca-K exchanger 5
ion transporter JSX
oculocutaneous albinism 6 (autosomal recessive)
solute carrier family 24 (sodium/potassium/calcium exchanger), member 5

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_011500.1 RefSeqGene

    Range
    5019..26701
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_205850.3NP_995322.1  sodium/potassium/calcium exchanger 5 precursor

    See identical proteins and their annotated locations for NP_995322.1

    Status: REVIEWED

    Source sequence(s)
    AC090526, AF348468, BC073944
    Consensus CDS
    CCDS10128.1
    UniProtKB/Swiss-Prot
    A5X8Z8, A5X8Z9, Q14CT4, Q6DKH3, Q71RS6
    Related
    ENSP00000341550.3, ENST00000341459.8
    Conserved Domains (1) summary
    cl27511
    Location:20224
    Na_Ca_ex; Sodium/calcium exchanger protein

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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    48120990..48142672
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047432394.1XP_047288350.1  sodium/potassium/calcium exchanger 5 isoform X1

  2. XM_047432395.1XP_047288351.1  sodium/potassium/calcium exchanger 5 isoform X2

  3. XM_024449901.2XP_024305669.2  sodium/potassium/calcium exchanger 5 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    45929094..45950765
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054377738.1XP_054233713.1  sodium/potassium/calcium exchanger 5 isoform X1

  2. XM_054377740.1XP_054233715.1  sodium/potassium/calcium exchanger 5 isoform X2

  3. XM_054377739.1XP_054233714.1  sodium/potassium/calcium exchanger 5 isoform X2