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SLC44A5 solute carrier family 44 member 5 [ Homo sapiens (human) ]

Gene ID: 204962, updated on 2-Nov-2024

Summary

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Official Symbol
SLC44A5provided by HGNC
Official Full Name
solute carrier family 44 member 5provided by HGNC
Primary source
HGNC:HGNC:28524
See related
Ensembl:ENSG00000137968 MIM:620329; AllianceGenome:HGNC:28524
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CTL5
Summary
Enables choline transmembrane transporter activity. Involved in choline transport. Located in plasma membrane. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in skin (RPKM 2.6), testis (RPKM 1.3) and 21 other tissues See more
Orthologs
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Genomic context

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See SLC44A5 in Genome Data Viewer
Location:
1p31.1
Exon count:
33
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (75202129..75724015, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (75043976..75561339, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (75667814..76081848, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak288 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:75597021-75598220 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:75600378-75600890 Neighboring gene LHX8 antisense RNA 1 Neighboring gene LIM homeobox 8 Neighboring gene RNA, U6 small nuclear 622, pseudogene Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:75841149-75842348 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:75842759-75843540 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:75942295-75942795 Neighboring gene MPRA-validated peak289 silencer Neighboring gene G protein nucleolar 3 pseudogene Neighboring gene RNA, U6 small nuclear 503, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 995 Neighboring gene ribosomal protein L29 pseudogene 5 Neighboring gene diphosphoinositol pentakisphosphate kinase 2 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1202 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:76143731-76144390 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:76185422-76186047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1203 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 996 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 997 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1204 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1206 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1207 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 998 Neighboring gene acyl-CoA dehydrogenase medium chain Neighboring gene dihydrolipoamide S-succinyltransferase pseudogene 1 Neighboring gene small nucleolar RNA, C/D box 45C Neighboring gene Rab geranylgeranyltransferase subunit beta

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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

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Related articles in PubMed

  1. Knockdown by shRNA identifies SLC44A5 as a potential therapeutic target in hepatocellular carcinoma. Peng GZ, et al. Mol Med Rep, 2016 Jun. PMID 27082540
  2. Choline transporter-like protein 4 (CTL4) links to non-neuronal acetylcholine synthesis. Song P, et al. J Neurochem, 2013 Aug. PMID 23651124, Free PMC Article
  3. Identification of novel germline polymorphisms governing capecitabine sensitivity. O'Donnell PH, et al. Cancer, 2012 Aug 15. PMID 22864933, Free PMC Article
  4. Molecular characterization of the family of choline transporter-like proteins and their splice variants. Traiffort E, et al. J Neurochem, 2005 Mar. PMID 15715662
  5. Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease. Furney SJ, et al. Mol Psychiatry, 2011 Nov. PMID 21116278, Free PMC Article

See all (17) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. the present study indicated the important role of SLC44A5 as a tumor promoter in HCC through the inhibition of choline uptake, suggesting that SLC44A5 may be a potential target for HCC therapy.
    Title: Knockdown by shRNA identifies SLC44A5 as a potential therapeutic target in hepatocellular carcinoma.
  2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association with MRI atrophy measures as a quantitative trait locus for Alzheimer's disease.
EBI GWAS Catalog
Identification of novel germline polymorphisms governing capecitabine sensitivity.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ34081, MGC34032

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables antiporter activity IEA
Inferred from Electronic Annotation
more info
  
enables choline transmembrane transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables choline transmembrane transporter activity TAS
Traceable Author Statement
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in choline transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in phosphatidylcholine biosynthetic process TAS
Traceable Author Statement
more info
  
involved_in transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in transmembrane transport TAS
Traceable Author Statement
more info
  
Component Evidence Code Pubs
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
choline transporter-like protein 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.

mRNA and Protein(s)

  1. NM_001130058.2 → NP_001123530.1  choline transporter-like protein 5 isoform B

    See identical proteins and their annotated locations for NP_001123530.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) has a distinct 3' coding region and UTR, compared to variant 1, resulting in a protein (isoform B) with a shorter and distinct C-terminus, compared to isoform A.
    Source sequence(s)
    AC118550, AK093170, AK128063, BC051740, DC374918
    Consensus CDS
    CCDS44164.1
    UniProtKB/TrEMBL
    B7Z470
    Related
    ENSP00000359896.3, ENST00000370859.8
    Conserved Domains (1) summary
    pfam04515
    Location:329 → 686
    Choline_transpo; Plasma-membrane choline transporter

  2. NM_001320283.3 → NP_001307212.1  choline transporter-like protein 5 isoform C

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and 5' coding region and uses an alternate start codon, compared to variant 1. It encodes isoform C, which is shorter and has a distinct N-terminus, compared to isoform A.
    Source sequence(s)
    AC107627, AC118550, AC118990, AL096829
    UniProtKB/TrEMBL
    B7Z5Y4
    Conserved Domains (1) summary
    pfam04515
    Location:323 → 680
    Choline_transpo; Plasma-membrane choline transporter

  3. NM_001320285.2 → NP_001307214.1  choline transporter-like protein 5 isoform D precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, uses a downstream in-frame start codon and contains an alternate 3' terminal exon, compared to variant 1. It encodes isoform D, which is shorter and has distinct N- and C-termini, compared to isoform A. Variants 4 and 5 encode the same isoform (D).
    Source sequence(s)
    AC118550, AI922912, AK093170, AK128063, AK299573, BC034580
    UniProtKB/TrEMBL
    B7Z5Y4
    Conserved Domains (1) summary
    pfam04515
    Location:288 → 645
    Choline_transpo; Plasma-membrane choline transporter

  4. NM_001320287.2 → NP_001307216.1  choline transporter-like protein 5 isoform D precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, uses a downstream in-frame start codon and contains an alternate 3' terminal exon, compared to variant 1. It encodes isoform D, which is shorter and has distinct N- and C-termini, compared to isoform A. Variants 4 and 5 encode the same isoform (D).
    Source sequence(s)
    AC118550, AI922912, AK128063, AK299573, BC034580, BG718149
    UniProtKB/TrEMBL
    B7Z5Y4
    Conserved Domains (1) summary
    pfam04515
    Location:288 → 645
    Choline_transpo; Plasma-membrane choline transporter

  5. NM_001394064.1 → NP_001380993.1  choline transporter-like protein 5 isoform E

    Status: VALIDATED

    Source sequence(s)
    AC107627, AC118550, AC118990, AL096829
    UniProtKB/TrEMBL
    B7Z5Y4

  6. NM_152697.6 → NP_689910.2  choline transporter-like protein 5 isoform A

    See identical proteins and their annotated locations for NP_689910.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the shorter transcript but encodes the longer isoform (A).
    Source sequence(s)
    AC093156, AC107627, AC118550, AC118990, AL096829
    Consensus CDS
    CCDS667.1
    UniProtKB/Swiss-Prot
    A0A0A0MRP1, B5MCU3, Q4G0K0, Q8NA44, Q8NB86, Q8NCS7
    UniProtKB/TrEMBL
    B7Z5Y4
    Related
    ENSP00000359892.5, ENST00000370855.5
    Conserved Domains (1) summary
    pfam04515
    Location:330 → 686
    Choline_transpo; Plasma-membrane choline transporter

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    75202129..75724015 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047449166.1 → XP_047305122.1  choline transporter-like protein 5 isoform X4

  2. XM_017000608.2 → XP_016856097.1  choline transporter-like protein 5 isoform X2

    UniProtKB/TrEMBL
    B7Z5Y4

  3. XM_017000610.2 → XP_016856099.1  choline transporter-like protein 5 isoform X3

    UniProtKB/Swiss-Prot
    A0A0A0MRP1, B5MCU3, Q4G0K0, Q8NA44, Q8NB86, Q8NCS7
    UniProtKB/TrEMBL
    B7Z5Y4
    Conserved Domains (1) summary
    pfam04515
    Location:330 → 686
    Choline_transpo; Plasma-membrane choline transporter

  4. XM_017000609.2 → XP_016856098.1  choline transporter-like protein 5 isoform X3

    UniProtKB/Swiss-Prot
    A0A0A0MRP1, B5MCU3, Q4G0K0, Q8NA44, Q8NB86, Q8NCS7
    UniProtKB/TrEMBL
    B7Z5Y4
    Conserved Domains (1) summary
    pfam04515
    Location:330 → 686
    Choline_transpo; Plasma-membrane choline transporter

  5. XM_017000607.2 → XP_016856096.1  choline transporter-like protein 5 isoform X1

    UniProtKB/TrEMBL
    B7Z5Y4

  6. XM_006710445.4 → XP_006710508.1  choline transporter-like protein 5 isoform X5

    See identical proteins and their annotated locations for XP_006710508.1

    UniProtKB/TrEMBL
    B7Z5Y4
    Conserved Domains (1) summary
    pfam04515
    Location:287 → 644
    Choline_transpo; Plasma-membrane choline transporter

  7. XM_047449167.1 → XP_047305123.1  choline transporter-like protein 5 isoform X5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    75043976..75561339 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054335054.1 → XP_054191029.1  choline transporter-like protein 5 isoform X4

  2. XM_054335051.1 → XP_054191026.1  choline transporter-like protein 5 isoform X2

  3. XM_054335052.1 → XP_054191027.1  choline transporter-like protein 5 isoform X3

    UniProtKB/Swiss-Prot
    A0A0A0MRP1, B5MCU3, Q4G0K0, Q8NA44, Q8NB86, Q8NCS7

  4. XM_054335053.1 → XP_054191028.1  choline transporter-like protein 5 isoform X3

    UniProtKB/Swiss-Prot
    A0A0A0MRP1, B5MCU3, Q4G0K0, Q8NA44, Q8NB86, Q8NCS7

  5. XM_054335050.1 → XP_054191025.1  choline transporter-like protein 5 isoform X1

  6. XM_054335055.1 → XP_054191030.1  choline transporter-like protein 5 isoform X5

  7. XM_054335056.1 → XP_054191031.1  choline transporter-like protein 5 isoform X5

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NCS7.5 GenPept UniProtKB/Swiss-Prot:Q8NCS7

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