U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Nucleotide

    • Showing Current items.

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

    Gene ID: 204962, updated on 10-Dec-2024

    Summary

    Go to the top of the page Help
    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, Dec 2024]
    Expression
    Broad expression in skin (RPKM 2.6), testis (RPKM 1.3) and 21 other tissues See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

    Go to the top of the pageHelp

    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

    Go to the top of the page Help

    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    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

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    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

    Go to the top of the page Help
    Preferred Names
    choline transporter-like protein 5

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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.

    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

      UniProtKB/TrEMBL
      B7Z5Y4

    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

      UniProtKB/TrEMBL
      B7Z5Y4

    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

      UniProtKB/TrEMBL
      B7Z5Y4

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

      UniProtKB/TrEMBL
      B7Z5Y4

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

      UniProtKB/Swiss-Prot
      A0A0A0MRP1, B5MCU3, Q4G0K0, Q8NA44, Q8NB86, Q8NCS7
      UniProtKB/TrEMBL
      B7Z5Y4

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

      UniProtKB/Swiss-Prot
      A0A0A0MRP1, B5MCU3, Q4G0K0, Q8NA44, Q8NB86, Q8NCS7
      UniProtKB/TrEMBL
      B7Z5Y4

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

      UniProtKB/TrEMBL
      B7Z5Y4

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

      UniProtKB/TrEMBL
      B7Z5Y4

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

      UniProtKB/TrEMBL
      B7Z5Y4
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NCS7.5 GenPept UniProtKB/Swiss-Prot:Q8NCS7

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous