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    SLC44A4 solute carrier family 44 member 4 [ Homo sapiens (human) ]

    Gene ID: 80736, updated on 7-Jul-2018

    Summary

    Official Symbol
    SLC44A4provided by HGNC
    Official Full Name
    solute carrier family 44 member 4provided by HGNC
    Primary source
    HGNC:HGNC:13941
    See related
    Ensembl:ENSG00000204385 MIM:606107; Vega:OTTHUMG00000031133
    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
    CTL4; NG22; TPPT; DFNA72; hTPPT1; C6orf29
    Summary
    The protein encoded by this gene may be a sodium-dependent transmembrane transport protein involved in the uptake of choline by cholinergic neurons. Defects in this gene can cause sialidosis, a lysosomal storage disease. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2010]
    Expression
    Biased expression in colon (RPKM 98.7), stomach (RPKM 72.4) and 9 other tissues See more
    Orthologs

    Genomic context

    See SLC44A4 in Genome Data Viewer
    Location:
    6p21.33
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 6 NC_000006.12 (31863192..31879046, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (31830969..31846823, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene chromosome 6 open reading frame 48 Neighboring gene small nucleolar RNA, C/D box 52 Neighboring gene neuraminidase 1 Neighboring gene uncharacterized LOC107986588 Neighboring gene euchromatic histone lysine methyltransferase 2 Neighboring gene zinc finger and BTB domain containing 12 Neighboring gene complement C2

    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 Jun 15 11:32:44 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    DEAFNESS, AUTOSOMAL DOMINANT 72
    MedGen: C4539886 OMIM: 617606 GeneReviews: Not available
    not available

    NHGRI GWAS Catalog

    Description
    Genome-wide association identifies OBFC1 as a locus involved in human leukocyte telomere biology.
    NHGRI GWA Catalog
    Genome-wide association scan in north Indians reveals three novel HLA-independent risk loci for ulcerative colitis.
    NHGRI GWA Catalog
    Genome-wide association study for vitiligo identifies susceptibility loci at 6q27 and the MHC.
    NHGRI GWA Catalog
    Loci at chromosomes 13, 19 and 20 influence age at natural menopause.
    NHGRI GWA Catalog

    Pathways from BioSystems

    • Choline metabolism in cancer, organism-specific biosystem (from KEGG)
      Choline metabolism in cancer, organism-specific biosystemAbnormal choline metabolism is emerging as a metabolic hallmark that is associated with oncogenesis and tumour progression. Following transformation, oncogenic signalling via pathways such as the RAS...
    • Choline metabolism in cancer, conserved biosystem (from KEGG)
      Choline metabolism in cancer, conserved biosystemAbnormal choline metabolism is emerging as a metabolic hallmark that is associated with oncogenesis and tumour progression. Following transformation, oncogenic signalling via pathways such as the RAS...
    • Glycerophospholipid biosynthesis, organism-specific biosystem (from REACTOME)
      Glycerophospholipid biosynthesis, organism-specific biosystemGlycerophospholipids are important structural and functional components of biological membranes and constituents of serum lipoproteins and the pulmonary surfactant. In addition, glycerophospholipids...
    • Metabolism, organism-specific biosystem (from REACTOME)
      Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
    • Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
      Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...
    • Phospholipid metabolism, organism-specific biosystem (from REACTOME)
      Phospholipid metabolism, organism-specific biosystemPhospholipids contain a polar head group and two long-chain fatty acyl moieties, one of which is generally unsaturated. The head group is a glycerol or serine phosphate attached to a polar group such...
    • 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...
    • Synthesis of PC, organism-specific biosystem (from REACTOME)
      Synthesis of PC, organism-specific biosystemDe novo (Kennedy pathway) synthesis of phosphatidylcholine (PC) involves phosphorylation of choline (Cho) to phosphocholine (PCho) followed by condensing with cytidine triphosphate (CTP) to form CDP-...
    • 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 glucose and other sugars, bile salts and organic acids, metal ions and amine compounds, organism-specific biosystem (from REACTOME)
      Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds, organism-specific biosystemHexoses like glucose, galactose and fructose serve as basic fuel molecules for eukaryotic cells. Indeed, glucose is the main energy source for mammalian cells. These sugars are unable to diffuse acro...

    General gene information

    Markers

    Potential readthrough

    Included gene: NEU1

    Homology

    Clone Names

    • FLJ14491

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    choline transmembrane transporter activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    choline transmembrane transporter activity TAS
    Traceable Author Statement
    more info
     
    thiamine pyrophosphate transmembrane transporter activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Process Evidence Code Pubs
    acetylcholine biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acetylcholine secretion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    choline transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    neuromast hair cell development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    otolith formation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    phosphatidylcholine biosynthetic process TAS
    Traceable Author Statement
    more info
     
    positive regulation of cell growth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    thiamine pyrophosphate transmembrane transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    thiamine pyrophosphate transmembrane transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    transmembrane transport TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    apical plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular exosome HDA PubMed 
    integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    choline transporter-like protein 4
    Names
    testicular tissue protein Li 48
    thiamine pyrophosphate transporter
    thiamine pyrophosphate transporter 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_023058.1 RefSeqGene

      Range
      5001..20855
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001178044.1NP_001171515.1  choline transporter-like protein 4 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AI956094, AK300550, AK301596, BC014659, DC300771
      Consensus CDS
      CCDS54990.1
      UniProtKB/Swiss-Prot
      Q53GD3
      Related
      ENSP00000364712.4, ENST00000375562.8
      Conserved Domains (1) summary
      pfam04515
      Location:271632
      Choline_transpo; Plasma-membrane choline transporter
    2. NM_001178045.1NP_001171516.1  choline transporter-like protein 4 isoform 3

      See identical proteins and their annotated locations for NP_001171516.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AI956094, AK300550, BC014659, DC392935
      Consensus CDS
      CCDS54989.1
      UniProtKB/Swiss-Prot
      Q53GD3
      UniProtKB/TrEMBL
      A0A1U9X8K7
      Related
      ENSP00000444109.1, ENST00000544672.5
      Conserved Domains (1) summary
      pfam04515
      Location:238598
      Choline_transpo; Plasma-membrane choline transporter
    3. NM_025257.2NP_079533.2  choline transporter-like protein 4 isoform 1

      See identical proteins and their annotated locations for NP_079533.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AI560195, AK222998, BC014659, DA924720, DC300771
      Consensus CDS
      CCDS4724.2
      UniProtKB/Swiss-Prot
      Q53GD3
      UniProtKB/TrEMBL
      A0A140VJH4
      Related
      ENSP00000229729.6, OTTHUMP00000029182, ENST00000229729.10, OTTHUMT00000076234
      Conserved Domains (1) summary
      pfam04515
      Location:313674
      Choline_transpo; Plasma-membrane choline transporter

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000006.12 Reference GRCh38.p12 Primary Assembly

      Range
      31863192..31879046 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p12 ALT_REF_LOCI_1

    Genomic

    1. NT_167244.2 Reference GRCh38.p12 ALT_REF_LOCI_1

      Range
      3195808..3211661 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p12 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.3 Reference GRCh38.p12 ALT_REF_LOCI_2

      Range
      3340610..3356471 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p12 ALT_REF_LOCI_3

    Genomic

    1. NT_167245.2 Reference GRCh38.p12 ALT_REF_LOCI_3

      Range
      3110970..3126820 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p12 ALT_REF_LOCI_5

    Genomic

    1. NT_167247.2 Reference GRCh38.p12 ALT_REF_LOCI_5

      Range
      3205262..3221111 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p12 ALT_REF_LOCI_6

    Genomic

    1. NT_167248.2 Reference GRCh38.p12 ALT_REF_LOCI_6

      Range
      3119164..3135019 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p12 ALT_REF_LOCI_7

    Genomic

    1. NT_167249.2 Reference GRCh38.p12 ALT_REF_LOCI_7

      Range
      3164419..3180268 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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