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

Gene ID: 80736, updated on 4-Oct-2020

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
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
109.20200815 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (31863192..31878997, 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 small nucleolar RNA host gene 32 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
DEAFNESS, AUTOSOMAL DOMINANT 72
MedGen: C4539886 OMIM: 617606 GeneReviews: Not available
Compare labs
Genome-wide association identifies OBFC1 as a locus involved in human leukocyte telomere biology.
GeneReviews: Not available
Genome-wide association scan in north Indians reveals three novel HLA-independent risk loci for ulcerative colitis.
GeneReviews: Not available
Genome-wide association study for vitiligo identifies susceptibility loci at 6q27 and the MHC.
GeneReviews: Not available
Loci at chromosomes 13, 19 and 20 influence age at natural menopause.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

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 
thiamine pyrophosphate transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
thiamine pyrophosphate transmembrane transporter activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
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 IBA
Inferred from Biological aspect of Ancestor
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 IBA
Inferred from Biological aspect of Ancestor
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 IBA
Inferred from Biological aspect of Ancestor
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
 
membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 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
    5050..20855
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001178044.2NP_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
    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_001178045.2NP_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_025257.3NP_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, ENST00000229729.11
    Conserved Domains (1) summary
    pfam04515
    Location:313674
    Choline_transpo; Plasma-membrane choline transporter

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    31863192..31878997 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_1

Genomic

  1. NT_167244.2 Reference GRCh38.p13 ALT_REF_LOCI_1

    Range
    3195808..3211612 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p13 ALT_REF_LOCI_2

    Range
    3340610..3356422 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p13 ALT_REF_LOCI_3

    Range
    3110970..3126771 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p13 ALT_REF_LOCI_5

    Range
    3205262..3221062 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p13 ALT_REF_LOCI_6

    Range
    3119164..3134970 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p13 ALT_REF_LOCI_7

    Range
    3164419..3180219 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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