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Aliases for SLC44A2 Gene

Aliases for SLC44A2 Gene

  • Solute Carrier Family 44 Member 2 2 3 4 5
  • Solute Carrier Family 44 (Choline Transporter), Member 2 2 3
  • CTL2 3 4
  • Choline Transporter-Like Protein 2 3
  • Testicular Tissue Protein Li 47 3
  • PP1292 3

External Ids for SLC44A2 Gene

Previous GeneCards Identifiers for SLC44A2 Gene

  • GC19P010713
  • GC19P010290

Summaries for SLC44A2 Gene

GeneCards Summary for SLC44A2 Gene

SLC44A2 (Solute Carrier Family 44 Member 2) is a Protein Coding gene. Diseases associated with SLC44A2 include Deafness, Autosomal Recessive 68 and Choline Deficiency Disease. Among its related pathways are Metabolism and Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds. GO annotations related to this gene include signal transducer activity and choline transmembrane transporter activity. An important paralog of this gene is SLC44A5.

UniProtKB/Swiss-Prot for SLC44A2 Gene

  • Isoform 1, but not isoform 3, exhibits some choline transporter activity.

Gene Wiki entry for SLC44A2 Gene

Additional gene information for SLC44A2 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLC44A2 Gene

Genomics for SLC44A2 Gene

Regulatory Elements for SLC44A2 Gene

Enhancers for SLC44A2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH19H010601 1.7 FANTOM5 ENCODE dbSUPER 34.3 +1.7 1679 4.4 ARID4B DMAP1 ZNF2 TCF12 ZNF121 ZNF766 GLIS2 ZNF143 KLF7 ATF7 SLC44A2 CDKN2D KRI1 ICAM3 ILF3 ZNF627 PRKCSH TYK2 DNM2 S1PR5
GH19H010615 1.8 FANTOM5 Ensembl ENCODE dbSUPER 25.1 +14.8 14842 4.1 HDGF PKNOX1 ATF1 ARNT ZBTB7B TCF12 ZNF766 GATA2 ELK1 ATF7 SLC44A2 KRI1 ILF3 TIMM29 PPAN ZNF627 ZNF561 AP1M2 FBXL12 ILF3-AS1
GH19H010595 1.6 FANTOM5 Ensembl ENCODE dbSUPER 26.8 -6.2 -6245 2 ZSCAN4 MAX EBF1 BATF ADNP ATF7 ETV6 RUNX3 IKZF2 MAZ KRI1 CDKN2D SLC44A2 ICAM3 ATG4D ILF3 TYK2 DNM2 C19orf38 S1PR5
GH19H010746 1.9 FANTOM5 Ensembl ENCODE dbSUPER 22 +147.8 147761 6.8 HDGF FOXA2 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 ZNF766 FOS SLC44A2 CDKN2D ILF3-AS1 ICAM3 DNM2 KRI1 HNRNPA1P10 TYK2 ICAM1 C19orf38
GH19H010729 1.6 FANTOM5 Ensembl ENCODE dbSUPER 20 +129.0 128982 4.1 HDGF CTCF PKNOX1 MAX ZIC2 POLR2A ATF7 ETV6 RUNX3 ZNF687 SLC44A2 CDKN2D KRI1 ILF3 ILF3-AS1 S1PR5 SMARCA4 DNM2 ICAM3 TYK2
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SLC44A2 on UCSC Golden Path with GeneCards custom track

Promoters for SLC44A2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000107048 356 1600 ARID4B ZNF2 TCF12 GLIS2 ATF7 KLF7 SP3 SP5 YY2 NCOA1

Genomic Locations for SLC44A2 Gene

Genomic Locations for SLC44A2 Gene
chr19:10,602,445-10,644,559
(GRCh38/hg38)
Size:
42,115 bases
Orientation:
Plus strand
chr19:10,713,121-10,755,235
(GRCh37/hg19)

Genomic View for SLC44A2 Gene

Genes around SLC44A2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC44A2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC44A2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC44A2 Gene

Proteins for SLC44A2 Gene

  • Protein details for SLC44A2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8IWA5-CTL2_HUMAN
    Recommended name:
    Choline transporter-like protein 2
    Protein Accession:
    Q8IWA5
    Secondary Accessions:
    • B2RBB1
    • B3KNH3
    • B4DFJ0
    • F2Q9D7
    • Q658V1
    • Q658Z2
    • Q6PJV7
    • Q8N2F0
    • Q9NY68

    Protein attributes for SLC44A2 Gene

    Size:
    706 amino acids
    Molecular mass:
    80124 Da
    Quaternary structure:
    • Interacts with COCH.
    SequenceCaution:
    • Sequence=BAC11662.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for SLC44A2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SLC44A2 Gene

Post-translational modifications for SLC44A2 Gene

  • Glycosylation at isoforms=2, 3187, Asn200, and Asn417
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SLC44A2 Gene

Domains & Families for SLC44A2 Gene

Gene Families for SLC44A2 Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Transporters

Protein Domains for SLC44A2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SLC44A2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8IWA5

UniProtKB/Swiss-Prot:

CTL2_HUMAN :
  • Belongs to the CTL (choline transporter-like) family.
Family:
  • Belongs to the CTL (choline transporter-like) family.
genes like me logo Genes that share domains with SLC44A2: view

Function for SLC44A2 Gene

Molecular function for SLC44A2 Gene

UniProtKB/Swiss-Prot Function:
Isoform 1, but not isoform 3, exhibits some choline transporter activity.

Phenotypes From GWAS Catalog for SLC44A2 Gene

Gene Ontology (GO) - Molecular Function for SLC44A2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004871 signal transducer activity IMP 12761501
GO:0015220 choline transmembrane transporter activity TAS 10677542
genes like me logo Genes that share ontologies with SLC44A2: view
genes like me logo Genes that share phenotypes with SLC44A2: view

Animal Models for SLC44A2 Gene

MGI Knock Outs for SLC44A2:

Animal Model Products

miRNA for SLC44A2 Gene

miRTarBase miRNAs that target SLC44A2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SLC44A2 Gene

Localization for SLC44A2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC44A2 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SLC44A2 gene
Compartment Confidence
plasma membrane 5
extracellular 5
lysosome 5
cytoskeleton 2
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cell Junctions (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SLC44A2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005765 lysosomal membrane IDA 17897319
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA,TAS 10677542
GO:0035579 specific granule membrane TAS --
genes like me logo Genes that share ontologies with SLC44A2: view

Pathways & Interactions for SLC44A2 Gene

genes like me logo Genes that share pathways with SLC44A2: view

Pathways by source for SLC44A2 Gene

Interacting Proteins for SLC44A2 Gene

Gene Ontology (GO) - Biological Process for SLC44A2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006656 phosphatidylcholine biosynthetic process TAS --
GO:0006810 transport IEA --
GO:0007165 signal transduction IEA --
GO:0015871 choline transport TAS 10677542
GO:0043123 positive regulation of I-kappaB kinase/NF-kappaB signaling IMP 12761501
genes like me logo Genes that share ontologies with SLC44A2: view

No data available for SIGNOR curated interactions for SLC44A2 Gene

Drugs & Compounds for SLC44A2 Gene

(1) Drugs for SLC44A2 Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Choline Approved Nutra Transporter, substrate 166
genes like me logo Genes that share compounds with SLC44A2: view

Transcripts for SLC44A2 Gene

Unigene Clusters for SLC44A2 Gene

Solute carrier family 44, member 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLC44A2 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b · 11c ^ 12a · 12b ^ 13 ^ 14a · 14b · 14c ^ 15a · 15b ^ 16a · 16b · 16c ·
SP1: - - -
SP2: - - - - -
SP3: - - -
SP4: - - -
SP5:
SP6:
SP7: - - - - - - - - - - - - - - - - - - -
SP8:
SP9: -
SP10: -
SP11:

ExUns: 16d · 16e ^ 17a · 17b · 17c ^ 18a · 18b · 18c ^ 19 ^ 20 ^ 21 ^ 22 ^ 23a · 23b ^ 24a · 24b
SP1: - -
SP2: - -
SP3: - - - -
SP4:
SP5:
SP6: -
SP7:
SP8:
SP9:
SP10:
SP11:

Relevant External Links for SLC44A2 Gene

GeneLoc Exon Structure for
SLC44A2
ECgene alternative splicing isoforms for
SLC44A2

Expression for SLC44A2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SLC44A2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SLC44A2 Gene

This gene is overexpressed in Whole Blood (x4.8).

Protein differential expression in normal tissues from HIPED for SLC44A2 Gene

This gene is overexpressed in Nasal epithelium (43.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SLC44A2 Gene



Protein tissue co-expression partners for SLC44A2 Gene

NURSA nuclear receptor signaling pathways regulating expression of SLC44A2 Gene:

SLC44A2

SOURCE GeneReport for Unigene cluster for SLC44A2 Gene:

Hs.534560

mRNA Expression by UniProt/SwissProt for SLC44A2 Gene:

Q8IWA5-CTL2_HUMAN
Tissue specificity: Present in supporting cells of the inner ear (at protein level). Only isoform 3 is expressed in inner ear vestibular tissue.

Evidence on tissue expression from TISSUES for SLC44A2 Gene

  • Nervous system(4.9)
  • Lung(4.5)
  • Stomach(4.5)
  • Eye(4.3)
  • Liver(4.3)
  • Kidney(2.9)
  • Intestine(2.4)
  • Muscle(2.4)
  • Blood(2.1)
genes like me logo Genes that share expression patterns with SLC44A2: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC44A2 Gene

Orthologs for SLC44A2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SLC44A2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SLC44A2 33 34
  • 99.76 (n)
dog
(Canis familiaris)
Mammalia SLC44A2 33 34
  • 89.73 (n)
cow
(Bos Taurus)
Mammalia SLC44A2 33 34
  • 87.77 (n)
oppossum
(Monodelphis domestica)
Mammalia SLC44A2 34
  • 85 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Slc44a2 33
  • 84.95 (n)
mouse
(Mus musculus)
Mammalia Slc44a2 33 16 34
  • 84.78 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SLC44A2 34
  • 56 (a)
OneToOne
chicken
(Gallus gallus)
Aves SLC44A2 34
  • 72 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SLC44A2 34
  • 80 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia slc44a2 33
  • 72.68 (n)
Str.7588 33
zebrafish
(Danio rerio)
Actinopterygii slc44a2 33 34
  • 69.24 (n)
SLC44A2 (1 of 2) 34
  • 63 (a)
OneToMany
sbcb39 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10852 33
fruit fly
(Drosophila melanogaster)
Insecta CG11880 34
  • 31 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea chtl-1 34
  • 35 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PNS1 34
  • 19 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G15380 33
  • 42.49 (n)
rice
(Oryza sativa)
Liliopsida Os04g0681600 33
  • 43.59 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 46 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.12838 33
Species where no ortholog for SLC44A2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SLC44A2 Gene

ENSEMBL:
Gene Tree for SLC44A2 (if available)
TreeFam:
Gene Tree for SLC44A2 (if available)

Paralogs for SLC44A2 Gene

Paralogs for SLC44A2 Gene

(4) SIMAP similar genes for SLC44A2 Gene using alignment to 8 proteins:

genes like me logo Genes that share paralogs with SLC44A2: view

Variants for SLC44A2 Gene

Sequence variations from dbSNP and Humsavar for SLC44A2 Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs1000108234 -- 10,608,206(+) CAACA(C/G)AGCGA intron-variant
rs1000115013 -- 10,629,747(+) GCCCT(A/G)TATAA intron-variant
rs1000202185 -- 10,644,282(+) CTGCC(C/T)ACACA utr-variant-3-prime
rs1000224973 -- 10,623,182(+) GACTT(C/T)GAGAA intron-variant
rs1000281983 -- 10,616,982(+) AGTGG(C/G/T)GCGAT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SLC44A2 Gene

Variant ID Type Subtype PubMed ID
nsv833745 CNV loss 17160897
nsv833744 CNV loss 17160897
nsv1160584 CNV deletion 26073780
nsv1127651 CNV deletion 24896259
nsv1071907 CNV deletion 25765185

Variation tolerance for SLC44A2 Gene

Residual Variation Intolerance Score: 20% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.44; 42.94% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SLC44A2 Gene

Human Gene Mutation Database (HGMD)
SLC44A2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SLC44A2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC44A2 Gene

Disorders for SLC44A2 Gene

MalaCards: The human disease database

(7) MalaCards diseases for SLC44A2 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
deafness, autosomal recessive 68
  • autosomal recessive nonsyndromic deafness 68
choline deficiency disease
  • choline deficiency
deafness, autosomal dominant 9
  • autosomal dominant nonsyndromic deafness 9
vitreous detachment
  • posterior vitreous detachment
meniere's disease
  • meniere disease
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for SLC44A2

Human Genome Epidemiology (HuGE) Navigator
SLC44A2
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SLC44A2
genes like me logo Genes that share disorders with SLC44A2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SLC44A2 Gene

Publications for SLC44A2 Gene

  1. Cochlin isoforms and their interaction with CTL2 (SLC44A2) in the inner ear. (PMID: 17926100) Kommareddi PK … Carey TE (Journal of the Association for Research in Otolaryngology : JARO 2007) 3 4 22 60
  2. Identification and characterization of choline transporter-like protein 2, an inner ear glycoprotein of 68 and 72 kDa that is the target of antibody-induced hearing loss. (PMID: 14973250) Nair TS … Carey TE (The Journal of neuroscience : the official journal of the Society for Neuroscience 2004) 3 4 22 60
  3. An electric lobe suppressor for a yeast choline transport mutation belongs to a new family of transporter-like proteins. (PMID: 10677542) O'Regan S … Meunier FM (Proceedings of the National Academy of Sciences of the United States of America 2000) 2 3 4 60
  4. Characterization of the human neutrophil alloantigen-3a. (PMID: 20037594) Greinacher A … Bux J (Nature medicine 2010) 3 22 60
  5. The neutrophil alloantigen HNA-3a (5b) is located on choline transporter-like protein 2 and appears to be encoded by an R>Q154 amino acid substitution. (PMID: 20040764) Curtis BR … Aster RH (Blood 2010) 3 22 60

Products for SLC44A2 Gene

Sources for SLC44A2 Gene

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