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SLC44A3 solute carrier family 44 member 3 [ Homo sapiens (human) ]

Gene ID: 126969, updated on 3-Apr-2024

Summary

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Official Symbol
SLC44A3provided by HGNC
Official Full Name
solute carrier family 44 member 3provided by HGNC
Primary source
HGNC:HGNC:28689
See related
Ensembl:ENSG00000143036 MIM:620328; AllianceGenome:HGNC:28689
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
CTL3
Summary
Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be located in plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in kidney (RPKM 8.6), colon (RPKM 8.5) and 20 other tissues See more
Orthologs
mouse all
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Genomic context

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See SLC44A3 in Genome Data Viewer
Location:
1p21.3
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (94820357..94895247)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (94668402..94743603)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (95285913..95360803)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene SLC44A3 antisense RNA 1 Neighboring gene piggyBac transposable element derived 4 pseudogene 7 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:95177148-95178105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1098 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1348 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:95188809-95189310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:95193997-95194497 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:95199763-95200705 Neighboring gene Sharpr-MPRA regulatory region 2553 Neighboring gene microRNA 378g Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:95248718-95249480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1099 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1349 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1350 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1100 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:95302044-95303243 Neighboring gene NANOG hESC enhancer GRCh37_chr1:95331914-95332415 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_9624 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:95349823-95350709 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:95376115-95377314 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:95385599-95386099 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1101 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1102 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:95401156-95402010 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:95402011-95402865 Neighboring gene calponin 3 Neighboring gene CNN3 divergent transcript Neighboring gene uncharacterized LOC124904224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1351 Neighboring gene ALG14 UDP-N-acetylglucosaminyltransferase subunit

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
  • 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. An electric lobe suppressor for a yeast choline transport mutation belongs to a new family of transporter-like proteins. O'Regan S, et al. Proc Natl Acad Sci U S A, 2000 Feb 15. PMID 10677542, Free PMC Article
  2. A genome-wide association search for type 2 diabetes genes in African Americans. Palmer ND, et al. PLoS One, 2012. PMID 22238593, Free PMC Article
  3. Molecular characterization of the family of choline transporter-like proteins and their splice variants. Traiffort E, et al. J Neurochem, 2005 Mar. PMID 15715662
  4. Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study. Yu B, et al. Genet Epidemiol, 2013 Dec. PMID 23934736, Free PMC Article
  5. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. Clark HF, et al. Genome Res, 2003 Oct. PMID 12975309, Free PMC Article

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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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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
A genome-wide association search for type 2 diabetes genes in African Americans.
EBI GWAS Catalog
Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study.
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)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC45474

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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 IEA
Inferred from Electronic Annotation
more info
  
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 TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
choline transporter-like protein 3

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_001114106.3 → NP_001107578.1  choline transporter-like protein 3 isoform 1

    See identical proteins and their annotated locations for NP_001107578.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AY358659, BC033858, DB331517, DC311042
    Consensus CDS
    CCDS44176.1
    UniProtKB/Swiss-Prot
    B4DVY4, B4E1M4, B7ZA08, E9PJH2, E9PJY8, Q6UWT1, Q7Z6C5, Q8N4M1, Q9BWY7
    UniProtKB/TrEMBL
    B4DTF4
    Related
    ENSP00000271227.6, ENST00000271227.11
    Conserved Domains (1) summary
    pfam04515
    Location:288 → 601
    Choline_transpo; Plasma-membrane choline transporter

  2. NM_001258340.2 → NP_001245269.1  choline transporter-like protein 3 isoform 3

    See identical proteins and their annotated locations for NP_001245269.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AK313574, AL530322, AY358659, BX648225, DB331517, DC311042
    UniProtKB/TrEMBL
    B4DTF4
    Conserved Domains (1) summary
    pfam04515
    Location:288 → 600
    Choline_transpo; Plasma-membrane choline transporter

  3. NM_001258341.2 → NP_001245270.1  choline transporter-like protein 3 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) uses two alternate splice sites in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
    Source sequence(s)
    AK316123, BX648225, DB331517, DC311042
    Consensus CDS
    CCDS58011.1
    UniProtKB/TrEMBL
    B4DTF4
    Related
    ENSP00000431836.1, ENST00000529450.5
    Conserved Domains (1) summary
    pfam04515
    Location:257 → 568
    Choline_transpo; Plasma-membrane choline transporter

  4. NM_001258342.2 → NP_001245271.1  choline transporter-like protein 3 isoform 5

    See identical proteins and their annotated locations for NP_001245271.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks an exon in the 5' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (5) is shorter than isoform 1.
    Source sequence(s)
    AK303906, AY358659, DB331517, DC311042
    Consensus CDS
    CCDS58013.1
    UniProtKB/TrEMBL
    B4DTF4
    Related
    ENSP00000389143.2, ENST00000446120.6
    Conserved Domains (1) summary
    pfam04515
    Location:252 → 565
    Choline_transpo; Plasma-membrane choline transporter

  5. NM_001258343.2 → NP_001245272.1  choline transporter-like protein 3 isoform 6

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) lacks an exon and uses an alternate splice site in the 5' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (6) is shorter than isoform 1.
    Source sequence(s)
    AK301288, AY358659, DB331517, DC311042
    Consensus CDS
    CCDS58012.1
    UniProtKB/TrEMBL
    B4DTF4
    Related
    ENSP00000433641.1, ENST00000527077.5
    Conserved Domains (1) summary
    pfam04515
    Location:221 → 533
    Choline_transpo; Plasma-membrane choline transporter

  6. NM_001301079.2 → NP_001288008.1  choline transporter-like protein 3 isoform 7

    See identical proteins and their annotated locations for NP_001288008.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) differs in the 5' UTR, contains multiple differences in the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (7) is shorter than isoform 1.
    Source sequence(s)
    AK300193, AY358659, DA538278, DB331517
    Consensus CDS
    CCDS72827.1
    UniProtKB/TrEMBL
    B4DTF4, E9PIC5
    Related
    ENSP00000436661.1, ENST00000532427.5
    Conserved Domains (1) summary
    pfam04515
    Location:209 → 521
    Choline_transpo; Plasma-membrane choline transporter

  7. NM_001350223.1 → NP_001337152.1  choline transporter-like protein 3 isoform 8

    Status: VALIDATED

    Source sequence(s)
    AC093429, AK300193, AY358659, BX648225, DB331517
    UniProtKB/TrEMBL
    B4DTF4
    Conserved Domains (1) summary
    pfam04515
    Location:192 → 504
    Choline_transpo; Plasma-membrane choline transporter

  8. NM_152369.5 → NP_689582.2  choline transporter-like protein 3 isoform 2

    See identical proteins and their annotated locations for NP_689582.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AY358659, BC053877, DA538278, DB331517
    Consensus CDS
    CCDS751.1
    UniProtKB/TrEMBL
    B4DTF4
    Related
    ENSP00000432789.1, ENST00000467909.5
    Conserved Domains (1) summary
    pfam04515
    Location:240 → 553
    Choline_transpo; Plasma-membrane choline transporter

RNA

  1. NR_146575.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC093429, AY358659, BC033858, DB331517, DC311042

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    94820357..94895247
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005270442.3 → XP_005270499.1  choline transporter-like protein 3 isoform X6

    UniProtKB/TrEMBL
    B4DTF4
    Conserved Domains (1) summary
    pfam04515
    Location:288 → 543
    Choline_transpo; Plasma-membrane choline transporter

  2. XM_017000264.3 → XP_016855753.1  choline transporter-like protein 3 isoform X7

    UniProtKB/TrEMBL
    B4DTF4

  3. XM_005270440.3 → XP_005270497.1  choline transporter-like protein 3 isoform X1

    UniProtKB/TrEMBL
    B4DTF4
    Conserved Domains (1) summary
    pfam04515
    Location:256 → 569
    Choline_transpo; Plasma-membrane choline transporter

  4. XM_017000265.2 → XP_016855754.1  choline transporter-like protein 3 isoform X8

    UniProtKB/TrEMBL
    B4DTF4

  5. XM_047444897.1 → XP_047300853.1  choline transporter-like protein 3 isoform X9

  6. XM_017000262.3 → XP_016855751.1  choline transporter-like protein 3 isoform X2

    UniProtKB/TrEMBL
    B4DTF4
    Conserved Domains (1) summary
    pfam04515
    Location:252 → 564
    Choline_transpo; Plasma-membrane choline transporter

  7. XM_047444888.1 → XP_047300844.1  choline transporter-like protein 3 isoform X5

  8. XM_011540636.4 → XP_011538938.1  choline transporter-like protein 3 isoform X15

    Conserved Domains (1) summary
    pfam04515
    Location:256 → 462
    Choline_transpo; Plasma-membrane choline transporter

  9. XM_011540635.4 → XP_011538937.1  choline transporter-like protein 3 isoform X12

    Conserved Domains (1) summary
    pfam04515
    Location:288 → 494
    Choline_transpo; Plasma-membrane choline transporter

  10. XM_017000266.3 → XP_016855755.1  choline transporter-like protein 3 isoform X11

  11. XM_047444909.1 → XP_047300865.1  choline transporter-like protein 3 isoform X13

  12. XM_047444914.1 → XP_047300870.1  choline transporter-like protein 3 isoform X16

  13. XM_005270441.3 → XP_005270498.1  choline transporter-like protein 3 isoform X3

    See identical proteins and their annotated locations for XP_005270498.1

    UniProtKB/TrEMBL
    B4DTF4
    Conserved Domains (1) summary
    pfam04515
    Location:240 → 553
    Choline_transpo; Plasma-membrane choline transporter

  14. XM_017000263.2 → XP_016855752.1  choline transporter-like protein 3 isoform X4

    UniProtKB/TrEMBL
    B4DTF4

  15. XM_047444912.1 → XP_047300868.1  choline transporter-like protein 3 isoform X14

  16. XM_011540633.3 → XP_011538935.1  choline transporter-like protein 3 isoform X10

    UniProtKB/TrEMBL
    B4DTF4
    Conserved Domains (1) summary
    pfam04515
    Location:159 → 472
    Choline_transpo; Plasma-membrane choline transporter

RNA

  1. XR_946543.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    94668402..94743603
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054334288.1 → XP_054190263.1  choline transporter-like protein 3 isoform X6

  2. XM_054334289.1 → XP_054190264.1  choline transporter-like protein 3 isoform X7

  3. XM_054334283.1 → XP_054190258.1  choline transporter-like protein 3 isoform X1

  4. XM_054334290.1 → XP_054190265.1  choline transporter-like protein 3 isoform X8

  5. XM_054334291.1 → XP_054190266.1  choline transporter-like protein 3 isoform X9

  6. XM_054334284.1 → XP_054190259.1  choline transporter-like protein 3 isoform X2

  7. XM_054334287.1 → XP_054190262.1  choline transporter-like protein 3 isoform X5

  8. XM_054334297.1 → XP_054190272.1  choline transporter-like protein 3 isoform X15

  9. XM_054334294.1 → XP_054190269.1  choline transporter-like protein 3 isoform X12

  10. XM_054334293.1 → XP_054190268.1  choline transporter-like protein 3 isoform X11

  11. XM_054334295.1 → XP_054190270.1  choline transporter-like protein 3 isoform X13

  12. XM_054334298.1 → XP_054190273.1  choline transporter-like protein 3 isoform X16

  13. XM_054334285.1 → XP_054190260.1  choline transporter-like protein 3 isoform X3

  14. XM_054334286.1 → XP_054190261.1  choline transporter-like protein 3 isoform X4

  15. XM_054334296.1 → XP_054190271.1  choline transporter-like protein 3 isoform X14

  16. XM_054334292.1 → XP_054190267.1  choline transporter-like protein 3 isoform X10

RNA

  1. XR_008485910.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N4M1.4 GenPept UniProtKB/Swiss-Prot:Q8N4M1

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