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

    Gene ID: 126969, updated on 10-Dec-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, Dec 2024]
    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_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (94820357..94895247)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (94668402..94743603)
    RS_2024_09 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. Genome-Wide Analysis of Exertional Rhabdomyolysis in Sickle Cell Trait Positive African Americans. Ren M, et al. Genes (Basel), 2024 Mar 26. PMID 38674343, Free PMC Article
    2. 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
    3. 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
    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 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

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Genome-Wide Analysis of Exertional Rhabdomyolysis in Sickle Cell Trait Positive African Americans.
      Title: Genome-Wide Analysis of Exertional Rhabdomyolysis in Sickle Cell Trait Positive African Americans.
    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

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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)

    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_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
      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

      UniProtKB/TrEMBL
      B4DTF4

    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

      UniProtKB/TrEMBL
      B4DTF4

    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

      UniProtKB/TrEMBL
      B4DTF4

    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

      UniProtKB/TrEMBL
      B4DTF4

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

      UniProtKB/TrEMBL
      B4DTF4

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

      UniProtKB/TrEMBL
      B4DTF4

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

      UniProtKB/TrEMBL
      B4DTF4

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

      UniProtKB/TrEMBL
      B4DTF4

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

      UniProtKB/TrEMBL
      B4DTF4

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

      UniProtKB/TrEMBL
      B4DTF4

    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

      UniProtKB/TrEMBL
      B4DTF4

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

      UniProtKB/TrEMBL
      B4DTF4

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

      UniProtKB/TrEMBL
      B4DTF4

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

      UniProtKB/TrEMBL
      B4DTF4

    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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