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SLC28A3 solute carrier family 28 member 3 [ Homo sapiens (human) ]

Gene ID: 64078, updated on 11-Apr-2024

Summary

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Official Symbol
SLC28A3provided by HGNC
Official Full Name
solute carrier family 28 member 3provided by HGNC
Primary source
HGNC:HGNC:16484
See related
Ensembl:ENSG00000197506 MIM:608269; AllianceGenome:HGNC:16484
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
CNT3
Summary
Nucleoside transporters, such as SLC28A3, regulate multiple cellular processes, including neurotransmission, vascular tone, adenosine concentration in the vicinity of cell surface receptors, and transport and metabolism of nucleoside drugs. SLC28A3 shows broad specificity for pyrimidine and purine nucleosides (Ritzel et al., 2001 [PubMed 11032837]).[supplied by OMIM, Mar 2008]
Expression
Biased expression in gall bladder (RPKM 4.2), bone marrow (RPKM 3.2) and 11 other tissues See more
Orthologs
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Genomic context

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See SLC28A3 in Genome Data Viewer
Location:
9q21.32-q21.33
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (84275457..84368727, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (96425798..96519059, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (86890372..86983642, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:86595393-86595900 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:86595901-86596409 Neighboring gene heterogeneous nuclear ribonucleoprotein K Neighboring gene uncharacterized LOC101927575 Neighboring gene RecQ mediated genome instability 1 Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 33 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:86766071-86767007 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:86787894-86788403 Neighboring gene Sharpr-MPRA regulatory region 11289 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19983 Neighboring gene NANOG hESC enhancer GRCh37_chr9:86891619-86892170 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr9:86892303-86893502 Neighboring gene SLC28A3 regulatory antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28502 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28503 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28504 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:86916903-86918102 Neighboring gene SLC28A3 intron nontranscribed chromatin-defined enhancer Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:86991346-86991846 Neighboring gene uncharacterized LOC102724036 Neighboring gene uncharacterized LOC124902192 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19984 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:87127109-87128308 Neighboring gene NANOG hESC enhancer GRCh37_chr9:87185076-87185832 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_108369 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28505 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19985 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28506 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28507 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28508 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:87323096-87324014 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28509 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28510 Neighboring gene neurotrophic receptor tyrosine kinase 2 Neighboring gene uncharacterized LOC124902193

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. Allosteric and transport modulation of human concentrative nucleoside transporter 3 at the atomic scale. Duan H, et al. Phys Chem Chem Phys, 2021 Nov 17. PMID 34751688
  2. Cryo-EM structure of the human concentrative nucleoside transporter CNT3. Zhou Y, et al. PLoS Biol, 2020 Aug. PMID 32776918, Free PMC Article
  3. Inward- and outward-facing homology modeling of human concentrative nucleoside transporter 3 (hCNT3) predicts an elevator-type transport mechanism. Yao SYM, et al. Channels (Austin), 2018. PMID 30096006, Free PMC Article
  4. Human Concentrative Nucleoside Transporter 3 (hCNT3, SLC28A3) Forms a Cyclic Homotrimer. Stecula A, et al. Biochemistry, 2017 Jul 11. PMID 28661652, Free PMC Article
  5. Concentrative nucleoside transporter 3 as a prognostic indicator for favorable outcome of t(8;21)-positive acute myeloid leukemia patients after cytarabine-based chemotherapy. Song JH, et al. Oncol Rep, 2015 Jul. PMID 25955569

See all (55) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The Role of RARG rs2229774, SLC28A3 rs7853758, and UGT1A6*4 rs17863783 Single-nucleotide Polymorphisms in the Doxorubicin-induced Cardiotoxicity in Solid Childhood Tumors.
    Title: The Role of RARG rs2229774, SLC28A3 rs7853758, and UGT1A6*4 rs17863783 Single-nucleotide Polymorphisms in the Doxorubicin-induced Cardiotoxicity in Solid Childhood Tumors.
  2. Gene-Gene Interactions of Gemcitabine Metabolizing-Enzyme Genes hCNT3 and WEE1 for Preventing Severe Gemcitabine-Induced Hematological Toxicity.
    Title: Gene-Gene Interactions of Gemcitabine Metabolizing-Enzyme Genes hCNT3 and WEE1 for Preventing Severe Gemcitabine-Induced Hematological Toxicity.
  3. Allosteric and transport modulation of human concentrative nucleoside transporter 3 at the atomic scale.
    Title: Allosteric and transport modulation of human concentrative nucleoside transporter 3 at the atomic scale.
  4. Characterization of deoxyribonucleoside transport mediated by concentrative nucleoside transporters.
    Title: Characterization of deoxyribonucleoside transport mediated by concentrative nucleoside transporters.
  5. Association of SLC28A3 Gene Expression and CYP2B6*6 Allele with the Response to Fludarabine Plus Cyclophosphamide in Chronic Lymphocytic Leukemia Patients.
    Title: Association of SLC28A3 Gene Expression and CYP2B6*6 Allele with the Response to Fludarabine Plus Cyclophosphamide in Chronic Lymphocytic Leukemia Patients.
  6. Cryo-EM structure of the human concentrative nucleoside transporter CNT3.
    Title: Cryo-EM structure of the human concentrative nucleoside transporter CNT3.
  7. human CNT3 homology models generated validate previously published PCMBS SCAM data, and confirm an elevator-type mechanism of membrane transport
    Title: Inward- and outward-facing homology modeling of human concentrative nucleoside transporter 3 (hCNT3) predicts an elevator-type transport mechanism.
  8. De novo structure prediction of three N-terminal transmembrane helices of the human concentrative nucleoside transporter 3 (hCNT3) homotrimer belonging to the solute carrier 28 family of transporters (SLC28) using Rosetta program and its Broker protocol.
    Title: Rosetta Broker for membrane protein structure prediction: concentrative nucleoside transporter 3 and corticotropin-releasing factor receptor 1 test cases.
  9. CYR61 negatively regulates the nucleoside transporters hENT1 and hCNT3 in pancreatic ductal adenocarcinoma.
    Title: TGF-β-induced stromal CYR61 promotes resistance to gemcitabine in pancreatic ductal adenocarcinoma through downregulation of the nucleoside transporters hENT1 and hCNT3.
  10. Data suggest that CNT3 forms a homotrimer in solution and membrane-bound inside cells; the quaternary structure creates an aqueous basin that significantly shortens the substrate translocation distance.
    Title: Human Concentrative Nucleoside Transporter 3 (hCNT3, SLC28A3) Forms a Cyclic Homotrimer.
Submit: New GeneRIF Correction See all GeneRIFs (45)

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
Gene-environment interactions and obesity traits among postmenopausal African-American and Hispanic women in the Women's Health Initiative SHARe Study.
EBI GWAS Catalog
Genome-wide association of lipid-lowering response to statins in combined study populations.
EBI GWAS Catalog
Genome-wide association study (GWAS) for molar-incisor hypomineralization (MIH).
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables nucleoside:sodium symporter activity TAS
Traceable Author Statement
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables purine nucleobase transmembrane transporter activity NAS
Non-traceable Author Statement
more info
 PubMed 
enables purine-specific nucleoside:sodium symporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables pyrimidine- and adenosine-specific:sodium symporter activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables uridine transmembrane transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in nucleoside transmembrane transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in purine nucleobase transmembrane transport NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in purine nucleoside transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in pyrimidine nucleobase transport IEA
Inferred from Electronic Annotation
more info
  
involved_in pyrimidine nucleoside transport IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in pyrimidine-containing compound transmembrane transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in sodium ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
involved_in uridine transmembrane transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in xenobiotic metabolic process TAS
Traceable Author Statement
more info
  
involved_in xenobiotic transmembrane transport TAS
Traceable Author Statement
more info
  
Component Evidence Code Pubs
located_in brush border membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma 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
solute carrier family 28 member 3
Names
concentrative Na(+)-nucleoside cotransporter 3
concentrative Na+-nucleoside cotransporter
solute carrier family 28 (concentrative nucleoside transporter), member 3
solute carrier family 28 (sodium-coupled nucleoside transporter), member 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_001199633.2 → NP_001186562.1  solute carrier family 28 member 3

    See identical proteins and their annotated locations for NP_001186562.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1 and 2 both encode the same protein.
    Source sequence(s)
    AA643687, AF305210, AK022042, AK314039, AL356134
    Consensus CDS
    CCDS6670.1
    UniProtKB/Swiss-Prot
    A8K9Y4, B1AML0, B2RA51, B4E2S8, F5GYE3, Q9HAS3
    Related
    ENSP00000365413.4, ENST00000376238.5
    Conserved Domains (4) summary
    TIGR00804
    Location:201 → 612
    nupC; nucleoside transporter
    pfam01773
    Location:206 → 275
    Nucleos_tra2_N; Na+ dependent nucleoside transporter N-terminus
    pfam07662
    Location:388 → 612
    Nucleos_tra2_C; Na+ dependent nucleoside transporter C-terminus
    pfam07670
    Location:287 → 383
    Gate; Nucleoside recognition

  2. NM_022127.3 → NP_071410.1  solute carrier family 28 member 3

    See identical proteins and their annotated locations for NP_071410.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same protein.
    Source sequence(s)
    AA643687, AF305210, AK022042, AL353787, AL356134
    Consensus CDS
    CCDS6670.1
    UniProtKB/Swiss-Prot
    A8K9Y4, B1AML0, B2RA51, B4E2S8, F5GYE3, Q9HAS3
    Conserved Domains (4) summary
    TIGR00804
    Location:201 → 612
    nupC; nucleoside transporter
    pfam01773
    Location:206 → 275
    Nucleos_tra2_N; Na+ dependent nucleoside transporter N-terminus
    pfam07662
    Location:388 → 612
    Nucleos_tra2_C; Na+ dependent nucleoside transporter C-terminus
    pfam07670
    Location:287 → 383
    Gate; Nucleoside recognition

RNA

  1. NR_037638.3 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) includes an alternate exon in the coding region compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AA643687, AF305210, AK022042, AK304406, AL353787, AL356134

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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    84275457..84368727 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011518907.3 → XP_011517209.1  solute carrier family 28 member 3 isoform X2

    Conserved Domains (4) summary
    TIGR00804
    Location:118 → 529
    nupC; nucleoside transporter
    pfam01773
    Location:123 → 192
    Nucleos_tra2_N; Na+ dependent nucleoside transporter N-terminus
    pfam07662
    Location:305 → 529
    Nucleos_tra2_C; Na+ dependent nucleoside transporter C-terminus
    pfam07670
    Location:204 → 300
    Gate; Nucleoside recognition

  2. XM_011518906.3 → XP_011517208.1  solute carrier family 28 member 3 isoform X1

    See identical proteins and their annotated locations for XP_011517208.1

    Conserved Domains (4) summary
    TIGR00804
    Location:229 → 640
    nupC; nucleoside transporter
    pfam01773
    Location:234 → 303
    Nucleos_tra2_N; Na+ dependent nucleoside transporter N-terminus
    pfam07662
    Location:416 → 640
    Nucleos_tra2_C; Na+ dependent nucleoside transporter C-terminus
    pfam07670
    Location:315 → 411
    Gate; Nucleoside recognition

  3. XM_011518905.3 → XP_011517207.1  solute carrier family 28 member 3 isoform X1

    See identical proteins and their annotated locations for XP_011517207.1

    Conserved Domains (4) summary
    TIGR00804
    Location:229 → 640
    nupC; nucleoside transporter
    pfam01773
    Location:234 → 303
    Nucleos_tra2_N; Na+ dependent nucleoside transporter N-terminus
    pfam07662
    Location:416 → 640
    Nucleos_tra2_C; Na+ dependent nucleoside transporter C-terminus
    pfam07670
    Location:315 → 411
    Gate; Nucleoside recognition

  4. XM_011518908.3 → XP_011517210.1  solute carrier family 28 member 3 isoform X4

    Conserved Domains (4) summary
    TIGR00804
    Location:11 → 399
    nupC; nucleoside transporter
    pfam01773
    Location:13 → 62
    Nucleos_tra2_N; Na+ dependent nucleoside transporter N-terminus
    pfam07662
    Location:175 → 399
    Nucleos_tra2_C; Na+ dependent nucleoside transporter C-terminus
    pfam07670
    Location:74 → 170
    Gate; Nucleoside recognition

  5. XM_047423712.1 → XP_047279668.1  solute carrier family 28 member 3 isoform X3

  6. XM_011518910.3 → XP_011517212.1  solute carrier family 28 member 3 isoform X5

    See identical proteins and their annotated locations for XP_011517212.1

    Conserved Domains (2) summary
    pfam01773
    Location:234 → 303
    Nucleos_tra2_N; Na+ dependent nucleoside transporter N-terminus
    pfam07670
    Location:315 → 370
    Gate; Nucleoside recognition

  7. XM_011518909.3 → XP_011517211.1  solute carrier family 28 member 3 isoform X5

    See identical proteins and their annotated locations for XP_011517211.1

    Conserved Domains (2) summary
    pfam01773
    Location:234 → 303
    Nucleos_tra2_N; Na+ dependent nucleoside transporter N-terminus
    pfam07670
    Location:315 → 370
    Gate; Nucleoside recognition

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    96425798..96519059 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054363509.1 → XP_054219484.1  solute carrier family 28 member 3 isoform X2

  2. XM_054363508.1 → XP_054219483.1  solute carrier family 28 member 3 isoform X1

  3. XM_054363507.1 → XP_054219482.1  solute carrier family 28 member 3 isoform X1

  4. XM_054363511.1 → XP_054219486.1  solute carrier family 28 member 3 isoform X4

  5. XM_054363510.1 → XP_054219485.1  solute carrier family 28 member 3 isoform X3

  6. XM_054363513.1 → XP_054219488.1  solute carrier family 28 member 3 isoform X5

  7. XM_054363512.1 → XP_054219487.1  solute carrier family 28 member 3 isoform X5

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9HAS3.1 GenPept UniProtKB/Swiss-Prot:Q9HAS3

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