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

Summary

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: mouse all
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Genomic context

Location:: 9q21.32-q21.33

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (84275457..84368727, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (96425798..96519059, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (86890372..86983642, complement)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
Characterization of deoxyribonucleoside transport mediated by concentrative nucleoside transporters.
Title: Characterization of deoxyribonucleoside transport mediated by concentrative nucleoside transporters.
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.
Cryo-EM structure of the human concentrative nucleoside transporter CNT3.
Title: Cryo-EM structure of the human concentrative nucleoside transporter CNT3.
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.
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.
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.
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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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 EBI GWAS CatalogPubMed
Genome-wide association of lipid-lowering response to statins in combined study populations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study (GWAS) for molar-incisor hypomineralization (MIH). EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

SHGC-149871 (e-PCR)
- UniSTS:177272

G17301 (e-PCR)
- UniSTS:5285

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)

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
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

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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000009.12 Reference GRCh38.p14 Primary Assembly

Range

84275457..84368727 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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