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SLC29A3 solute carrier family 29 member 3 [ Homo sapiens (human) ]

Gene ID: 55315, updated on 11-Apr-2024

Summary

Official Symbol
SLC29A3provided by HGNC
Official Full Name
solute carrier family 29 member 3provided by HGNC
Primary source
HGNC:HGNC:23096
See related
Ensembl:ENSG00000198246 MIM:612373; AllianceGenome:HGNC:23096
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ENT3; HJCD; PHID; HCLAP
Summary
This gene encodes a nucleoside transporter. The encoded protein plays a role in cellular uptake of nucleosides, nucleobases, and their related analogs. Mutations in this gene have been associated with H syndrome, which is characterized by cutaneous hyperpigmentation and hypertrichosis, hepatosplenomegaly, heart anomalies, and hypogonadism. A related disorder, PHID (pigmented hypertrichosis with insulin-dependent diabetes mellitus), has also been associated with mutations at this locus. Alternatively spliced transcript variants have been described.[provided by RefSeq, Mar 2010]
Expression
Ubiquitous expression in placenta (RPKM 7.5), urinary bladder (RPKM 5.5) and 25 other tissues See more
Orthologs
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Genomic context

See SLC29A3 in Genome Data Viewer
Location:
10q22.1
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (71319259..71381423)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (72188806..72250962)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (73079016..73123142)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC112268061 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72980575-72981076 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72992253-72992763 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72992809-72993562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72995071-72995822 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72995831-72996578 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72996579-72997325 Neighboring gene UNC5B antisense RNA 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:73006150-73007349 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73019454-73020306 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:73025690-73026683 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:73026875-73027596 Neighboring gene Sharpr-MPRA regulatory region 4598 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:73030481-73031200 Neighboring gene unc-5 netrin receptor B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:73038590-73039114 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:73039115-73039640 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73044725-73045226 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73045227-73045726 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:73055217-73056024 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:73063697-73064197 Neighboring gene uncharacterized LOC124902445 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2461 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73086403-73086902 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:73087283-73087858 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:73087859-73088434 Neighboring gene uncharacterized LOC105378353 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:73103993-73104698 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:73105405-73106110 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73110710-73111210 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73111211-73111711 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2462 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3513 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73136384-73136944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3514 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2463 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2464 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73156969-73157480 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:73202099-73202263 Neighboring gene cadherin related 23 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:73222965-73223156 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73225529-73226250 Neighboring gene uncharacterized LOC105378356 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73246156-73246656 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73246657-73247157 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73254765-73255264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73261097-73261617 Neighboring gene CDH23 antisense RNA 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
H syndrome
MedGen: C1864445 OMIM: 602782 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Association analyses identify three susceptibility Loci for vitiligo in the Chinese Han population.
EBI GWAS Catalog
Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with systemic lupus erythematosus in Asians.
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ11160

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in adenosine transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in adenosine transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cytidine transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in dopamine transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in guanine transmembrane transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in inosine transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in neurotransmitter transport IEA
Inferred from Electronic Annotation
more info
 
involved_in norepinephrine transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in nucleobase transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in nucleoside transmembrane transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in nucleoside transmembrane transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in nucleoside transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in nucleoside transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in purine nucleobase transmembrane transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in pyrimidine nucleobase transmembrane transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in serotonin transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in uracil transmembrane transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in uridine transmembrane transport IDA
Inferred from Direct Assay
more info
PubMed 
involved_in xenobiotic metabolic process TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
is_active_in Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
located_in late endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in lysosomal membrane HDA PubMed 
located_in lysosomal membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in lysosomal membrane TAS
Traceable Author Statement
more info
 
located_in mitochondrial outer membrane TAS
Traceable Author Statement
more info
 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
 

General protein information

Preferred Names
equilibrative nucleoside transporter 3
Names
solute carrier family 29 (equilibrative nucleoside transporter), member 3
solute carrier family 29 (nucleoside transporters), 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.

Genomic

  1. NG_017066.2 RefSeqGene

    Range
    5001..49127
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1318

mRNA and Protein(s)

  1. NM_001174098.2NP_001167569.1  equilibrative nucleoside transporter 3 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. It encodes isoform b, which is shorter than isoform a.
    Source sequence(s)
    BC063019, BC120997, DC319920
    UniProtKB/Swiss-Prot
    Q9BZD2
    Conserved Domains (1) summary
    cl15430
    Location:57258
    Nucleoside_tran; Nucleoside transporter
  2. NM_001363518.2NP_001350447.1  equilibrative nucleoside transporter 3 isoform c

    Status: REVIEWED

    Source sequence(s)
    AL359183, AL359384
    Consensus CDS
    CCDS86099.1
    UniProtKB/TrEMBL
    A0A2R8YDR8
    Related
    ENSP00000493995.1, ENST00000479577.2
    Conserved Domains (1) summary
    cl15430
    Location:16397
    Nucleoside_tran; Nucleoside transporter
  3. NM_018344.6NP_060814.4  equilibrative nucleoside transporter 3 isoform a

    See identical proteins and their annotated locations for NP_060814.4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (a).
    Source sequence(s)
    BC050589, BC120997, DC319920
    Consensus CDS
    CCDS7310.1
    UniProtKB/Swiss-Prot
    B2RB50, B4E2Z9, B7ZA37, Q0VAM9, Q5T465, Q7RTT8, Q8IVZ0, Q9BWI2, Q9BZD2, Q9NUS9
    Related
    ENSP00000362285.5, ENST00000373189.6
    Conserved Domains (1) summary
    cl15430
    Location:57475
    Nucleoside_tran; Nucleoside transporter

RNA

  1. NR_033413.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate internal exon, 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)
    BC050589, BC120997, DC319920
    Related
    ENST00000644591.1
  2. NR_033414.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks two alternate internal exons, 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)
    BC050589, BC120997, DC319920
    Related
    ENST00000644088.1

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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    71319259..71381423
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047425425.1XP_047281381.1  equilibrative nucleoside transporter 3 isoform X2

  2. XM_047425424.1XP_047281380.1  equilibrative nucleoside transporter 3 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    72188806..72250962
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054366210.1XP_054222185.1  equilibrative nucleoside transporter 3 isoform X2

  2. XM_054366209.1XP_054222184.1  equilibrative nucleoside transporter 3 isoform X1