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    SLC35A3 solute carrier family 35 member A3 [ Homo sapiens (human) ]

    Gene ID: 23443, updated on 9-Dec-2024

    Summary

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    Official Symbol
    SLC35A3provided by HGNC
    Official Full Name
    solute carrier family 35 member A3provided by HGNC
    Primary source
    HGNC:HGNC:11023
    See related
    Ensembl:ENSG00000117620 MIM:605632; AllianceGenome:HGNC:11023
    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
    AMRS
    Summary
    This gene encodes a UDP-N-acetylglucosamine transporter found in the golgi apparatus membrane. In cattle, a missense mutation in this gene causes complex vertebral malformation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]
    Expression
    Broad expression in colon (RPKM 21.3), duodenum (RPKM 16.3) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC35A3 in Genome Data Viewer
    Location:
    1p21.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (99969996..100035634)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (99818116..99883750)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (100435552..100501190)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:100315063-100316037 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:100316038-100317011 Neighboring gene ribosomal protein L39 pseudogene 9 Neighboring gene amylo-alpha-1,6-glucosidase and 4-alpha-glucanotransferase Neighboring gene uncharacterized LOC124904230 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:100415895-100416089 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1363 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1364 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1115 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1365 Neighboring gene RNA, U6 small nuclear 750, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:100471652-100472152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:100472153-100472653 Neighboring gene RNA, U6 small nuclear 1318, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:100503123-100503725 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1366 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1367 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1368 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:100514024-100514739 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1369 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1370 Neighboring gene major facilitator superfamily domain containing 14A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1371 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1372 Neighboring gene SAS-6 centriolar assembly protein Neighboring gene ReSE screen-validated silencer GRCh37_chr1:100578889-100579078 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1373 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:100598108-100598271 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:100598267-100598869

    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. Molecular cloning and functional expression of the human Golgi UDP-N-acetylglucosamine transporter. Ishida N, et al. J Biochem, 1999 Jul. PMID 10393322
    2. Identification of HIF-dependent alternative splicing in gastrointestinal cancers and characterization of a long, coding isoform of SLC35A3. Markolin P, et al. Genomics, 2021 Mar. PMID 33418078
    3. Biosynthesis of GlcNAc-rich N- and O-glycans in the Golgi apparatus does not require the nucleotide sugar transporter SLC35A3. Szulc B, et al. J Biol Chem, 2020 Nov 27. PMID 32938718, Free PMC Article
    4. Evaluation of SLC35A3 as a candidate gene for human vertebral malformations. Ghebranious N, et al. Am J Med Genet A, 2006 Jun 15. PMID 16691598
    5. A human case of SLC35A3-related skeletal dysplasia. Edmondson AC, et al. Am J Med Genet A, 2017 Oct. PMID 28777481

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Colorectal cancer with low SLC35A3 is associated with immune infiltrates and poor prognosis.
      Title: Colorectal cancer with low SLC35A3 is associated with immune infiltrates and poor prognosis.
    2. Identification of HIF-dependent alternative splicing in gastrointestinal cancers and characterization of a long, coding isoform of SLC35A3.
      Title: Identification of HIF-dependent alternative splicing in gastrointestinal cancers and characterization of a long, coding isoform of SLC35A3.
    3. Serum bikunin isoforms in congenital disorders of glycosylation and linkeropathies.
      Title: Serum bikunin isoforms in congenital disorders of glycosylation and linkeropathies.
    4. Biosynthesis of GlcNAc-rich N- and O-glycans in the Golgi apparatus does not require the nucleotide sugar transporter SLC35A3.
      Title: Biosynthesis of GlcNAc-rich N- and O-glycans in the Golgi apparatus does not require the nucleotide sugar transporter SLC35A3.
    5. SLC35A3 missense homozygous mutation is associated with skeletal dysplasia.
      Title: A human case of SLC35A3-related skeletal dysplasia.
    6. Recessive mutations in SLC35A3 caused early onset epileptic encephalopathy with skeletal defects in two siblings in an Italian non-consanguineous family.
      Title: Recessive mutations in SLC35A3 cause early onset epileptic encephalopathy with skeletal defects.
    7. UDP-galactose (SLC35A2) and UDP-N-acetylglucosamine (SLC35A3) Transporters Form Glycosylation-related Complexes with Mannoside Acetylglucosaminyltransferases (Mgats).
      Title: UDP-galactose (SLC35A2) and UDP-N-acetylglucosamine (SLC35A3) Transporters Form Glycosylation-related Complexes with Mannoside Acetylglucosaminyltransferases (Mgats).
    8. Identified deleterious mutations in SLC35A3 in eight patients from a large kindred, who suffered from autism spectrum disorder, arthrogryposis and epilepsy.
      Title: Mutations in SLC35A3 cause autism spectrum disorder, epilepsy and arthrogryposis.
    9. The data further supports the hypothesis that UGT and NGT cooperate in the UDP-Gal delivery for glycosyltransferases located in the Golgi apparatus.
      Title: UDP-Gal/UDP-GlcNAc chimeric transporter complements mutation defect in mammalian cells deficient in UDP-Gal transporter.
    10. A mutation in the SLC35A3 gene is associated with vertebral malformations in cattle. A missense mutation likely effects signal transduction which relies on glycosylation.
      Title: A missense mutation in the bovine SLC35A3 gene, encoding a UDP-N-acetylglucosamine transporter, causes complex vertebral malformation.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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

    Associated conditions

    Description Tests
    Autism spectrum disorder - epilepsy - arthrogryposis syndrome
    MedGen: C3809910 OMIM: 615553 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope transmembrane glycoprotein gp41 env Mannose-containing, N-linked oligosaccharide side-chains of HIV-1 gp41 are involved in the initial stage of infection by HIV-1; glycosylation inhibitors block virus-cell and cell-cell fusion and release of the virions PubMed

    Go to the HIV-1, Human Interaction Database

    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

    Clone Names

    • DKFZp781P1297

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables UDP-N-acetylglucosamine transmembrane transporter activity TAS
    Traceable Author Statement
    more info
    		  
    enables UDP-galactose transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables antiporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in UDP-N-acetylglucosamine metabolic process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in UDP-N-acetylglucosamine transmembrane transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus TAS
    Traceable Author Statement
    more info
    		 PubMed 
    is_active_in Golgi membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Golgi membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    UDP-N-acetylglucosamine transporter
    Names
    golgi UDP-GlcNAc transporter
    solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member 3
    solute carrier family 35 (UDP-N-acetylglucosamine (UDP-GlcNAc) transporter), member A3

    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_033857.2 RefSeqGene

      Range
      5002..70640
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001271684.2 → NP_001258613.1  UDP-N-acetylglucosamine transporter isoform 2

      See identical proteins and their annotated locations for NP_001258613.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks two exons in the coding region, which results in a frameshift and an early stop codon, compared to variant 1. It encodes isoform 2, which has a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC093019, AC118553, AV698459, BC005136, CR749816
      Consensus CDS
      CCDS60205.1
      UniProtKB/TrEMBL
      A0A1W2PQD6
      Related
      ENSP00000491145.1, ENST00000638336.1
      Conserved Domains (1) summary
      pfam04142
      Location:4 → 220
      Nuc_sug_transp; Nucleotide-sugar transporter

    2. NM_001271685.2 → NP_001258614.1  UDP-N-acetylglucosamine transporter isoform 3

      See identical proteins and their annotated locations for NP_001258614.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate 5' exon structure, which introduces an upstream start codon, compared to variant 1. It encodes isoform 3, which has a longer N-terminus, compared to isoform 1.
      Source sequence(s)
      AC093019, AC118553, CR749816
      Consensus CDS
      CCDS60204.1
      UniProtKB/TrEMBL
      A0A1W2PQH2
      Related
      ENSP00000359172.1, ENST00000370153.6
      Conserved Domains (2) summary
      TIGR00803
      Location:128 → 354
      nst; UDP-galactose transporter
      pfam04142
      Location:46 → 355
      Nuc_sug_transp; Nucleotide-sugar transporter

    3. NM_012243.3 → NP_036375.1  UDP-N-acetylglucosamine transporter isoform 1

      See identical proteins and their annotated locations for NP_036375.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes isoform 1.
      Source sequence(s)
      AB021981, AC093019, AC118553, CR749816
      Consensus CDS
      CCDS762.1
      UniProtKB/Swiss-Prot
      A8K3F8, D3DT54, Q68CR2, Q9BSB7, Q9Y2D2
      UniProtKB/TrEMBL
      A0A1W2PQH2
      Related
      ENSP00000433849.1, ENST00000533028.8
      Conserved Domains (2) summary
      TIGR00803
      Location:86 → 312
      nst; UDP-galactose transporter
      pfam04142
      Location:4 → 313
      Nuc_sug_transp; Nucleotide-sugar transporter

    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
      99969996..100035634
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005270691.6 → XP_005270748.1  UDP-N-acetylglucosamine transporter isoform X2

      See identical proteins and their annotated locations for XP_005270748.1

      UniProtKB/Swiss-Prot
      A8K3F8, D3DT54, Q68CR2, Q9BSB7, Q9Y2D2
      UniProtKB/TrEMBL
      A0A1W2PQH2
      Related
      ENSP00000414947.2, ENST00000427993.7
      Conserved Domains (2) summary
      TIGR00803
      Location:86 → 312
      nst; UDP-galactose transporter
      pfam04142
      Location:4 → 313
      Nuc_sug_transp; Nucleotide-sugar transporter

    2. XM_017000870.3 → XP_016856359.1  UDP-N-acetylglucosamine transporter isoform X5

      UniProtKB/TrEMBL
      A0A1W2PRN3, A0A1W2PSD1
      Related
      ENSP00000492801.1, ENST00000640715.1

    3. XM_017000869.3 → XP_016856358.1  UDP-N-acetylglucosamine transporter isoform X4

      UniProtKB/TrEMBL
      A0A1W2PRT7, A0A1W2PS45
      Related
      ENSP00000492771.1, ENST00000640732.1

    4. XM_017000871.3 → XP_016856360.1  UDP-N-acetylglucosamine transporter isoform X7

      UniProtKB/TrEMBL
      A0A1W2PQL8, A0A1W2PRN3
      Related
      ENSP00000492169.1, ENST00000639221.1

    5. XM_047416587.1 → XP_047272543.1  UDP-N-acetylglucosamine transporter isoform X9

    6. XM_047416588.1 → XP_047272544.1  UDP-N-acetylglucosamine transporter isoform X10

      UniProtKB/TrEMBL
      A0A1W2PR66
      Related
      ENSP00000492128.1, ENST00000640726.1

    7. XM_011541137.4 → XP_011539439.1  UDP-N-acetylglucosamine transporter isoform X3

      UniProtKB/TrEMBL
      A0A1W2PRN3
      Conserved Domains (1) summary
      TIGR00803
      Location:128 → 293
      nst; UDP-galactose transporter

    8. XM_011541138.4 → XP_011539440.1  UDP-N-acetylglucosamine transporter isoform X6

      UniProtKB/TrEMBL
      A0A1W2PQD6
      Conserved Domains (1) summary
      cl23754
      Location:128 → 258
      EamA; EamA-like transporter family

    9. XM_011541135.4 → XP_011539437.1  UDP-N-acetylglucosamine transporter isoform X1

      Conserved Domains (2) summary
      TIGR00803
      Location:128 → 313
      nst; UDP-galactose transporter
      pfam04142
      Location:46 → 314
      Nuc_sug_transp; Nucleotide-sugar transporter

    10. XM_047416586.1 → XP_047272542.1  UDP-N-acetylglucosamine transporter isoform X8

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      99818116..99883750
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054335691.1 → XP_054191666.1  UDP-N-acetylglucosamine transporter isoform X2

      UniProtKB/Swiss-Prot
      A8K3F8, D3DT54, Q68CR2, Q9BSB7, Q9Y2D2
      UniProtKB/TrEMBL
      A0A1W2PQH2

    2. XM_054335694.1 → XP_054191669.1  UDP-N-acetylglucosamine transporter isoform X5

      UniProtKB/TrEMBL
      A0A1W2PRN3, A0A1W2PSD1

    3. XM_054335693.1 → XP_054191668.1  UDP-N-acetylglucosamine transporter isoform X4

      UniProtKB/TrEMBL
      A0A1W2PRT7, A0A1W2PS45

    4. XM_054335696.1 → XP_054191671.1  UDP-N-acetylglucosamine transporter isoform X7

      UniProtKB/TrEMBL
      A0A1W2PQL8, A0A1W2PRN3

    5. XM_054335698.1 → XP_054191673.1  UDP-N-acetylglucosamine transporter isoform X9

    6. XM_054335699.1 → XP_054191674.1  UDP-N-acetylglucosamine transporter isoform X10

      UniProtKB/TrEMBL
      A0A1W2PR66

    7. XM_054335692.1 → XP_054191667.1  UDP-N-acetylglucosamine transporter isoform X3

      UniProtKB/TrEMBL
      A0A1W2PRN3

    8. XM_054335695.1 → XP_054191670.1  UDP-N-acetylglucosamine transporter isoform X6

      UniProtKB/TrEMBL
      A0A1W2PQD6

    9. XM_054335690.1 → XP_054191665.1  UDP-N-acetylglucosamine transporter isoform X1

    10. XM_054335697.1 → XP_054191672.1  UDP-N-acetylglucosamine transporter isoform X8

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y2D2.1 GenPept UniProtKB/Swiss-Prot:Q9Y2D2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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