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    EXTL2 exostosin like glycosyltransferase 2 [ Homo sapiens (human) ]

    Gene ID: 2135, updated on 2-Nov-2024

    Summary

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    Official Symbol
    EXTL2provided by HGNC
    Official Full Name
    exostosin like glycosyltransferase 2provided by HGNC
    Primary source
    HGNC:HGNC:3516
    See related
    Ensembl:ENSG00000162694 MIM:602411; AllianceGenome:HGNC:3516
    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
    EXTR2
    Summary
    Enables alpha-1,4-N-acetylgalactosaminyltransferase activity and glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity. Involved in N-acetylglucosamine metabolic process and UDP-N-acetylgalactosamine metabolic process. Located in cytosol; endoplasmic reticulum; and nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in adrenal (RPKM 10.0), placenta (RPKM 9.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See EXTL2 in Genome Data Viewer
    Location:
    1p21.2
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (100872372..100895179, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (100721212..100744883, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (101337928..101360735, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904231 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:101121642-101121817 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:101177825-101179024 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1385 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1386 Neighboring gene vascular cell adhesion molecule 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:101301135-101302334 Neighboring gene Sharpr-MPRA regulatory region 5467 Neighboring gene MPRA-validated peak338 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:101359730-101360453 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:101360454-101361176 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1389 Neighboring gene solute carrier family 30 member 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1390 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 68 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:101490870-101492069 Neighboring gene diphthamide biosynthesis 5

    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 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. Two-step mechanism that determines the donor binding specificity of human UDP-N-acetylhexosaminyltransferase. Sobhany M, et al. J Biol Chem, 2005 Jun 24. PMID 15831490
    2. Structure, chromosomal location, and expression profile of EXTR1 and EXTR2, new members of the multiple exostoses gene family. Saito T, et al. Biochem Biophys Res Commun, 1998 Feb 4. PMID 9473480
    3. Gene silencing of EXTL2 and EXTL3 as a substrate deprivation therapy for heparan sulphate storing mucopolysaccharidoses. Kaidonis X, et al. Eur J Hum Genet, 2010 Feb. PMID 19690583, Free PMC Article
    4. EXTL2, a member of the EXT family of tumor suppressors, controls glycosaminoglycan biosynthesis in a xylose kinase-dependent manner. Nadanaka S, et al. J Biol Chem, 2013 Mar 29. PMID 23395820, Free PMC Article
    5. The tumor suppressor EXT-like gene EXTL2 encodes an alpha1, 4-N-acetylhexosaminyltransferase that transfers N-acetylgalactosamine and N-acetylglucosamine to the common glycosaminoglycan-protein linkage region. The key enzyme for the chain initiation of heparan sulfate. Kitagawa H, et al. J Biol Chem, 1999 May 14. PMID 10318803

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Glycosyltransferases EXTL2 and EXTL3 cellular balance dictates heparan sulfate biosynthesis and shapes gastric cancer cell motility and invasion.
      Title: Glycosyltransferases EXTL2 and EXTL3 cellular balance dictates heparan sulfate biosynthesis and shapes gastric cancer cell motility and invasion.
    2. Altered Expression of Aggrecan, FAM20B, B3GALT6, and EXTL2 in Patients with Osteoarthritis and Kashin-Beck Disease.
      Title: Altered Expression of Aggrecan, FAM20B, B3GALT6, and EXTL2 in Patients with Osteoarthritis and Kashin-Beck Disease.
    3. The glycosyltransferase EXTL2 promotes proteoglycan deposition and injurious neuroinflammation following demyelination.
      Title: The glycosyltransferase EXTL2 promotes proteoglycan deposition and injurious neuroinflammation following demyelination.
    4. EXTL2 functions to suppress GAG biosynthesis that is enhanced by a xylose kinase and the EXTL2-dependent mechanism that regulates GAG biosynthesis might be a "quality control system" for proteoglycans
      Title: EXTL2, a member of the EXT family of tumor suppressors, controls glycosaminoglycan biosynthesis in a xylose kinase-dependent manner.
    5. Lysosomal glycosaminoglycan levels in mucopolysaccharidosis are reduced by EXTL2 gene silencing.
      Title: Gene silencing of EXTL2 and EXTL3 as a substrate deprivation therapy for heparan sulphate storing mucopolysaccharidoses.
    6. donor binding appears to undergo two distinct steps, beginning with the N-acetyl group expelling water from the donor- enzyme complex into the bulk solvent followed by positioning of the donor into the binding site for interactions with the enzyme
      Title: Two-step mechanism that determines the donor binding specificity of human UDP-N-acetylhexosaminyltransferase.
    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
    Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.
    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 alpha-1,4-N-acetylgalactosaminyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables glycosaminoglycan binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables manganese ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in N-acetylglucosamine metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in UDP-N-acetylgalactosamine metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in heparan sulfate proteoglycan biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    exostosin-like 2
    Names
    EXT-related protein 2
    alpha-1,4-N-acetylhexosaminyltransferase EXTL2
    alpha-GalNAcT EXTL2
    exostoses (multiple)-like 2
    glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase
    processed exostosin-like 2
    NP_001028197.1
    NP_001248369.1
    NP_001248370.1
    NP_001248371.1
    NP_001430.1
    XP_005270678.1
    XP_011539297.1
    XP_011539298.1
    XP_016856140.1
    XP_047305361.1
    XP_047305362.1
    XP_047305363.1
    XP_047305364.1
    XP_047305365.1
    XP_047305366.1
    XP_054191071.1
    XP_054191072.1
    XP_054191073.1
    XP_054191074.1
    XP_054191075.1
    XP_054191076.1
    XP_054191077.1
    XP_054191078.1
    XP_054191079.1
    XP_054191080.1
    XP_054191081.1
    XP_054191082.1
    XP_054191083.1
    XP_054191084.1
    XP_054191085.1
    XP_054191086.1
    XP_054191087.1
    XP_054191088.1

    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_001033025.3 → NP_001028197.1  exostosin-like 2 isoform 1

      See identical proteins and their annotated locations for NP_001028197.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AC104506, AK312895
      Consensus CDS
      CCDS775.1
      UniProtKB/Swiss-Prot
      B2R795, D3DT60, Q9UBQ6
      UniProtKB/TrEMBL
      Q49A43, Q8IYF4
      Related
      ENSP00000359132.3, ENST00000370114.8
      Conserved Domains (1) summary
      pfam09258
      Location:66 → 313
      Glyco_transf_64; Glycosyl transferase family 64 domain

    2. NM_001261440.2 → NP_001248369.1  exostosin-like 2 isoform 2

      See identical proteins and their annotated locations for NP_001248369.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in the 5' UTR and an alternate splice site in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC104506, AK096914
      UniProtKB/TrEMBL
      Q49A43, Q8IYF4, Q8N8F1
      Conserved Domains (1) summary
      pfam09258
      Location:66 → 312
      Glyco_transf_64; Glycosyl transferase family 64 domain

    3. NM_001261441.2 → NP_001248370.1  exostosin-like 2 isoform 3

      See identical proteins and their annotated locations for NP_001248370.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate splice site in the 5' UTR and includes an alternate exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (3) is longer than isoform 1.
      Source sequence(s)
      AC104506, AU130571
      UniProtKB/TrEMBL
      Q49A43, Q8IYF4
      Conserved Domains (1) summary
      pfam09258
      Location:74 → 321
      Glyco_transf_64; Glycosyl transferase family 64 domain

    4. NM_001261442.2 → NP_001248371.1  exostosin-like 2 isoform 4

      See identical proteins and their annotated locations for NP_001248371.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) lacks an exon in the coding region, which results in a frameshift, compared to variant 1. The encoded isoform (4) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC104506, BX103291
      Consensus CDS
      CCDS72831.1
      UniProtKB/TrEMBL
      F5GZK1
      Related
      ENSP00000444385.2, ENST00000535414.5
      Conserved Domains (1) summary
      pfam09258
      Location:66 → 146
      Glyco_transf_64; Glycosyl transferase family 64 domain

    5. NM_001439.4 → NP_001430.1  exostosin-like 2 isoform 1

      See identical proteins and their annotated locations for NP_001430.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes isoform 1. Variants and 2 encode the same isoform.
      Source sequence(s)
      AC104506, AF000416
      Consensus CDS
      CCDS775.1
      UniProtKB/Swiss-Prot
      B2R795, D3DT60, Q9UBQ6
      UniProtKB/TrEMBL
      Q49A43, Q8IYF4
      Related
      ENSP00000359131.3, ENST00000370113.7
      Conserved Domains (1) summary
      pfam09258
      Location:66 → 313
      Glyco_transf_64; Glycosyl transferase family 64 domain

    RNA

    1. NR_048570.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC104506, AK298124, BP202626

    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
      100872372..100895179 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047449409.1 → XP_047305365.1  exostosin-like 2 isoform X4

      UniProtKB/TrEMBL
      Q8N8F1

    2. XM_047449407.1 → XP_047305363.1  exostosin-like 2 isoform X3

      UniProtKB/Swiss-Prot
      B2R795, D3DT60, Q9UBQ6

    3. XM_047449405.1 → XP_047305361.1  exostosin-like 2 isoform X1

    4. XM_017000651.3 → XP_016856140.1  exostosin-like 2 isoform X4

      UniProtKB/TrEMBL
      Q49A43, Q8IYF4, Q8N8F1
      Conserved Domains (1) summary
      pfam09258
      Location:66 → 312
      Glyco_transf_64; Glycosyl transferase family 64 domain

    5. XM_005270621.2 → XP_005270678.1  exostosin-like 2 isoform X3

      See identical proteins and their annotated locations for XP_005270678.1

      UniProtKB/Swiss-Prot
      B2R795, D3DT60, Q9UBQ6
      UniProtKB/TrEMBL
      Q49A43, Q8IYF4
      Conserved Domains (1) summary
      pfam09258
      Location:66 → 313
      Glyco_transf_64; Glycosyl transferase family 64 domain

    6. XM_047449406.1 → XP_047305362.1  exostosin-like 2 isoform X1

    7. XM_011540996.3 → XP_011539298.1  exostosin-like 2 isoform X2

      UniProtKB/TrEMBL
      Q49A43, Q8IYF4
      Conserved Domains (1) summary
      pfam09258
      Location:74 → 320
      Glyco_transf_64; Glycosyl transferase family 64 domain

    8. XM_047449410.1 → XP_047305366.1  exostosin-like 2 isoform X4

      UniProtKB/TrEMBL
      Q8N8F1

    9. XM_047449408.1 → XP_047305364.1  exostosin-like 2 isoform X3

      UniProtKB/Swiss-Prot
      B2R795, D3DT60, Q9UBQ6

    10. XM_011540995.3 → XP_011539297.1  exostosin-like 2 isoform X1

      See identical proteins and their annotated locations for XP_011539297.1

      UniProtKB/TrEMBL
      Q49A43, Q8IYF4
      Conserved Domains (1) summary
      pfam09258
      Location:74 → 321
      Glyco_transf_64; Glycosyl transferase family 64 domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      100721212..100744883 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054335108.1 → XP_054191083.1  exostosin-like 2 isoform X3

      UniProtKB/Swiss-Prot
      B2R795, D3DT60, Q9UBQ6

    2. XM_054335113.1 → XP_054191088.1  exostosin-like 2 isoform X4

      UniProtKB/TrEMBL
      Q8N8F1

    3. XM_054335105.1 → XP_054191080.1  exostosin-like 2 isoform X3

      UniProtKB/Swiss-Prot
      B2R795, D3DT60, Q9UBQ6

    4. XM_054335098.1 → XP_054191073.1  exostosin-like 2 isoform X1

    5. XM_054335107.1 → XP_054191082.1  exostosin-like 2 isoform X3

      UniProtKB/Swiss-Prot
      B2R795, D3DT60, Q9UBQ6

    6. XM_054335104.1 → XP_054191079.1  exostosin-like 2 isoform X3

      UniProtKB/Swiss-Prot
      B2R795, D3DT60, Q9UBQ6

    7. XM_054335099.1 → XP_054191074.1  exostosin-like 2 isoform X1

    8. XM_054335103.1 → XP_054191078.1  exostosin-like 2 isoform X3

      UniProtKB/Swiss-Prot
      B2R795, D3DT60, Q9UBQ6

    9. XM_054335110.1 → XP_054191085.1  exostosin-like 2 isoform X4

      UniProtKB/TrEMBL
      Q8N8F1

    10. XM_054335111.1 → XP_054191086.1  exostosin-like 2 isoform X4

      UniProtKB/TrEMBL
      Q8N8F1

    11. XM_054335097.1 → XP_054191072.1  exostosin-like 2 isoform X1

    12. XM_054335100.1 → XP_054191075.1  exostosin-like 2 isoform X1

    13. XM_054335106.1 → XP_054191081.1  exostosin-like 2 isoform X3

      UniProtKB/Swiss-Prot
      B2R795, D3DT60, Q9UBQ6

    14. XM_054335102.1 → XP_054191077.1  exostosin-like 2 isoform X2

    15. XM_054335109.1 → XP_054191084.1  exostosin-like 2 isoform X4

      UniProtKB/TrEMBL
      Q8N8F1

    16. XM_054335096.1 → XP_054191071.1  exostosin-like 2 isoform X1

    17. XM_054335112.1 → XP_054191087.1  exostosin-like 2 isoform X4

      UniProtKB/TrEMBL
      Q8N8F1

    18. XM_054335101.1 → XP_054191076.1  exostosin-like 2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UBQ6.1 GenPept UniProtKB/Swiss-Prot:Q9UBQ6

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