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XYLT2 Gene

protein-coding   GIFtS: 57

GC17P045778
xylosyltransferase II
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Aliases
EC 2.4.2.26 3
XT-II 1, 2, 3
XT2 2, 3, 5
XylT-II 3
xylT-II 2
Descriptions
Peptide O-xylosyltransferase 1 2, 3
UDP-D-xylose:proteoglycan core protein
beta-D-xylosyltransferase 2
xylosyltransferase II 2, 3
External Ids
HGNC: 155171
Entrez Gene: 641322
UniProtKB: Q9H1B53
Ensembl: ENSG000000155327
Search outside databases for aliases for XYLT2 gene

Previous GC identifers: GC17P048136 GC17P050905 GC17P048765 GC17P048899 GC17P048900

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

EntrezGene summary for XYLT2:
The protein encoded by this gene is an isoform of xylosyltransferase, which belongs to a family of
glycosyltransferases. This enzyme transfers xylose from UDP-xylose to specific serine residues of
the core protein and initiates the biosynthesis of glycosaminoglycan chains in proteoglycans
including chondroitin sulfate, heparan sulfate, heparin and dermatan sulfate. The enzyme activity,
which is increased in scleroderma patients, is a diagnostic marker for the determination of
sclerotic activity in systemic sclerosis. [provided by RefSeq]

UniProtKB/Swiss-Prot: XYLT2_HUMAN, Q9H1B5
Function: Probably catalyzes the first step in biosynthesis of glycosaminoglycan. Transfers
D-xylose from UDP-D-xylose to specific serine residues of the core protein. Initial enzyme in the
biosynthesis of chondroitin sulfate and dermatan sulfate proteoglycans in fibroblasts and
chondrocytes (By similarity). Its enzyme activity has not been demonstrated

Gene Wiki entry for XYLT2

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the XYLT2 gene  

Entrez Gene cytogenetic band: 17q21.3-q22   Ensembl cytogenetic band:  17q21.33   HGNC cytogenetic band: 17q21.33

XYLT2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17P045778:     (about GC identifiers)

Start:
45,778,392 bp from pter
End:
45,793,511 bp from pter
Size:
15,120 bases
Orientation:
plus strand
RefSeq DNA sequence:
NC_000017.9  NT_010783.14  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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UniProtKB/Swiss-Prot: XYLT2_HUMAN, Q9H1B5 (See protein sequence)
Recommended Name: Xylosyltransferase 2  
Size: 865 amino acids; 96767 Da
Cofactor: Divalent cations (By similarity)
Subunit: Monomer (By similarity)
Subcellular location: Endoplasmic reticulum membrane; Single-pass type II membrane protein (By
similarity). Golgi apparatus membrane; Single-pass type II membrane protein (By similarity)
Secondary accessions: Q6UY41 Q86V00
Alternative splicing: 2 isoforms:  Q9H1B5-1   Q9H1B5-2   

Post-translational modifications:

  • Contains disulfide bonds (By similarity)1


  • REFSEQ proteins: NP_071450.2  

    ENSEMBL proteins: 
    ENSP00000017003 ENSP00000365733 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
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    Recombinant Proteins from Abcam (XYLT2)
    Browse Abnova for Human Recombinant Proteins
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

    5/7 Gene Ontology (GO) cellular component terms (links to tree view) (see all 7 ):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000139 Golgi membrane IEA--
    GO:0005575 cellular_component ND--
    GO:0005783 endoplasmic reticulum IEA--
    GO:0005789 endoplasmic reticulum membrane IEA--
    GO:0005794 Golgi apparatus IEA--
    About this table

    Antibodies for XYLT2: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Sigma-Aldrich Antibodies for XYLT2
    Browse R&D Systems for Antibodies
    Antibodies from Abcam (XYLT2), each with their AbpromiseSM
    Browse Abnova for Monoclonal and Polyclonal Antibodies
    Search Novus for antibodies for XYLT2

    Assays for XYLT2: 
    Browse Invitrogen for biochemical assays
    Browse Kits and Assays available from Millipore
    Browse R&D Systems for biochemical assays
    Browse biochemical assays available from Enzo Life Sciences

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    1 InterPro domain/family:
     IPR003406 Glyco_trans_14


       GeneDecks  XYLT2 for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry Q9H1B5

    ProtoNet protein and cluster: Q9H1B5

    UniProtKB/Swiss-Prot: XYLT2_HUMAN, Q9H1B5
    Similarity: Belongs to the glycosyltransferase 14 family. XylT subfamily

    (According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
    RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (XYLT2)
    Browse for Gene Knock-down Tools from Millipore
    Browse Abnova for Chimera RNAi Products
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_022167

                  Applied Biosystems Silencer® siRNAs for XYLT2

                  Sigma-Aldrich siRNA for XYLT2  
                         Sigma-Aldrich shRNA for XYLT2  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Browse Clone Ranger at Invitrogen for clones
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_022167
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_022167
                                     untagged cDNA clone in CMV expression vector: NM_022167 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_022167

    UniProtKB/Swiss-Prot: XYLT2_HUMAN, Q9H1B5
    Function: Probably catalyzes the first step in biosynthesis of glycosaminoglycan. Transfers
    D-xylose from UDP-D-xylose to specific serine residues of the core protein. Initial enzyme in the
    biosynthesis of chondroitin sulfate and dermatan sulfate proteoglycans in fibroblasts and
    chondrocytes (By similarity). Its enzyme activity has not been demonstrated
    Catalytic activity: Transfers a beta-D-xylosyl residue from UDP-D-xylose to the serine hydroxy
    group of an acceptor protein substrate
    Enzyme Number (IUBMB): EC 2.4.2.26 

    3 MGI mutant phenotypes (inferred from 1 allele(MGI details for Xylt2):

    homeostasis/metabolismliver/biliary systemrenal/urinary system

    3 Gene Ontology (GO) molecular function terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008375 acetylglucosaminyltransferase activity IEA--
    GO:0016757 transferase activity, transferring glycosyl groups IEA--
    GO:0030158 protein xylosyltransferase activity NAS11099377
    About this table

    (Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
    Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section


    1 Sigma-Aldrich "Your Favorite Gene" Pathway for  XYLT2  (Your Favorite Gene powered by Ingenuity) 
     Chondroitin Sulfate Biosynthesis

       GeneDecks  XYLT2 for the pathways selected above  
    About GeneDecksing

    2 Kegg Pathways  (Kegg details for XYLT2):
     hsa00532 Chondroitin sulfate biosynthesis
     hsa00534 Heparan sulfate biosynthesis

       GeneDecks  XYLT2 for the pathways selected above  
    About GeneDecksing
    UniProtKB/Swiss-Prot: XYLT2_HUMAN, Q9H1B5
    Pathway: Glycan metabolism; chondroitin sulfate biosynthesis
    Pathway: Glycan metabolism; heparan sulfate biosynthesis


    5 Interacting proteins for XYLT2 (ENSP000000170033) via UniProtKB, MINT, and/or STRING

    InteractantInteraction Details
    GeneCardExternal ID(s)
    B4GALT7ENSP000000294103STRING (score=.899)
    XYLT1ENSP000002613813STRING (score=.809)
    EXTL2ENSP000003591323STRING (score=.72)
    SLC6A20ENSP000003462983STRING (score=.72)
    SLC6A18ENSP000003235493STRING (score=.702)
    About this table

    1 Gene Ontology (GO) biological process term (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006024 glycosaminoglycan biosynthetic process NAS11099377
    About this table
    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    Browse drugs & compounds from Enzo Life Sciences
    Browse Small Molecules at Sigma-Aldrich

    Browse Tocris compounds for XYLT2
    6 Novoseek chemical compound relationships for XYLT2 gene
    Compound   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    glycosaminoglycan 78.06 5 18023272 (1), 17517600 (1), 17635914 (1)
    xylose 76.59 3 17189265 (1), 18789912 (1)
    tetrasaccharide 63.69 1 17189265 (1)
    chondroitin 61.32 2 17189266 (2)
    heparan sulfate 60.74 5 17189265 (2), 17189266 (2)
    chondroitin sulfate 46.97 4 17189265 (3)
    About this table


    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Invitrogen, Millipore, and/or Abnova,
    siRNAs from Applied Biosystems, Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene,
    Tagged/untagged cDNA clones from OriGene,
    Expression Assays from Applied Biosystems)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (XYLT2)
    Browse for Gene Knock-down Tools from Millipore
    Browse Abnova for Chimera RNAi Products
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_022167

                  Sigma-Aldrich siRNA for XYLT2  
                         Sigma-Aldrich shRNA for XYLT2  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_022167  

    REFSEQ mRNAs for XYLT2 gene: 

    NM_022167.2   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_022167  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_022167
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_022167
                                     untagged cDNA clone in CMV expression vector: NM_022167 

    Additional cDNA sequence: 

    AJ277442.1 AK299999.1 AL833210.1 AY358090.1 BC017084.2 BC036069.1 BC052262.1 

    6 DOTS entries:

    DT.456072  DT.102836161  DT.91729963  DT.95200429  DT.102836162  DT.102836163 

    24/130 AceView cDNA sequences (see all 130 ):

    BM461889 AA973869 BQ676498 CD515125 BQ877897 AI184929 AI967940 BQ681038 
    AI951943 BQ681871 BE550491 AI828310 BQ684294 AI874337 AI917812 BE673073 
    AY358090 AI801383 BF062232 AW593999 AI631553 AW593411 AA306503 BE503675 

    highest scoring ESTs for XYLT2:

    AA043495 AA149258 AA149273 AA338943 AA401674 AA412019 AA720916 AA973869 AI004612 AI128000 

    Unigene Cluster for XYLT2:

    Xylosyltransferase II
    Hs.463416  [show with all ESTs]
    Unigene Representative Sequence: AJ277442


    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for XYLT2

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10a · 10b ^ 11
    SP1:                                                                                    
    SP2:                                                        -     -                     
    SP3:                                                        -                           

    About this scheme

    ECgene alternative splicing isoforms for XYLT2

    2 Ensembl transcripts including schematic representations:
    ENST00000017003  ENST00000376550  
    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Expression Assays from Applied Biosystems )
    About This Section

    XYLT2 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for XYLT2

    1 / 2 / 3

    4 probe-sets matching XYLT2 gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

    44675_at2, 3 U95-B 2 1.00 0.97 1.00 1.00 AA043495 1.00 1.00 1.00 1

    219401_at2, 3 U133-A 1 1.00 1.00 -- -- NM_022167 0.60 1.00 0.82 1

    1570528_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

    219401_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
    About this table
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: AGCAGCGTGG

    SOURCE GeneReport for Unigene cluster: Hs.463416

    UniProtKB/Swiss-Prot: XYLT2_HUMAN, Q9H1B5
    Tissue specificity: Widely expressed. Expressed at higher level in kidney and pancreas

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section


    Orthologs for XYLT2 gene from 5/9 species (see all 9 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    XYLT21   -- xylosyltransferase II 92.45(n)
    95.26(a)
    493990  NM_001008714.1  NP_001008714.1 
    chimpanzee
    (Pan troglodytes)
    XYLT21   -- xylosyltransferase II 99.61(n)
    99.54(a)
    455118  NM_001009086.1  NP_001009086.1 
    cow
    (Bos taurus)
    XYLT21   -- xylosyltransferase II 88.19(n)
    88.19(a)
    493989  NM_001008667.1  NP_001008667.1 
    rat
    (Rattus norvegicus)
    Xylt21   -- xylosyltransferase II 89.54(n)
    93.63(a)
    64134  NM_022296.2  NP_071632.2 
    mouse
    (Mus musculus)
    Xylt21, 5 115
    xylosyltransferase II1, 5 89.37(n)1
    92.66(a)1
    2171191  NM_145828.21  NP_665827.11 
     AJ2917515  AK0834825  (see all 13)
    About this table        Species with no ortholog for XYLT2

    ENSEMBL Gene Tree for XYLT2
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

    Paralogs for XYLT2 gene
    XYLT12  

    (According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
    About This Section


    10/116 NCBI SNPs in XYLT2 are shown (see all 116 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 59)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 17 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs65046491,2
    A,C,F,H45792455(+) GCACAC/GACAGC 1 T/R mis1 ese316Minor allele frequency- G:0.19EA NA EU WA 1394
    rs25265371,2
    A,C,F,H45793054(-) AAGCCA/CCTGCT 1 -- ut31 ese38Minor allele frequency- C:0.27MN NA EU EA WA 702
    rs110799131,2
    A,C,F45777058(+) AAAGCG/ACAGAA 1 -- ng512Minor allele frequency- A:0.04EA 180
    --
    rs110799111,2
    A,C45776566(+) gggagG/Tcagag 1 -- ng510--------
    --
    rs110799121,2
    A,C45776634(+) cgtctC/Taaaaa 1 -- ng510--------
    rs98987771,2
    F,H45792967(+) GAAAAT/CGGGTG 1 -- ut314Minor allele frequency- C:0.02EU EA WA 418
    rs124512991,2
    A,C45787323(+) CCTGAC/GGATGT 1 R/T mis1 ese30--------
    --
    rs47941371,2
    A45792934(+) tctttC/Tttttt 1 -- ut310--------
    rs47941361,2
    A,C,F,H45788957(+) CTGTAT/CGGCAG 1 Y/Y syn1 ese36Minor allele frequency- C:0.24EU EA WA 600
    rs7399901,2
    F,O45786031(-) GAACCC/TTCGCC 1 E/E syn11Minor allele frequency- T:0.30MN 184
    About this table

    HapMap Linkage Disequilibrium images for XYLT2 (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

    OMIM: 608125   disorders: 264800  

    2 Novoseek disease relationships for XYLT2 gene

    Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
    diabetic nephropathies 47.00 5 17003309 (2), 18789912 (1), 16164625 (1)
    renal disease 24.07 4 18789912 (1), 16164625 (1), 17517600 (1)
    About this table

    Human Gene Mutation Database: XYLT2
    Genetic Association Database: XYLT2
    Human Genome Epidemiology Navigator: XYLT2 (5 documents)

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

    (in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
    About This Section

    10/27 PubMed articles for XYLT2 gene (see all 27 ):
    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section

     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)
    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
    About This Section

    Entrez Gene: 64132 HGNC: 15517 AceView: XYLT2 Ensembl:ENSG00000015532 euGenes: HUgn64132
    ECgene: XYLT2 H-InvDB: XYLT2
    (According to HUGE)
    About This Section

      --
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

    NameDescription
    ATLAS Chromosomes in Cancer entry for XYLT2 Genetics and Cytogenetics in Oncology and Haematology
    GGDBhttp://riodb.ibase.aist.go.jp/rcmg/ggdb/Homolog?cat=symbol&symbol=XYLT2
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for XYLT2:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



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     Predesigned and custom siRNAs for XYLT2 Antibodies for XYLT2
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