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XXYLT1 Gene

protein-coding   GIFtS: 40
GCID: GC03M194790

Xyloside Xylosyltransferase 1

(Previous name: chromosome 3 open reading frame 21)
(Previous symbol: C3orf21)
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Xyloside Xylosyltransferase 11 2
C3orf211 2 3 5
UDP-Xylose:Alpha-Xyloside Alpha-1,3-Xylosyltransferase2 3
Chromosome 3 Open Reading Frame 211
EC 2.4.2.n33

External Ids:    HGNC: 266391   Entrez Gene: 1520022   Ensembl: ENSG000001739507   OMIM: 6145525   UniProtKB: Q8NBI63   

Export aliases for XXYLT1 gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for XXYLT1 Gene:
XXYLT1 (xyloside xylosyltransferase 1) is a protein-coding gene. GO annotations related to this gene include transferase activity, transferring pentosyl groups. An important paralog of this gene is LARGE.

UniProtKB/Swiss-Prot: XXLT1_HUMAN, Q8NBI6
Function: Alpha-1,3-xylosyltransferase, which elongates the O-linked xylose-glucose disaccharide attached to
EGF-like repeats in the extracellular domain of Notch proteins by catalyzing the addition of the second xylose




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000003.11  NT_005612.17  NC_018914.2  
Regulatory elements:
   Search for regulatory transcription factor binding sites for XXYLT1
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidXXYLT1 promoter sequence
   Search Chromatin IP Primers for XXYLT1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat XXYLT1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 3q29   Ensembl cytogenetic band:  3q29   HGNC cytogenetic band: 3q29

XXYLT1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
XXYLT1 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03M194790:  view genomic region     (about GC identifiers)

Start:
194,789,008 bp from pter      End:
194,991,896 bp from pter
Size:
202,889 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: XXLT1_HUMAN, Q8NBI6 (See protein sequence)
Recommended Name: Xyloside xylosyltransferase 1  
Size: 393 amino acids; 43807 Da
Subunit: Monomer. Homodimer. Dimer formation may be essential for the retention in endoplasmic reticulum
Caution: It is uncertain whether Met-1 or Met-14 is the initiator
Sequence caution: Sequence=AAH19036.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Secondary accessions: D3DNW5 Q8NAL3 Q8WV03 Q96ME0
Alternative splicing: 3 isoforms:  Q8NBI6-1   Q8NBI6-2   Q8NBI6-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for XXYLT1: NX_Q8NBI6

Explore proteomics data for XXYLT1 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys321
  • Glycosylation2 at Ser67, Ser77
  • Modification sites at PhosphoSitePlus

  • See XXYLT1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_689744.3  
    ENSEMBL proteins: 
     ENSP00000309640   ENSP00000409865   ENSP00000399422   ENSP00000349179   ENSP00000393989  
     ENSP00000405583   ENSP00000347967  

    XXYLT1 Human Recombinant Protein Products:

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    Browse Proteins at Cloud-Clone Corp.

     
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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    GLT8: Glycosyltransferase family 8 domain containing

    1 InterPro protein domain:
     IPR002495 Glyco_trans_8

    Graphical View of Domain Structure for InterPro Entry Q8NBI6

    ProtoNet protein and cluster: Q8NBI6

    1 Blocks protein domain: IPB002495 Glycosyl transferase

    UniProtKB/Swiss-Prot: XXLT1_HUMAN, Q8NBI6
    Similarity: Belongs to the glycosyltransferase 8 family


    Find genes that share domains with XXYLT1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: XXLT1_HUMAN, Q8NBI6
    Function: Alpha-1,3-xylosyltransferase, which elongates the O-linked xylose-glucose disaccharide attached to
    EGF-like repeats in the extracellular domain of Notch proteins by catalyzing the addition of the second xylose
    Catalytic activity: UDP-D-xylose + alpha-D-xylose-(1->3)-beta-D-glucosyl-R = UDP +
    alpha-D-xylose-(1->3)-alpha-D-xylose-(1->3)-beta-D-glucosyl-R

         Enzyme Number (IUBMB): EC 2.4.2.n31

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016757transferase activity, transferring glycosyl groups ----
    GO:0016763transferase activity, transferring pentosyl groups IEA--
         
    Find genes that share ontologies with XXYLT1           About GenesLikeMe


    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for XXYLT1
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    XXLT1_HUMAN, Q8NBI6: Endoplasmic reticulum membrane; Single-pass type II membrane protein

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005789endoplasmic reticulum membrane IEA--
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with XXYLT1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for XXYLT1
    Interactions:

        Search GeneGlobe Interaction Network for XXYLT1

    STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

    4 Interacting proteins for XXYLT1 (ENSP000003096404) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ENSG00000225553ENSP000003919014STRING: ENSP00000391901
    GCSAMENSP000003094874STRING: ENSP00000309487
    ELAVL1ENSP000003852694STRING: ENSP00000385269
    --ENSP000004033774STRING: ENSP00000403377
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for XXYLT1 (XXLT1)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for XXYLT1 gene: 
    NM_152531.4  

    Unigene Cluster for XXYLT1:

    Xyloside xylosyltransferase 1
    Hs.478741  [show with all ESTs]
    Unigene Representative Sequence: AK024181
    13 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000310380(uc003fuk.3 uc003fum.4) ENST00000437101(uc003ful.3)
    ENST00000460582 ENST00000473200 ENST00000429994(uc011bsw.1) ENST00000356740
    ENST00000418940 ENST00000491138 ENST00000496644 ENST00000476897 ENST00000494175
    ENST00000455281 ENST00000355729
    miRNA
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    SwitchGear 3'UTR luciferase reporter plasmidXXYLT1 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat XXYLT1
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    Primer
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    OriGene qPCR primer pairs and template standards for XXYLT1
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      QuantiTect SYBR Green Assays in human, mouse, rat XXYLT1
      QuantiFast Probe-based Assays in human, mouse, rat XXYLT1

    Additional mRNA sequence: 

    AK024181.1 AK057046.1 AK092474.1 

    6 DOTS entries:

    DT.97841771  DT.91741423  DT.40229786  DT.91722176  DT.91741418  DT.97773649 

    Selected AceView cDNA sequences (see all 116):

    BE515127 AI863661 BG753678 AI225062 AI459991 BE794557 BQ669651 BI915160 
    BG752631 BX385479 AK092474 AA340323 BU184281 BE220593 CR614018 AI298918 
    AI459077 AA338587 CR626411 BQ440035 CR591622 AI954532 AU122209 AX747562 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for XXYLT1 (see all 7)    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b · 13c · 13d · 13e
    SP1:                                            -     -     -     -     -                                 
    SP2:              -     -     -     -           -     -     -     -     -                                 
    SP3:                                                                                                      
    SP4:                                                  -     -     -     -                                 
    SP5:                                                        -     -     -                                 


    ECgene alternative splicing isoforms for XXYLT1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    XXYLT1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AGTGAGGATA
    XXYLT1 Expression
    About this image

    XXYLT1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    XXYLT1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.478741
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for XXYLT1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for XXYLT1 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia AI4806535
    Xxylt11
    expressed sequence AI4806535
    xyloside xylosyltransferase 11
    89.46(n)1
    91.84(a)1
      16 (21.34 cM)5
    2688801  NM_198626.21  NP_941028.21 
     309556275 
    chicken
    (Gallus gallus)
    Aves XXYLT11 xyloside xylosyltransferase 1 70.55(n)
    71.04(a)
      424896  XM_422707.4  XP_422707.3 
    lizard
    (Anolis carolinensis)
    Reptilia XXYLT16
    xyloside xylosyltransferase 1
    65(a)
    1 ↔ 1
    GL343538.1(517621-521728)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.195042 Xenopus laevis transcribed sequences 81.75(n)    BX847992.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC1003346691 xyloside xylosyltransferase 1-like 64.53(n)
    62.4(a)
      100334669  XM_002663810.3  XP_002663856.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG113881 CG11388 54.43(n)
    44.41(a)
      37833  NM_138027.2  NP_611871.2 


    ENSEMBL Gene Tree for XXYLT1 (if available)
    TreeFam Gene Tree for XXYLT1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for XXYLT1 gene
    LARGE2  B3GNT12  GYLTL1B2  

    Find genes that share paralogs with XXYLT1           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for XXYLT1 (see all 4725)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs361235931,2
    C--194697604(+) CAAAC-/A/    
       AAAAA
    AAAAA
    1 -- int10--------
    rs1813218741,2
    --194788523(+) AGACAC/TAATGA 1 -- int10--------
    rs775173881,2
    C,F--194788550(+) ATAAAC/TATTAT 1 -- int11Minor allele frequency- T:0.06WA 118
    rs580907491,2
    C,F--194788638(+) TCAAGT/CAGGTG 1 -- int12Minor allele frequency- C:0.09WA EA 238
    rs557811301,2
    C,F--194788791(+) TGCCAA/GTACCT 1 -- int16Minor allele frequency- G:0.36WA CSA NA EA 364
    rs1398175731,2
    --194788816(+) CCTTGC/TTTTGA 1 -- int10--------
    rs1155104921,2
    F--194788858(+) CCCTCT/CCAGAT 1 -- int11Minor allele frequency- C:0.03WA 118
    rs796404141,2
    C,F--194788941(+) CATTGA/GGTACA 1 -- int11Minor allele frequency- G:0.06WA 118
    rs781825541,2
    C,F--194788995(+) AACAAA/CCAACA 1 -- int11Minor allele frequency- C:0.04WA 118
    rs27209301,2
    C,F,A,H--194789032(+) TTATTA/GGCTAT 1 -- ut3122Minor allele frequency- G:0.27EA NS NA WA CSA 2302

    HapMap Linkage Disequilibrium report for XXYLT1 (194789008 - 194991896 bp)

    Structural Variations
          Database of Genomic Variants (DGV) variations for XXYLT1: --
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing XXYLT1
    DNA2.0 Custom Variant and Variant Library Synthesis for XXYLT1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 614552    OMIM disorders: --


    Find genes that share disorders with XXYLT1           About GenesLikeMe


    Export disorders for XXYLT1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for XXYLT1 gene, integrated from 10 sources (see all 11):
    (articles sorted by number of sources associating them with XXYLT1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular cloning of a xylosyltransferase that transfers the second xylose to O-glucosylated epidermal growth factor repeats of Notch. (PubMed id 22117070)1, 2, 3 Sethi M.K.... Bakker H. (J. Biol. Chem. 2012)
    2. Signal sequence and keyword trap in silico for selection of full- length human cDNAs encoding secretion or membrane proteins from oligo- capped cDNA libraries. (PubMed id 16303743)1, 2 Otsuki T....Isogai T. (DNA Res. 2005)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    5. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)
    6. Global identification of modular cullin-RING ligase substrates. (PubMed id 21963094)1 Emanuele M.J....Elledge S.J. (Cell 2011)
    7. A genome-wide association study reveals susceptibility variants for non-small cell lung cancer in the Korean population. (PubMed id 20876614)1 Yoon K.A....Lee J.S. (Hum. Mol. Genet. 2010)
    8. Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. (PubMed id 21145461)1 Bennett E.J....Harper J.W. (Cell 2010)
    9. Ubiquitin-mediated proteolysis of HuR by heat shock. (PubMed id 19322201)1 Abdelmohsen K....Gorospe M. (EMBO J. 2009)
    10. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 152002 HGNC: 26639 AceView: FLJ35155 Ensembl:ENSG00000173950 euGenes: HUgn152002
    ECgene: XXYLT1 H-InvDB: XXYLT1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for XXYLT1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for XXYLT1 gene:
    Search GeneIP for patents involving XXYLT1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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