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XXYLT1 xyloside xylosyltransferase 1 [ Homo sapiens (human) ]

Gene ID: 152002, updated on 11-Apr-2024

Summary

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Official Symbol
XXYLT1provided by HGNC
Official Full Name
xyloside xylosyltransferase 1provided by HGNC
Primary source
HGNC:HGNC:26639
See related
Ensembl:ENSG00000173950 MIM:614552; AllianceGenome:HGNC:26639
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
C3orf21
Summary
Enables magnesium ion binding activity; manganese ion binding activity; and xylosyl alpha-1,3-xylosyltransferase activity. Involved in O-glycan processing. Is integral component of endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in placenta (RPKM 1.4), esophagus (RPKM 1.2) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
3q29
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (195068284..195271159, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (197765933..197969040, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (194789013..194991888, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374294 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:194707036-194707536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:194708829-194709329 Neighboring gene uncharacterized LOC105374295 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194751125-194752122 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194752123-194753121 Neighboring gene Sharpr-MPRA regulatory region 6289 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:194781985-194782758 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:194789061-194790260 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:194793833-194794333 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:194799753-194800269 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21037 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_67503 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21038 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21039 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21040 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:194815702-194816901 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:194823367-194824566 Neighboring gene uncharacterized LOC124909476 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15030 Neighboring gene XXYLT1 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:194838030-194838572 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194838573-194839113 Neighboring gene Sharpr-MPRA regulatory region 14086 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194846542-194847072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21042 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21043 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21044 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21045 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21046 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:194859771-194860272 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:194860273-194860772 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21048 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21047 Neighboring gene uncharacterized LOC105374296 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21049 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194873291-194873932 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194873933-194874573 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21050 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:194880491-194880991 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194881004-194881518 Neighboring gene XXYLT1 antisense RNA 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21051 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21052 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:194884078-194884245 Neighboring gene microRNA 3137 Neighboring gene RNA, 7SL, cytoplasmic 36, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194900787-194901364 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194901365-194901942 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:194904967-194906166 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194908389-194908904 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194927427-194927954 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194927955-194928480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:194932550-194933131 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194947105-194947699 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:194960771-194961333 Neighboring gene RNA, U6 small nuclear 25, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15031 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21053 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:194974283-194975070 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:194976828-194977002 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15032 Neighboring gene uncharacterized LOC124909475 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:194991127-194991918 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15035 Neighboring gene ArfGAP with coiled-coil, ankyrin repeat and PH domains 2 Neighboring gene ribosomal protein L31 pseudogene 22 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21054 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:195154512-195155012 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21055 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15036 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:195163293-195163792 Neighboring gene uncharacterized LOC124906341

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. XXYLT1 methylation contributes to the occurrence of lung adenocarcinoma: Methylation and lung adenocarcinoma. Zeng H, et al. Medicine (Baltimore), 2021 Jan 8. PMID 33429795, Free PMC Article
  2. C3orf21 ablation promotes the proliferation of lung adenocarcinoma, and its mutation at the rs2131877 locus may serve as a susceptibility marker. Yang L, et al. Oncotarget, 2017 May 16. PMID 28422717, Free PMC Article
  3. A genome-wide association study reveals susceptibility variants for non-small cell lung cancer in the Korean population. Yoon KA, et al. Hum Mol Genet, 2010 Dec 15. PMID 20876614
  4. Detection of UDP-D-xylose: alpha-D-xyloside alpha 1-->3xylosyltransferase activity in human hepatoma cell line HepG2. Minamida S, et al. J Biochem, 1996 Nov. PMID 8982869
  5. Molecular cloning of a xylosyltransferase that transfers the second xylose to O-glucosylated epidermal growth factor repeats of notch. Sethi MK, et al. J Biol Chem, 2012 Jan 20. PMID 22117070, Free PMC Article

See all (33) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. XXYLT1 methylation contributes to the occurrence of lung adenocarcinoma: Methylation and lung adenocarcinoma.
    Title: XXYLT1 methylation contributes to the occurrence of lung adenocarcinoma: Methylation and lung adenocarcinoma.
  2. our study concluded that C30rf21 rs 2131877 T/C+C/C genotype patients may experience increased nicotine addiction and that C30rf21 can likely serve as a susceptibility marker for lung adenocarcinoma with a higher degree of malignancy.
    Title: C3orf21 ablation promotes the proliferation of lung adenocarcinoma, and its mutation at the rs2131877 locus may serve as a susceptibility marker.
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
A genome-wide association study reveals susceptibility variants for non-small cell lung cancer in the Korean population.
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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ35155

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables UDP-xylosyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables magnesium ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables manganese ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables xylosyl alpha-1,3-xylosyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables xylosyl alpha-1,3-xylosyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in O-glycan processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in O-glycan processing IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in endoplasmic reticulum membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
xyloside xylosyltransferase 1
Names
UDP-xylose:alpha-xyloside alpha-1,3-xylosyltransferase
NP_001294998.1
NP_001397783.1
NP_689744.3
XP_005269343.1
XP_016861238.1
XP_047303453.1
XP_054201330.1
XP_054201331.1
XP_054201332.1

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_001308069.2 → NP_001294998.1  xyloside xylosyltransferase 1 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate 5' exon, contains an alternate 5' terminal exon, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a shorter and distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AC106705, AI952430, BG721419
    Consensus CDS
    CCDS77874.1
    UniProtKB/TrEMBL
    A0A140T9D0
    Related
    ENSP00000399422.1, ENST00000429994.5
    Conserved Domains (1) summary
    cl11394
    Location:18 → 237
    Glyco_tranf_GTA_type; Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold

  2. NM_001410854.1 → NP_001397783.1  xyloside xylosyltransferase 1 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC090018, AC106705
    Consensus CDS
    CCDS93439.1
    Related
    ENSP00000409865.1, ENST00000437101.5

  3. NM_152531.5 → NP_689744.3  xyloside xylosyltransferase 1 isoform 1

    See identical proteins and their annotated locations for NP_689744.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC106705, AK075551, BC039067, DA575404
    Consensus CDS
    CCDS43188.1
    UniProtKB/Swiss-Prot
    D3DNW5, Q8NAL3, Q8NBI6, Q8WV03, Q96ME0
    Related
    ENSP00000309640.6, ENST00000310380.11
    Conserved Domains (2) summary
    COG1442
    Location:162 → 353
    RfaJ; Lipopolysaccharide biosynthesis protein, LPS:glycosyltransferase [Cell wall/membrane/envelope biogenesis]
    cl11394
    Location:120 → 383
    Glyco_tranf_GTA_type; Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    195068284..195271159 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005269286.6 → XP_005269343.1  xyloside xylosyltransferase 1 isoform X2

    See identical proteins and their annotated locations for XP_005269343.1

    Conserved Domains (1) summary
    cl11394
    Location:11 → 196
    Glyco_tranf_GTA_type; Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold

  2. XM_047447497.1 → XP_047303453.1  xyloside xylosyltransferase 1 isoform X3

  3. XM_017005749.3 → XP_016861238.1  xyloside xylosyltransferase 1 isoform X1

RNA

  1. XR_924105.4 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    197765933..197969040 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054345356.1 → XP_054201331.1  xyloside xylosyltransferase 1 isoform X2

  2. XM_054345357.1 → XP_054201332.1  xyloside xylosyltransferase 1 isoform X3

  3. XM_054345355.1 → XP_054201330.1  xyloside xylosyltransferase 1 isoform X1

RNA

  1. XR_008486664.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NBI6.1 GenPept UniProtKB/Swiss-Prot:Q8NBI6

Gene LinkOut

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