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XG Xg glycoprotein (Xg blood group) [ Homo sapiens (human) ]

Gene ID: 7499, updated on 11-Apr-2024

Summary

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Official Symbol
XGprovided by HGNC
Official Full Name
Xg glycoprotein (Xg blood group)provided by HGNC
Primary source
HGNC:HGNC:12806
See related
Ensembl:ENSG00000124343 MIM:300879; AllianceGenome:HGNC:12806
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
PBDX
Summary
This gene encodes the XG blood group antigen, and is located at the pseudoautosomal boundary on the short (p) arm of chromosome X. The three 5' exons reside in the pseudoautosomal region and the remaining exons within the X-specific end. A truncated copy of this gene is found on the Y chromosome at the pseudoautosomal boundary. It is transcribed, but not expected to make a Y-chromosome specific gene product. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2008]
Expression
Biased expression in skin (RPKM 8.7), fat (RPKM 4.1) and 4 other tissues See more
Orthologs
all
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Genomic context

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Location:
Xp22.33
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (2752040..2816500)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (2365029..2429443)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (2670081..2734541)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 102 Neighboring gene CD99 molecule pseudogene 1 Neighboring gene CD99 molecule (Xg blood group) Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:2699593-2700274 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2700956-2701636 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2701637-2702317 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2711950-2712538 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2717356-2718298 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2718299-2719240 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2721222-2721887 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chrX:2722445-2723644 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:2764748-2764850 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2766248-2766874 Neighboring gene glycogenin 2 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:2807746-2808337 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:2809856-2810546 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2815103-2815898 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:2815899-2816694 Neighboring gene ARSD antisense RNA 1 Neighboring gene arylsulfatase D

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. Sex-specific association of a common variant of the XG gene with autism spectrum disorders. Chang SC, et al. Am J Med Genet B Neuropsychiatr Genet, 2013 Oct. PMID 24132906
  2. [Xg gene frequencies in Tunisia]. Gandouz R, et al. Transfus Clin Biol, 2008 Sep. PMID 18789743
  3. PBDX is the XG blood group gene. Ellis NA, et al. Nat Genet, 1994 Nov. PMID 7533029
  4. Inherited chondrodysplasia punctata due to a deletion of the terminal short arm of an X chromosome. Curry CJ, et al. N Engl J Med, 1984 Oct 18. PMID 6482910
  5. X-linked ichthyosis, due to steroid sulphatase deficiency, associated with Kallmann syndrome (hypogonadotropic hypogonadism and anosmia): linkage relationships with Xg and cloned DNA sequences from the distal short arm of the X chromosome. Ballabio A, et al. Hum Genet, 1986 Mar. PMID 3007328

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The present findings identify the genetic basis of the erythroid-specific Xg(a)/CD99 blood group phenotypes and reveal the molecular background of their formation.
    Title: The molecular genetic background leading to the formation of the human erythroid-specific Xg(a)/CD99 blood groups.
  2. The pseudoautosomal boundary on Xp22.33/Yp11.31 may harbor male-specific genetic variants for autism spectrum disorders.
    Title: Sex-specific association of a common variant of the XG gene with autism spectrum disorders.
  3. Gene frequency in France is similar to that reported in predominantly white populations.
    Title: [Xg gene frequencies in Tunisia].
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

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

General gene information

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Markers

Homology

Clone Names

  • MGC118758, MGC118759, MGC118760, MGC118761

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables molecular_function ND
No biological Data available
more info
  
Process Evidence Code Pubs
involved_in T cell extravasation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in biological_process ND
No biological Data available
more info
  
involved_in homotypic cell-cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of neutrophil extravasation IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
glycoprotein Xg
Names
Xg blood group (pseudoautosomal boundary-divided on the X chromosome)

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_011627.1 RefSeqGene

    Range
    4989..69449
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_805

mRNA and Protein(s)

  1. NM_001141919.2 → NP_001135391.1  glycoprotein Xg isoform 2 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an additional in-frame coding exon compared to transcript variant 1. This results in a longer isoform (2) with a 15 aa segment not found in isoform 1.
    Source sequence(s)
    AC006209, AC138085, AF380356, AK304164, BX098030, BX379565
    Consensus CDS
    CCDS48073.1
    UniProtKB/TrEMBL
    A0A2U3U020
    Related
    ENSP00000494087.1, ENST00000644266.2

  2. NM_001141920.2 → NP_001135392.1  glycoprotein Xg isoform 3 precursor

    See identical proteins and their annotated locations for NP_001135392.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate donor splice site at one of the coding exons compared to transcript variant 1, resulting in an isoform (3) containing one additional aa compared to isoform 1.
    Source sequence(s)
    AC006209, AC138085, AF380356, AK304164, BC100767, BX098030, BX379565
    UniProtKB/TrEMBL
    A0A2U3U020

  3. NM_175569.3 → NP_780778.1  glycoprotein Xg isoform 1 precursor

    See identical proteins and their annotated locations for NP_780778.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript and encodes isoform 1.
    Source sequence(s)
    AC006209, AC138085, AF380356, AK304164, BX098030, BX379565
    Consensus CDS
    CCDS14120.1
    UniProtKB/Swiss-Prot
    E9PCH1, P55808, Q496N8, Q496N9, Q496P0, Q71BZ5
    UniProtKB/TrEMBL
    A0A2U3U020
    Related
    ENSP00000370566.5, ENST00000381174.10

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_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    2752040..2816500
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005274587.5 → XP_005274644.1  glycoprotein Xg isoform X1

  2. XM_011545575.4 → XP_011543877.1  glycoprotein Xg isoform X3

  3. XM_017029787.3 → XP_016885276.1  glycoprotein Xg isoform X2

    Related
    ENSP00000411004.3, ENST00000419513.7

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    2365029..2429443
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P55808.1 GenPept UniProtKB/Swiss-Prot:P55808

Gene LinkOut

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