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TNXA tenascin XA (pseudogene) [ Homo sapiens (human) ]

Gene ID: 7146, updated on 10-Oct-2023

Summary

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Official Symbol
TNXAprovided by HGNC
Official Full Name
tenascin XA (pseudogene)provided by HGNC
Primary source
HGNC:HGNC:11975
See related
AllianceGenome:HGNC:11975
Gene type
pseudo
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
XA; TNX; HXBL; D6S103E
Summary
Predicted to be involved in collagen fibril organization. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in adrenal (RPKM 162.5), fat (RPKM 32.2) and 10 other tissues See more
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Genomic context

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Location:
6p21.33
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (32008420..32013023, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (31861626..31866229, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (31976197..31980800, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:31939702-31940412 Neighboring gene serine/threonine kinase 19 Neighboring gene decapping exoribonuclease Neighboring gene complement C4A (Chido/Rodgers blood group) Neighboring gene CYP21A1P recombination region Neighboring gene tenascin XA (pseudogene) recombination region Neighboring gene cytochrome P450 family 21 subfamily A member 1, pseudogene Neighboring gene serine/threonine kinase 19B (pseudogene) Neighboring gene complement C4B (Chido/Rodgers blood group) Neighboring gene CYP21A2 5' regulatory region

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. Sequences promoting the transcription of the human XA gene overlapping P450c21A correctly predict the presence of a novel, adrenal-specific, truncated form of tenascin-X. Tee MK, et al. Genomics, 1995 Jul 20. PMID 8530023
  2. Mechanism and consequences of the duplication of the human C4/P450c21/gene X locus. Gitelman SE, et al. Mol Cell Biol, 1992 May. PMID 1373808, Free PMC Article
  3. Genetic basis of tobacco smoking: strong association of a specific major histocompatibility complex haplotype on chromosome 6 with smoking behavior. Füst G, et al. Int Immunol, 2004 Oct. PMID 15339882
  4. Transcript encoded on the opposite strand of the human steroid 21-hydroxylase/complement component C4 gene locus. Morel Y, et al. Proc Natl Acad Sci U S A, 1989 Sep. PMID 2475872, Free PMC Article
  5. An unequal crossover between the RCCX modules of the human MHC leading to the presence of a CYP21B gene and a tenascin TNXB/TNXA-RP2 recombinant between C4A and C4B genes in a patient with juvenile rheumatoid arthritis. Rupert KL, et al. Exp Clin Immunogenet, 1999. PMID 10343159

See all (11) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic basis of tobacco smoking: strong association of a specific major histocompatibility complex haplotype on chromosome 6 with smoking behavior.
  2. molecular studies on RCCX haplotypes revealing a unique recombination giving rise to a TNXB/TNXA hybrid gene, CYP21A deletion and CYP21B duplication on one chromosome
    Title: An unequal crossover event in RCCX modules of the human MHC resulting in the formation of a TNXB/TNXA hybrid and deletion of the CYP21A.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
EBI GWAS Catalog

Variation

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See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

General gene information

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Markers

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 biological_process ND
No biological Data available
more info
  
Component Evidence Code Pubs
located_in extracellular exosome HDA PubMed 

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.

RNA

  1. NR_001284.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL645922

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    32008420..32013023 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

    Range
    3256195..3260798 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

    Range
    3350456..3355059 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

    Range
    3309609..3314212 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    31861626..31866229 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_007116.1: Suppressed sequence

    Description
    NM_007116.1: This RefSeq was permanently suppressed because it is now thought that this gene is a pseudogene.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q16473.2 GenPept UniProtKB/Swiss-Prot:Q16473

Gene LinkOut

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Chemical Information
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