TNXB tenascin XB [Homo sapiens (human)] - Gene

Summary

Official Symbol: TNXBprovided by HGNC
Official Full Name: tenascin XBprovided by HGNC
Primary source: HGNC:HGNC:11976
See related: Ensembl:ENSG00000168477 MIM:600985; AllianceGenome:HGNC:11976
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: XB; TNX; XBS; EDS3; HXBL; TENX; TN-X; VUR8; TNXB1; TNXB2; TNXBS; EDSCLL; EDSCLL1
Summary: This gene encodes a member of the tenascin family of extracellular matrix glycoproteins. The tenascins have anti-adhesive effects, as opposed to fibronectin which is adhesive. This protein is thought to function in matrix maturation during wound healing, and its deficiency has been associated with the connective tissue disorder Ehlers-Danlos syndrome. This gene localizes to the major histocompatibility complex (MHC) class III region on chromosome 6. It is one of four genes in this cluster which have been duplicated. The duplicated copy of this gene is incomplete and is a pseudogene which is transcribed but does not encode a protein. The structure of this gene is unusual in that it overlaps the CREBL1 and CYP21A2 genes at its 5' and 3' ends, respectively. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression: Broad expression in adrenal (RPKM 35.5), fat (RPKM 21.3) and 17 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p21.33-p21.32

Exon count:: 45

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (32041153..32109338, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (31894357..31962530, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (32008930..32077115, complement)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Aberrant methylation and expression of TNXB promote chondrocyte apoptosis and extracullar matrix degradation in hemophilic arthropathy via AKT signaling.
Title: Aberrant methylation and expression of TNXB promote chondrocyte apoptosis and extracullar matrix degradation in hemophilic arthropathy via AKT signaling.
Tenascins and osteopontin in biological response in cornea.
Title: Tenascins and osteopontin in biological response in cornea.
Congenital adrenal hyperplasia with a CYP21A2 deletion overlapping the tenascin-X gene: an atypical presentation.
Title: Congenital adrenal hyperplasia with a CYP21A2 deletion overlapping the tenascin-X gene: an atypical presentation.
A TNXB splice donor site variant as a cause of hypermobility type Ehlers-Danlos syndrome in patients with congenital adrenal hyperplasia.
Title: A TNXB splice donor site variant as a cause of hypermobility type Ehlers-Danlos syndrome in patients with congenital adrenal hyperplasia.
Differential DNA methylation patterns in human Schlemm's canal endothelial cells with glaucoma.
Title: Differential DNA methylation patterns in human Schlemm's canal endothelial cells with glaucoma.
TNX-deficient patients with Ehlers-Danlos syndrome have upper gastric dysfunction.
Title: A novel role for the extracellular matrix glycoprotein-Tenascin-X in gastric function.
These results suggest that fetal membranes may be a source of amniotic fluid TNX whereby protein and mRNA expression seem to be significantly impacted by inflammation independent of fetal membrane status.
Title: Tenascin-X in amniotic fluid and reproductive tissues of pregnancies complicated by infection and preterm prelabor rupture of membranes†.
Data indicate that tenascin XB protein (TNXB) mRNA expression was downregulated in esophageal squamous-cell carcinoma (ESCC) compared with adjacent normal tissues.
Title: A functional variant in TNXB promoter associates with the risk of esophageal squamous-cell carcinoma.
Loss of TNXB expression is associated with Gastrointestinal diseases.
Title: The extracellular matrix glycoprotein tenascin-X regulates peripheral sensory and motor neurones.
Data demonstrates gene expression changes in differentially methylated TNXB gene in patients with age-related macular degeneration.
Title: Whole-genome methylation profiling of the retinal pigment epithelium of individuals with age-related macular degeneration reveals differential methylation of the SKI, GTF2H4, and TNXB genes.

Submit: New GeneRIF Correction See all GeneRIFs (49)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Ehlers-Danlos syndrome due to tenascin-X deficiency MedGen: C1848029 OMIM: 606408 GeneReviews: TNXB-Related Classical-Like Ehlers-Danlos Syndrome	not available
Vesicoureteral reflux 8 MedGen: C4014831 OMIM: 615963 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
A genome-wide association study of atopic dermatitis identifies loci with overlapping effects on asthma and psoriasis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common genetic variation and the control of HIV-1 in humans. EBI GWAS Catalog EBI GWAS CatalogPubMed
Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study for serum complement C3 and C4 levels in healthy Chinese subjects. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study in Chinese identifies novel loci for blood pressure and hypertension. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of age-related macular degeneration identifies associated variants in the TNXB-FKBPL-NOTCH4 region of chromosome 6p21.3. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array. EBI GWAS Catalog EBI GWAS CatalogPubMed
Many sequence variants affecting diversity of adult human height. EBI GWAS Catalog EBI GWAS CatalogPubMed
Sequence variants affecting eosinophil numbers associate with asthma and myocardial infarction. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

CYP21A2_2362 (e-PCR)
- UniSTS:280636

MARC_2920-2921:991933729:7 (e-PCR)
- UniSTS:230979

RH11436 (e-PCR)
- UniSTS:85393

WI-7720 (e-PCR)
- UniSTS:38571

D6S2670 (e-PCR)
- UniSTS:256758

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables collagen binding	IEA Inferred from Electronic Annotation more info
enables collagen fibril binding	IDA Inferred from Direct Assay more info	PubMed
enables extracellular matrix structural constituent	ISS Inferred from Sequence or Structural Similarity more info
enables extracellular matrix structural constituent	RCA inferred from Reviewed Computational Analysis more info	PubMed
enables heparin binding	ISS Inferred from Sequence or Structural Similarity more info
enables integrin binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in actin cytoskeleton organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell adhesion	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell-cell adhesion	IEA Inferred from Electronic Annotation more info
involved_in cell-matrix adhesion	IEA Inferred from Electronic Annotation more info
involved_in collagen fibril organization	IEA Inferred from Electronic Annotation more info
involved_in collagen metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in elastic fiber assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in fatty acid metabolic process	IEA Inferred from Electronic Annotation more info
involved_in neuron projection development	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of cell fate determination	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of collagen fibril organization	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of epithelial to mesenchymal transition	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of vascular endothelial growth factor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of cell adhesion	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell differentiation	NAS Non-traceable Author Statement more info	PubMed
involved_in regulation of cell migration	ISO Inferred from Sequence Orthology more info
involved_in triglyceride metabolic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
colocalizes_with collagen-containing extracellular matrix	HDA more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
colocalizes_with collagen-containing extracellular matrix	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in collagen-containing extracellular matrix	NAS Non-traceable Author Statement more info	PubMed
located_in extracellular exosome	HDA more info	PubMed
located_in extracellular matrix	NAS Non-traceable Author Statement more info	PubMed
located_in extracellular region	HDA more info	PubMed
located_in extracellular space	HDA more info	PubMed
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
part_of tenascin complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: tenascin-X

Names: growth-inhibiting protein 45; hexabrachion-like protein; tenascin XB1; tenascin XB2

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

NG_008337.2 RefSeqGene

Range

5037..73222

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001365276.2 → NP_001352205.1 tenascin-X isoform 3 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (3). It should be noted that the exon combination of this variant lacks full-length transcript support in human; it is predicted based on a combination of partial human and homologous transcript alignments.

Source sequence(s)

AL645922, AL662884, AL772248

Consensus CDS

CCDS93886.1

UniProtKB/Swiss-Prot

P22105, P78530, P78531, Q08424, Q08AM0, Q08AM1, Q59GU7, Q5SQD3, Q5ST74, Q7L8Q4, Q8N4R1, Q9NPK9, Q9UC10, Q9UC11, Q9UC12, Q9UC13, Q9UMG7

UniProtKB/TrEMBL

A0A140TA52

Related

ENSP00000496448.1, ENST00000644971.2

Conserved Domains (5) summary

cd00063
Location:1156 → 1238

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

pfam00147
Location:4026 → 4235

Fibrinogen_C; Fibrinogen beta and gamma chains, C-terminal globular domain

pfam07974
Location:621 → 647

EGF_2; EGF-like domain

pfam00041
Location:3758 → 3836

fn3; Fibronectin type III domain

cl28643
Location:254 → 669

VSP; Giardia variant-specific surface protein
NM_001428335.1 → NP_001415264.1 tenascin-X isoform 4 precursor

Status: REVIEWED

Source sequence(s)

AL645922, AL662884, AL772248

UniProtKB/TrEMBL

A0A140TA52, A0A3B3ISX9

Related

ENSP00000497649.1, ENST00000647633.1
NM_019105.8 → NP_061978.6 tenascin-X isoform 1 precursor

See identical proteins and their annotated locations for NP_061978.6

Status: REVIEWED

Description

Transcript Variant: This variant (XB) uses an alternate in-frame splice junction compared to variant 3. The resulting isoform (1) has the same N- and C-termini but is shorter compared to isoform 3. It should be noted that the exon combination of this variant lacks full-length transcript support in human; it is predicted based on a combination of partial human and homologous transcript alignments.

Source sequence(s)

AL645922, AL662884, AL772248

UniProtKB/TrEMBL

A0A140TA52

Conserved Domains (4) summary

cd00063
Location:1156 → 1238

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

pfam00041
Location:3757 → 3834

fn3; Fibronectin type III domain

pfam00147
Location:4024 → 4233

Fibrinogen_C; Fibrinogen beta and gamma chains, C-terminal globular domain

pfam07974
Location:621 → 647

EGF_2; EGF-like domain
NM_032470.4 → NP_115859.2 tenascin-X isoform 2

See identical proteins and their annotated locations for NP_115859.2

Status: REVIEWED

Description

Transcript Variant: This variant (XB-S) is transcribed from a cryptic internal promoter sequence and is substantially shorter than variant 3 at the 5' end. It encodes isoform 2, which is identical to the C-terminus of the full-length protein, isoform 3.

Source sequence(s)

AL645922, BC071883, BC130037, BQ446909, U24488

Consensus CDS

CCDS4736.1

UniProtKB/Swiss-Prot

P22105

UniProtKB/TrEMBL

Q6IPK3

Related

ENSP00000407685.1, ENST00000451343.4

Conserved Domains (3) summary

cd00063
Location:274 → 360

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

pfam00041
Location:188 → 265

fn3; Fibronectin type III domain

pfam00147
Location:455 → 664

Fibrinogen_C; Fibrinogen beta and gamma chains, C-terminal globular domain