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TNXB tenascin XB [ Homo sapiens (human) ]

Gene ID: 7148, updated on 4-Feb-2018
Official Symbol
TNXBprovided by HGNC
Official Full Name
tenascin XBprovided by HGNC
Primary source
HGNC:HGNC:11976
See related
Ensembl:ENSG00000168477 MIM:600985; Vega:OTTHUMG00000031088
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
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
Location:
6p21.33-p21.32
Exon count:
44
Annotation release Status Assembly Chr Location
108 current GRCh38.p7 (GCF_000001405.33) 6 NC_000006.12 (32041155..32109374, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (32008932..32077151, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene serine/threonine kinase 19B (pseudogene) Neighboring gene complement C4B (Chido blood group) Neighboring gene cytochrome P450 family 21 subfamily A member 2 Neighboring gene RNA, 5S ribosomal pseudogene 206 Neighboring gene activating transcription factor 6 beta Neighboring gene FK506 binding protein like

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Ehlers-Danlos-like syndrome due to tenascin-X deficiency
MedGen: C1848029 OMIM: 606408 GeneReviews: Not available
Compare labs
Vesicoureteral reflux 8
MedGen: C4014831 OMIM: 615963 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
A genome-wide association study of atopic dermatitis identifies loci with overlapping effects on asthma and psoriasis.
NHGRI GWA Catalog
Common genetic variation and the control of HIV-1 in humans.
NHGRI GWA Catalog
Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production.
NHGRI GWA Catalog
Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium.
NHGRI GWA Catalog
Genome-wide association study for serum complement C3 and C4 levels in healthy Chinese subjects.
NHGRI GWA Catalog
Genome-wide association study in Chinese identifies novel loci for blood pressure and hypertension.
NHGRI GWA Catalog
Genome-wide association study of age-related macular degeneration identifies associated variants in the TNXB-FKBPL-NOTCH4 region of chromosome 6p21.3.
NHGRI GWA Catalog
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
NHGRI GWA Catalog
Many sequence variants affecting diversity of adult human height.
NHGRI GWA Catalog
Sequence variants affecting eosinophil numbers associate with asthma and myocardial infarction.
NHGRI GWA Catalog
  • ECM proteoglycans, organism-specific biosystem (from REACTOME)
    ECM proteoglycans, organism-specific biosystemProteoglycans are major components of the extracellular matrix. In cartilage the matrix constitutes more than 90% of tissue dry weight. Proteoglycans are proteins substituted with glycosaminoglycans ...
  • ECM-receptor interaction, organism-specific biosystem (from KEGG)
    ECM-receptor interaction, organism-specific biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
  • ECM-receptor interaction, conserved biosystem (from KEGG)
    ECM-receptor interaction, conserved biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
  • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
    Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...
  • Focal Adhesion, organism-specific biosystem (from WikiPathways)
    Focal Adhesion, organism-specific biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
  • Focal adhesion, organism-specific biosystem (from KEGG)
    Focal adhesion, organism-specific biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
  • Focal adhesion, conserved biosystem (from KEGG)
    Focal adhesion, conserved biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
  • MicroRNAs in cancer, organism-specific biosystem (from KEGG)
    MicroRNAs in cancer, organism-specific biosystemMicroRNA (miRNA) is a cluster of small non-encoding RNA molecules of 21 - 23 nucleotides in length, which controls gene expression post-transcriptionally either via the degradation of target mRNAs or...
  • MicroRNAs in cancer, conserved biosystem (from KEGG)
    MicroRNAs in cancer, conserved biosystemMicroRNA (miRNA) is a cluster of small non-encoding RNA molecules of 21 - 23 nucleotides in length, which controls gene expression post-transcriptionally either via the degradation of target mRNAs or...
  • PI3K-Akt signaling pathway, organism-specific biosystem (from KEGG)
    PI3K-Akt signaling pathway, organism-specific biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
  • PI3K-Akt signaling pathway, conserved biosystem (from KEGG)
    PI3K-Akt signaling pathway, conserved biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
  • miRNA targets in ECM and membrane receptors, organism-specific biosystem (from WikiPathways)
    miRNA targets in ECM and membrane receptors, organism-specific biosystemBased on the KEGG ECM-receptor interactions pathway (hsa04512), a depiction a plausible mechanism, where miRNAs regulate components of both extracellular matrix (top panel) and transmembrane receptor...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
heparin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
integrin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
actin cytoskeleton organization ISS
Inferred from Sequence or Structural Similarity
more info
 
cell adhesion ISS
Inferred from Sequence or Structural Similarity
more info
 
collagen fibril organization IEA
Inferred from Electronic Annotation
more info
 
collagen metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
elastic fiber assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
extracellular exosome HDA PubMed 
extracellular matrix IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with extracellular matrix IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with extracellular matrix ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
extracellular region IDA
Inferred from Direct Assay
more info
PubMed 
extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with fibrillar collagen trimer IDA
Inferred from Direct Assay
more info
PubMed 
intracellular IDA
Inferred from Direct Assay
more info
PubMed 
proteinaceous extracellular matrix NAS
Non-traceable Author Statement
more info
PubMed 
Preferred Names
tenascin-X
Names
growth-inhibiting protein 45
hexabrachion-like protein
tenascin XB1
tenascin XB2

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_008337.2 RefSeqGene

    Range
    5001..73220
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_019105.6NP_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) represents the longer transcript and encodes the full length protein (isoform 1). 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)
    AB209012, AK310080, AL044866, AL645922, AL662884, AL772248, BC033740, BI010479, BP233293, BP420628, BQ446909, U52699, Y17865, Y17866, Y17867
    UniProtKB/Swiss-Prot
    P22105
    UniProtKB/TrEMBL
    O95680, O95681, Q9Y464
    Related
    ENSP00000364393.3, OTTHUMP00000174881, ENST00000375244.7, OTTHUMT00000268927
    Conserved Domains (4) summary
    cd00063
    Location:11561238
    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:37573834
    fn3; Fibronectin type III domain
    pfam00147
    Location:40244233
    Fibrinogen_C; Fibrinogen beta and gamma chains, C-terminal globular domain
    pfam07974
    Location:621647
    EGF_2; EGF-like domain
  2. NM_032470.3NP_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 XB at the 5' end. It encodes isoform 2 which is identical to the C-terminus of the full-length protein, isoform 1.
    Source sequence(s)
    AL645922, BC071883, BC130037, BQ446909, U24488
    Consensus CDS
    CCDS4736.1
    UniProtKB/Swiss-Prot
    P22105
    UniProtKB/TrEMBL
    Q6IPK3
    Related
    ENSP00000407685.1, OTTHUMP00000216549, ENST00000451343.4, OTTHUMT00000268932
    Conserved Domains (3) summary
    cd00063
    Location:274360
    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:188265
    fn3; Fibronectin type III domain
    pfam00147
    Location:455664
    Fibrinogen_C; Fibrinogen beta and gamma chains, C-terminal globular domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p7 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p7 Primary Assembly

    Range
    32041155..32109374 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p7 ALT_REF_LOCI_1

Genomic

  1. NT_167244.2 Reference GRCh38.p7 ALT_REF_LOCI_1

    Range
    3406268..3418727 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p7 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p7 ALT_REF_LOCI_2

    Range
    3479477..3547707 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p7 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p7 ALT_REF_LOCI_3

    Range
    3282563..3350740 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p7 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p7 ALT_REF_LOCI_4

    Range
    3369799..3403209 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p7 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p7 ALT_REF_LOCI_5

    Range
    3383188..3451394 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p7 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p7 ALT_REF_LOCI_6

    Range
    3264390..3309331 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p7 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p7 ALT_REF_LOCI_7

    Range
    3342342..3369633 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018917.2 Alternate CHM1_1.1

    Range
    32011143..32079361 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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