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    TNXB tenascin XB [ Homo sapiens (human) ]

    Gene ID: 7148, updated on 3-Dec-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See TNXB in Genome Data Viewer
    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_000006.12Genomic Context describing neighboring genes Neighboring gene serine/threonine kinase 19B (pseudogene) Neighboring gene complement C4B (Chido/Rodgers blood group) Neighboring gene CYP21A2 5' regulatory region Neighboring gene CYP21A2 recombination region Neighboring gene tenascin XB recombination region Neighboring gene ReSE screen-validated silencer GRCh37_chr6:32013699-32013950 Neighboring gene cytochrome P450 family 21 subfamily A member 2 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:32014364-32015563 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:32015753-32016386 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:32038327-32039327 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:32040222-32041078 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:32041114-32041614 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:32049385-32049900 Neighboring gene RNA, 5S ribosomal pseudogene 206 Neighboring gene Sharpr-MPRA regulatory region 2290 Neighboring gene activating transcription factor 6 beta Neighboring gene FKBP prolyl isomerase like

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    A genome-wide association study of atopic dermatitis identifies loci with overlapping effects on asthma and psoriasis.
    EBI GWAS Catalog
    Common genetic variation and the control of HIV-1 in humans.
    EBI GWAS Catalog
    Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production.
    EBI GWAS Catalog
    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
    Genome-wide association study for serum complement C3 and C4 levels in healthy Chinese subjects.
    EBI GWAS Catalog
    Genome-wide association study in Chinese identifies novel loci for blood pressure and hypertension.
    EBI GWAS Catalog
    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
    Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
    EBI GWAS Catalog
    Many sequence variants affecting diversity of adult human height.
    EBI GWAS Catalog
    Sequence variants affecting eosinophil numbers associate with asthma and myocardial infarction.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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
     

    General protein information

    Preferred Names
    tenascin-X
    Names
    growth-inhibiting protein 45
    hexabrachion-like protein
    tenascin XB1
    tenascin XB2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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
      5037..73222
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001365276.2NP_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: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 ...
      pfam00147
      Location:40264235
      Fibrinogen_C; Fibrinogen beta and gamma chains, C-terminal globular domain
      pfam07974
      Location:621647
      EGF_2; EGF-like domain
      pfam00041
      Location:37583836
      fn3; Fibronectin type III domain
      cl28643
      Location:254669
      VSP; Giardia variant-specific surface protein
    2. NM_001428335.1NP_001415264.1  tenascin-X isoform 4 precursor

      Status: REVIEWED

      Source sequence(s)
      AL645922, AL662884, AL772248
      UniProtKB/TrEMBL
      A0A140TA52, A0A3B3ISX9
      Related
      ENSP00000497649.1, ENST00000647633.1
    3. NM_019105.8NP_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: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
    4. NM_032470.4NP_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: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: GCF_000001405.40-RS_2024_08

    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
      32041153..32109338 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_167244.2 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      3406268..3420263 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      3479475..3547671 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
      3282561..3350704 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_4

    Genomic

    1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

      Range
      3369799..3403209 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
      3383186..3451358 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_6

    Genomic

    1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

      Range
      3264388..3310650 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
      3342340..3369633 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      31894357..31962530 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)