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THBS4 thrombospondin 4 [ Homo sapiens (human) ]

Gene ID: 7060, updated on 21-Dec-2019

Summary

Official Symbol
THBS4provided by HGNC
Official Full Name
thrombospondin 4provided by HGNC
Primary source
HGNC:HGNC:11788
See related
Ensembl:ENSG00000113296 MIM:600715
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
TSP4; TSP-4
Summary
The protein encoded by this gene belongs to the thrombospondin protein family. Thrombospondin family members are adhesive glycoproteins that mediate cell-to-cell and cell-to-matrix interactions. This protein forms a pentamer and can bind to heparin and calcium. It is involved in local signaling in the developing and adult nervous system, and it contributes to spinal sensitization and neuropathic pain states. This gene is activated during the stromal response to invasive breast cancer. It may also play a role in inflammatory responses in Alzheimer's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]
Expression
Biased expression in fat (RPKM 161.8), heart (RPKM 56.3) and 1 other tissue See more
Orthologs

Genomic context

See THBS4 in Genome Data Viewer
Location:
5q14.1
Exon count:
27
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (79991296..80083753)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (79331170..79379111)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105379048 Neighboring gene long intergenic non-protein coding RNA 1455 Neighboring gene metaxin 3 Neighboring gene tRNA methyltransferase subunit 11-2 pseudogene 2 Neighboring gene RBX1 pseudogene 2 Neighboring gene uncharacterized LOC101929215 Neighboring gene serine incorporator 5 Neighboring gene keratin 18 pseudogene 45

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

NHGRI GWAS Catalog

Description
Genetic Variants Associated with Serum Thyroid Stimulating Hormone (TSH) Levels in European Americans and African Americans from the eMERGE Network.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IDA
Inferred from Direct Assay
more info
PubMed 
growth factor activity IEA
Inferred from Electronic Annotation
more info
 
heparin binding IDA
Inferred from Direct Assay
more info
PubMed 
integrin binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
behavioral response to pain ISS
Inferred from Sequence or Structural Similarity
more info
 
endothelial cell-cell adhesion IDA
Inferred from Direct Assay
more info
PubMed 
myoblast migration IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of angiogenesis IEP
Inferred from Expression Pattern
more info
PubMed 
positive regulation of cell division IEA
Inferred from Electronic Annotation
more info
 
positive regulation of endothelial cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of neutrophil chemotaxis IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of peptidyl-tyrosine phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
regulation of tissue remodeling ISS
Inferred from Sequence or Structural Similarity
more info
 
response to endoplasmic reticulum stress IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
response to endoplasmic reticulum stress ISS
Inferred from Sequence or Structural Similarity
more info
 
response to unfolded protein IEA
Inferred from Electronic Annotation
more info
 
signal transduction IEA
Inferred from Electronic Annotation
more info
 
tissue remodeling IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
basement membrane IDA
Inferred from Direct Assay
more info
PubMed 
collagen-containing extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen-containing extracellular matrix ISS
Inferred from Sequence or Structural Similarity
more info
 
endoplasmic reticulum ISS
Inferred from Sequence or Structural Similarity
more info
 
extracellular exosome HDA PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
sarcoplasmic reticulum ISS
Inferred from Sequence or Structural Similarity
more info
 

NCBI Reference Sequences (RefSeq)

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_047084.1 RefSeqGene

    Range
    4986..96977
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001306212.1NP_001293141.1  thrombospondin-4 isoform b

    See identical proteins and their annotated locations for NP_001293141.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains alternate 5' exon structure, and it thus differs in the 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a. Variants 2, 3 and 4 all encode isoform b.
    Source sequence(s)
    BC050456, DC310687, DC342285
    Consensus CDS
    CCDS78027.1
    UniProtKB/Swiss-Prot
    P35443
    UniProtKB/TrEMBL
    E7ES19
    Conserved Domains (8) summary
    cd00054
    Location:288322
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
    sd00001
    Location:500522
    TSP3; TSP3 repeat_short [structural motif]
    sd00002
    Location:405440
    TSP3; TSP3 repeat_long [structural motif]
    pfam00008
    Location:199229
    EGF; EGF-like domain
    pfam02412
    Location:406440
    TSP_3; Thrombospondin type 3 repeat
    pfam05735
    Location:654851
    TSP_C; Thrombospondin C-terminal region
    cd16080
    Location:128171
    TSP-4cc; Coiled coil region of thrombospondin-4 (TSP-4)
    cl22861
    Location:1101
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
  2. NM_001306213.1NP_001293142.1  thrombospondin-4 isoform b

    See identical proteins and their annotated locations for NP_001293142.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains alternate 5' exon structure, and it thus differs in the 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a. Variants 2, 3 and 4 all encode isoform b.
    Source sequence(s)
    BC050456, DC310687, DC342285, DC376500
    Consensus CDS
    CCDS78027.1
    UniProtKB/Swiss-Prot
    P35443
    UniProtKB/TrEMBL
    E7ES19
    Conserved Domains (8) summary
    cd00054
    Location:288322
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
    sd00001
    Location:500522
    TSP3; TSP3 repeat_short [structural motif]
    sd00002
    Location:405440
    TSP3; TSP3 repeat_long [structural motif]
    pfam00008
    Location:199229
    EGF; EGF-like domain
    pfam02412
    Location:406440
    TSP_3; Thrombospondin type 3 repeat
    pfam05735
    Location:654851
    TSP_C; Thrombospondin C-terminal region
    cd16080
    Location:128171
    TSP-4cc; Coiled coil region of thrombospondin-4 (TSP-4)
    cl22861
    Location:1101
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
  3. NM_001306214.1NP_001293143.1  thrombospondin-4 isoform b

    See identical proteins and their annotated locations for NP_001293143.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains an alternate 5' terminal exon, and it thus differs in the 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a. Variants 2, 3 and 4 all encode isoform b.
    Source sequence(s)
    AK302842, BC050456
    Consensus CDS
    CCDS78027.1
    UniProtKB/Swiss-Prot
    P35443
    UniProtKB/TrEMBL
    B7Z832, E7ES19
    Related
    ENSP00000422298.1, ENST00000511733.1
    Conserved Domains (8) summary
    cd00054
    Location:288322
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
    sd00001
    Location:500522
    TSP3; TSP3 repeat_short [structural motif]
    sd00002
    Location:405440
    TSP3; TSP3 repeat_long [structural motif]
    pfam00008
    Location:199229
    EGF; EGF-like domain
    pfam02412
    Location:406440
    TSP_3; Thrombospondin type 3 repeat
    pfam05735
    Location:654851
    TSP_C; Thrombospondin C-terminal region
    cd16080
    Location:128171
    TSP-4cc; Coiled coil region of thrombospondin-4 (TSP-4)
    cl22861
    Location:1101
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
  4. NM_003248.6NP_003239.2  thrombospondin-4 isoform a precursor

    See identical proteins and their annotated locations for NP_003239.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a).
    Source sequence(s)
    AC112184, BC050456
    Consensus CDS
    CCDS4049.1
    UniProtKB/Swiss-Prot
    P35443
    Related
    ENSP00000339730.2, ENST00000350881.6
    Conserved Domains (8) summary
    smart00210
    Location:24192
    TSPN; Thrombospondin N-terminal -like domains
    cd00054
    Location:379413
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
    sd00001
    Location:591613
    TSP3; TSP3 repeat_short [structural motif]
    sd00002
    Location:496531
    TSP3; TSP3 repeat_long [structural motif]
    pfam00008
    Location:290320
    EGF; EGF-like domain
    pfam02412
    Location:497531
    TSP_3; Thrombospondin type 3 repeat
    pfam05735
    Location:745942
    TSP_C; Thrombospondin C-terminal region
    cd16080
    Location:219262
    TSP-4cc; Coiled coil region of thrombospondin-4 (TSP-4)

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    79991296..80083753
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017009798.2XP_016865287.1  thrombospondin-4 isoform X1

  2. XM_017009799.2XP_016865288.1  thrombospondin-4 isoform X2

RNA

  1. XR_002956176.1 RNA Sequence

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