Human Gene THBS4 (ENST00000350881.6) from GENCODE V44
  Description: Homo sapiens thrombospondin 4 (THBS4), transcript variant 1, mRNA. (from RefSeq NM_003248)
RefSeq Summary (NM_003248): 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].
Gencode Transcript: ENST00000350881.6
Gencode Gene: ENSG00000113296.14
Transcript (Including UTRs)
   Position: hg38 chr5:80,035,348-80,083,287 Size: 47,940 Total Exon Count: 22 Strand: +
Coding Region
   Position: hg38 chr5:80,035,538-80,083,141 Size: 47,604 Coding Exon Count: 22 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:80,035,348-80,083,287)mRNA (may differ from genome)Protein (961 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: TSP4_HUMAN
DESCRIPTION: RecName: Full=Thrombospondin-4; Flags: Precursor;
FUNCTION: Acts as an extracellular mitogen and stimulates early erythroid progenitors proliferation in presence of EPO. Adhesive glycoprotein that mediates cell-to-cell and cell-to-matrix interactions. Can bind to fibrinogen, fibronectin, laminin and type V collagen.
SUBUNIT: Homopentamer; disulfide-linked. Interacts with PTBP3.
SIMILARITY: Belongs to the thrombospondin family.
SIMILARITY: Contains 4 EGF-like domains.
SIMILARITY: Contains 1 laminin G-like domain.
SIMILARITY: Contains 1 TSP C-terminal (TSPC) domain.
SIMILARITY: Contains 8 TSP type-3 repeats.
WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/thbs4/";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: THBS4
Diseases sorted by gene-association score: mycetoma (10), myocardial infarction (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 53.62 RPKM in Nerve - Tibial
Total median expression: 338.66 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -100.50190-0.529 Picture PostScript Text
3' UTR -17.90146-0.123 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR008985 - ConA-like_lec_gl_sf
IPR013320 - ConA-like_subgrp
IPR000742 - EG-like_dom
IPR001881 - EGF-like_Ca-bd
IPR013032 - EGF-like_CS
IPR018097 - EGF_Ca-bd_CS
IPR001791 - Laminin_G
IPR024665 - Thbs/COMP_coiled-coil
IPR003367 - Thrombospondin_3-like_rpt
IPR017897 - Thrombospondin_3_rpt
IPR008859 - Thrombospondin_C

Pfam Domains:
PF11598 - Cartilage oligomeric matrix protein
PF07645 - Calcium-binding EGF domain
PF02412 - Thrombospondin type 3 repeat
PF05735 - Thrombospondin C-terminal region

ModBase Predicted Comparative 3D Structure on P35443
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005178 integrin binding
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0008083 growth factor activity
GO:0008201 heparin binding

Biological Process:
GO:0001938 positive regulation of endothelial cell proliferation
GO:0006986 response to unfolded protein
GO:0007155 cell adhesion
GO:0010469 regulation of receptor activity
GO:0016525 negative regulation of angiogenesis
GO:0030198 extracellular matrix organization
GO:0034103 regulation of tissue remodeling
GO:0034976 response to endoplasmic reticulum stress
GO:0048266 behavioral response to pain
GO:0048771 tissue remodeling
GO:0050731 positive regulation of peptidyl-tyrosine phosphorylation
GO:0051451 myoblast migration
GO:0051781 positive regulation of cell division
GO:0071603 endothelial cell-cell adhesion
GO:0090023 positive regulation of neutrophil chemotaxis

Cellular Component:
GO:0005576 extracellular region
GO:0005604 basement membrane
GO:0005615 extracellular space
GO:0005783 endoplasmic reticulum
GO:0016529 sarcoplasmic reticulum
GO:0031012 extracellular matrix
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  BC050456 - Homo sapiens thrombospondin 4, mRNA (cDNA clone MGC:54257 IMAGE:6191808), complete cds.
AK313587 - Homo sapiens cDNA, FLJ94152, highly similar to Homo sapiens thrombospondin 4 (THBS4), mRNA.
Z19585 - H.sapiens mRNA for thrombospondin-4.
AK302842 - Homo sapiens cDNA FLJ51409 complete cds, highly similar to Thrombospondin-4 precursor.
JD326355 - Sequence 307379 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04350 - TGF-beta signaling pathway
hsa04510 - Focal adhesion
hsa04512 - ECM-receptor interaction

Reactome (by CSHL, EBI, and GO)

Protein P35443 (Reactome details) participates in the following event(s):

R-HSA-382054 PDGF binds to extracellular matrix proteins
R-HSA-186797 Signaling by PDGF
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: B2R909, ENST00000350881.1, ENST00000350881.2, ENST00000350881.3, ENST00000350881.4, ENST00000350881.5, NM_003248, P35443, Q86TG2, TSP4, TSP4_HUMAN, uc021yaw.1, uc021yaw.2
UCSC ID: ENST00000350881.6
RefSeq Accession: NM_003248
Protein: P35443 (aka TSP4_HUMAN)
CCDS: CCDS4049.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.