Thbs3 thrombospondin 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Thbs3provided by RGD
Official Full Name: thrombospondin 3provided by RGD
Primary source: RGD:1596780
See related: EnsemblRapid:ENSRNOG00000059903 AllianceGenome:RGD:1596780
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable heparin binding activity. Predicted to be involved in cell adhesion. Predicted to act upstream of or within bone trabecula formation; growth plate cartilage development; and ossification involved in bone maturation. Predicted to be located in perinuclear region of cytoplasm. Orthologous to human THBS3 (thrombospondin 3). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Lung (RPKM 57.0), Uterus (RPKM 57.0) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 2q34

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (176919549..176931357)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (174621788..174633594)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (188528979..188540738)

Chromosome 2 - NC_086020.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables heparin binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within bone trabecula formation	ISO Inferred from Sequence Orthology more info
involved_in cell adhesion	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within growth plate cartilage development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ossification involved in bone maturation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: thrombospondin-3

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.

mRNA and Protein(s)

NM_001305458.1 → NP_001292387.1 thrombospondin-3 precursor

Status: VALIDATED

Source sequence(s)

JAXUCZ010000002

UniProtKB/TrEMBL

A0A0G2JZH3, A0A8I6G4F0

Related

ENSRNOP00000071047.2, ENSRNOT00000087934.3

Conserved Domains (9) summary

cd00054
Location:315 → 351

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:527 → 549

TSP3; TSP3 repeat_short [structural motif]

sd00002
Location:550 → 585

TSP3; TSP3 repeat_long [structural motif]

sd00003
Location:456 → 490

TSP3_1C; TSP3 repeat_1C [structural motif]

pfam02412
Location:551 → 585

TSP_3; Thrombospondin type 3 repeat

pfam05735
Location:740 → 937

TSP_C; Thrombospondin C-terminal region

pfam12947
Location:377 → 406

EGF_3; EGF domain

cd16079
Location:226 → 268

TSP-3cc; Coiled coil region of thrombospondin-3 (TSP-3)

cl22861
Location:20 → 192

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 ...

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086020.1 Reference GRCr8

Range

176919549..176931357

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063282533.1 → XP_063138603.1 thrombospondin-3 isoform X3
XM_039103121.2 → XP_038959049.1 thrombospondin-3 isoform X2

UniProtKB/TrEMBL

A6J6D1

Conserved Domains (8) summary

cd00054
Location:315 → 351

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:527 → 549

TSP3; TSP3 repeat_short [structural motif]

sd00002
Location:550 → 585

TSP3; TSP3 repeat_long [structural motif]

sd00003
Location:456 → 490

TSP3_1C; TSP3 repeat_1C [structural motif]

cd16079
Location:226 → 268

TSP-3cc; Coiled coil region of thrombospondin-3 (TSP-3)

pfam02412
Location:550 → 585

TSP_3; Thrombospondin type 3 repeat

pfam12947
Location:377 → 406

EGF_3; EGF domain

cl22861
Location:20 → 192

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 ...
XM_039103123.2 → XP_038959051.1 thrombospondin-3 isoform X1

Conserved Domains (8) summary

cd00054
Location:27 → 63

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:239 → 261

TSP3; TSP3 repeat_short [structural motif]

sd00002
Location:262 → 297

TSP3; TSP3 repeat_long [structural motif]

sd00003
Location:168 → 202

TSP3_1C; TSP3 repeat_1C [structural motif]

pfam02412
Location:262 → 297

TSP_3; Thrombospondin type 3 repeat

pfam05735
Location:452 → 649

TSP_C; Thrombospondin C-terminal region

pfam12947
Location:89 → 118

EGF_3; EGF domain

NF033845
Location:167 → 409

MSCRAMM_ClfB; MSCRAMM family adhesin clumping factor ClfB