Col5a3 collagen, type V, alpha 3 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Col5a3provided by MGI
Official Full Name: collagen, type V, alpha 3provided by MGI
Primary source: MGI:MGI:1858212
See related: Ensembl:ENSMUSG00000004098 AllianceGenome:MGI:1858212
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Summary: Enables heparin binding activity. Acts upstream of or within cell-matrix adhesion. Part of collagen type V trimer. Is expressed in several structures, including bone; embryo mesenchyme; extraembryonic component; placenta; and tongue. Orthologous to human COL5A3 (collagen type V alpha 3 chain). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in subcutaneous fat pad adult (RPKM 60.2), adrenal adult (RPKM 48.3) and 7 other tissues See more
Orthologs: human all
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Genomic context

Location:: 9 A3; 9 7.63 cM

Exon count:: 67

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	9	NC_000075.7 (20681353..20726363, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	9	NC_000075.6 (20770050..20815117, complement)

Chromosome 9 - NC_000075.7 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: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Present study examined the expression of pro-alpha3(V) collagen gene in a mouse model of wound healing.
Title: Transient expression of mouse pro-α3(V) collagen gene (Col5a3) in wound healing.
data show the alpha3(V) collagen chain to constitute an important element of the microenvironment of certain highly specialized cell types in white adipose tissue, skeletal muscle and pancreatic islets and to have profound effects on function of such cells
Title: α3(V) collagen is critical for glucose homeostasis in mice due to effects in pancreatic islets and peripheral tissues.
The Sp1 and CBF/NF-Y transcription factors cooperatively regulate the mouse pro-alpha3(V) collagen gene (Col5a3) in osteoblastic cells.
Title: The Sp1 and CBF/NF-Y transcription factors cooperatively regulate the mouse pro-alpha3(V) collagen gene (Col5a3) in osteoblastic cells.
Sp7/Osterix promotes the expression of the collagen gene, Col5a3, and thereby playing a role in bone formation.
Title: Sp7/Osterix up-regulates the mouse pro-alpha3(V) collagen gene (Col5a3) during the osteoblast differentiation.
analysis of processing of the Pro-alpha1(V)Pro-alpha2(V)Pro-alpha3(V) procollagen heterotrimer
Title: Biosynthetic processing of the Pro-alpha1(V)Pro-alpha2(V)Pro-alpha3(V) procollagen heterotrimer.
N-terminal globular domain of the pro-alpha3(V) chain influence bone formation of osteoblasts through proteoglycan on the cell surface during development or regeneration
Title: Pro-alpha3(V) collagen chain is expressed in bone and its basic N-terminal peptide adheres to osteosarcoma cells.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (1)
Targeted (1) 1 citation

General gene information

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Markers

Col5a3 (e-PCR), detects polymorphism
- UniSTS:164918

Col5a3 (e-PCR), detects polymorphism
- UniSTS:531585

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info
enables heparin binding	IBA Inferred from Biological aspect of Ancestor more info
enables heparin binding	IDA Inferred from Direct Assay more info	PubMed
enables proteoglycan binding	ISO Inferred from Sequence Orthology more info
enables structural molecule activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within cell-matrix adhesion	IDA Inferred from Direct Assay more info	PubMed
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within extracellular matrix organization	ISS Inferred from Sequence or Structural Similarity more info	PubMed

Component	Evidence Code	Pubs
part_of collagen type V trimer	IDA Inferred from Direct Assay more info	PubMed
part_of collagen type V trimer	ISS Inferred from Sequence or Structural Similarity more info	PubMed
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in collagen-containing extracellular matrix	ISO Inferred from Sequence Orthology more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: collagen alpha-3(V) chain

Names: Pro-alpha3(V); procollagen, type V, alpha 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_001317388.1 → NP_001304317.1 collagen alpha-3(V) chain isoform 2 precursor

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. It encodes isoform 2 which is shorter than isoform 1.

Source sequence(s)

AC166365, AI482539, AI585575, BC138417, BX511958, BY783304

UniProtKB/TrEMBL

Q9JLI2

Conserved Domains (3) summary

pfam01391
Location:1002 → 1059

Collagen; Collagen triple helix repeat (20 copies)

pfam01410
Location:1509 → 1736

COLFI; Fibrillar collagen C-terminal domain

cl22861
Location:31 → 210

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 ...
NM_016919.3 → NP_058615.1 collagen alpha-3(V) chain isoform 1 precursor

See identical proteins and their annotated locations for NP_058615.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC166365, AI482539, AI585575, BC138417, BX511958, BY783304

Consensus CDS

CCDS22883.1

UniProtKB/TrEMBL

Q9JLI2

Related

ENSMUSP00000004201.8, ENSMUST00000004201.8

Conserved Domains (3) summary

pfam01391
Location:1003 → 1060

Collagen; Collagen triple helix repeat (20 copies)

pfam01410
Location:1510 → 1737

COLFI; Fibrillar collagen C-terminal domain

cl22861
Location:32 → 211

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 ...