mmp13a matrix metallopeptidase 13a [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: mmp13aprovided by ZNC
Official Full Name: matrix metallopeptidase 13aprovided by ZNC
Primary source: ZFIN:ZDB-GENE-031202-2
See related: Ensembl:ENSDARG00000012395 AllianceGenome:ZFIN:ZDB-GENE-031202-2
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: mmp13; cb1034
Summary: Predicted to enable metalloendopeptidase activity. Acts upstream of or within macrophage chemotaxis. Predicted to be located in extracellular matrix. Predicted to be active in extracellular space. Is expressed in several structures, including extension; heart; intermediate cell mass of mesoderm; leukocyte; and post-vent region. Human ortholog(s) of this gene implicated in anodontia; artery disease (multiple); bone disease (multiple); and ovarian carcinoma. Orthologous to human MMP13 (matrix metallopeptidase 13). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 10

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	10	NC_007121.7 (38593657..38619868)
105	previous assembly	GRCz10 (GCF_000002035.5)	10	NC_007121.6 (38649900..38676124)

Chromosome 10 - NC_007121.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The data suggest that MMP9 and MMP13 might play a key role in the inflammatory phase of heart regeneration in zebrafish, by mediating leukocyte recruitment via the activation of chemokines, in particular, CXCL8.
Title: Matrix metalloproteinases (MMPs) mediate leukocyte recruitment during the inflammatory phase of zebrafish heart regeneration.
MeHg impairs tail development at least partially by activation of the tissue remodeling proteases Mmp9 and Mmp13.
Title: Methyl mercury suppresses the formation of the tail primordium in developing zebrafish embryos.
JNK-Mmp13 signaling pathway plays an essential role in regulating the innate immune cell migration in response to severe injury in vivo
Title: In vivo interstitial migration of primitive macrophages mediated by JNK-matrix metalloproteinase 13 signaling in response to acute injury.
Zebra fish embryogenesis requires MMP-13 and dexamethasone and hydrocortisone modulate the expression of this gene, leading to increased activity and potentially contributing to subsequent dysmorphogenesis.
Title: Matrix metalloproteinase-13 is required for zebra fish (Danio rerio) development and is a target for glucocorticoids.

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General gene information

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Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables metalloendopeptidase activity	IBA Inferred from Biological aspect of Ancestor more info
enables metalloendopeptidase activity	IEA Inferred from Electronic Annotation more info
enables metallopeptidase activity	IEA Inferred from Electronic Annotation more info
enables peptidase activity	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in collagen catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within macrophage chemotaxis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within proteolysis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in extracellular matrix	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: collagenase 3a

Names: MMPLg; MMPLh; matrix metallopeptidase 13a (collagenase 3); matrix metalloproteinase 13; matrix metalloproteinase 13a

NP_001277408.1

EC 3.4.24.-

XP_009303831.1

EC 3.4.24.-

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_001290479.1 → NP_001277408.1 collagenase 3a precursor

Status: VALIDATED

Source sequence(s)

LO018336

UniProtKB/TrEMBL

A0A8M1P6J4

Conserved Domains (3) summary

cd00094
Location:286 → 475

HX; Hemopexin-like repeats.; Hemopexin is a heme-binding protein that transports heme to the liver. Hemopexin-like repeats occur in vitronectin and some matrix metalloproteinases family (matrixins). The HX repeats of some matrixins bind tissue inhibitor of ...

pfam00413
Location:112 → 268

Peptidase_M10; Matrixin

pfam01471
Location:28 → 91

PG_binding_1; Putative peptidoglycan binding domain

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

NC_007121.7 Reference GRCz11 Primary Assembly

Range

38593657..38619868

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_009305556.3 → XP_009303831.1 collagenase 3a isoform X1

UniProtKB/TrEMBL

A0A8M3AX13, F1QCX8

Related

ENSDARP00000012407.7, ENSDART00000011573.9

Conserved Domains (4) summary

cd00094
Location:286 → 475

HX; Hemopexin-like repeats.; Hemopexin is a heme-binding protein that transports heme to the liver. Hemopexin-like repeats occur in vitronectin and some matrix metalloproteinases family (matrixins). The HX repeats of some matrixins bind tissue inhibitor of ...

cd04278
Location:112 → 268

ZnMc_MMP; Zinc-dependent metalloprotease, matrix metalloproteinase (MMP) sub-family. MMPs are responsible for a great deal of pericellular proteolysis of extracellular matrix and cell surface molecules, playing crucial roles in morphogenesis, cell fate ...

pfam00413
Location:112 → 268

Peptidase_M10; Matrixin

pfam01471
Location:28 → 91

PG_binding_1; Putative peptidoglycan binding domain

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_201503.1: Suppressed sequence

Description

NM_201503.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.