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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

MMP13 Gene

protein-coding GIFtS: 72
GCID: GC11M102847

matrix metallopeptidase 13 (collagenase 3)

(Previous name: matrix metalloproteinase 13 (collagenase 3) )

Explore 105 diseases affiliated with
MMP13 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
Matrix Metallopeptidase 13 (Collagenase 3)¹ ²		Matrix Metalloproteinase-13³
CLG3¹ ² ⁵		EC 3.4.24⁸
Matrix Metalloproteinase 13 (Collagenase 3)¹ ²		EC 3.4.24.22⁸
MMP-13² ³		EC 3.4.24.24⁸
MANDP1² ⁵		EC 3.4.24.35⁸
Collagenase 3²		EC 3.4.24.65⁸
EC 3.4.24.-³		EC 3.4.24.7⁸

External Ids:	HGNC: 7159¹	Entrez Gene: 4322²	Ensembl: ENSG00000137745⁷	OMIM: 600108⁵	UniProtKB: P45452³

Export aliases for MMP13 gene to outside databases

Previous GC identifers: GC11M105007 GC11M104170 GC11M102351 GC11M102318 GC11M098741

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for MMP13:

Proteins of the matrix metalloproteinase (MMP) family are involved in the breakdown of extracellular matrix in normal

physiological processes, such as embryonic development, reproduction, and tissue remodeling, as well as in disease

processes, such as arthritis and metastasis. Most MMP's are secreted as inactive proproteins which are activated when

cleaved by extracellular proteinases. The protein encoded by this gene cleaves type II collagen more efficiently than

types I and III. It may be involved in articular cartilage turnover and cartilage pathophysiology associated with

osteoarthritis. The gene is part of a cluster of MMP genes which localize to chromosome 11q22.3. (provided by RefSeq,

Jul 2008)

UniProtKB/Swiss-Prot: MMP13_HUMAN, P45452

Function: Degrades collagen type I. Does not act on gelatin or casein. Could have a role in tumoral process

summary for MMP13:

Matrix metalloproteases (matrix metalloproteinase, MMPs), also called matrixins, are zinc-dependent

endopeptidases that are the major proteases involved in ECM degradation. MMPs are capable of degrading a

wide range of extracellular molecules and a number of bioactive molecules. 24 matrixin genes have been

identified in humans, which can be organized into six groups based on domain organization and substrate

preference: Collagenases (MMP-1, -8 and -13), Gelatinases (MMP-2 and MMP-9), Stromelysins (MMP-3, -10 and

-11), Matrilysin (MMP-7 and MMP-26), Membrane-type (MT)-MMPs (MMP-14, -15, -16, -17, -24 and -25) and others

(MMP-12, -19, -20, -21, -23, -27 and -28). MMP activity is regulated by two major endogenous inhibitors:

alpha2-macroglobulin and tissue inhibitors of metalloproteases (TIMPs). MMPs play a central role in cell

proliferation, migration, differentiation, angiogenesis, apoptosis and host defences. Dysregulatoin of MMPs

has been implicated in many diseases including arthritis, chronic ulcers, encephalomyelitis and cancer.

Tumour metastasis is a multistep process involving the dessemination of tumor cells from the primary tumor

to secondarys at a distant organ or tissue. One of the first steps in metastasis is the degradation of the

basement membrane, a process in which MMPs have been implicated. MMPs are secreted by tumor cells themselves

or by surrounding stromal cells stimulated by the nearby tumor. Numerous studies have linked altered MMP

expression in different human cancers with poor disease prognosis. MMP-1, -2, -3, -7, -9, -13 and -14 all

have elevated expression in primary tumors and/or metastases. Synthetic or natural inhibitors of MMPs result

in inhibition of metastasis, while up-regulation of MMPs led to enhanced cancer cell invasion.

Gene Wiki entry for MMP13 (Matrix metallopeptidase 13)

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000011.9 NC_018922.1 NT_033899.8

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the MMP13 gene promoter:
CREB STAT1 deltaCREB FOXO3a FOXO3 FOXO3b
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: MMP13 promoter sequence

Search SABiosciences Chromatin IP Primers for MMP13

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat MMP13

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 11q22.3 Ensembl cytogenetic band: 11q22.2 HGNC cytogenetic band: 11q22.3

MMP13 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
MMP13 gene location

GeneLoc information about chromosome 11 GeneLoc Exon Structure

GeneLoc location for GC11M102847: view genomic region (about GC identifiers)

Start:	102,813,721 bp from pter	End:	102,826,463 bp from pter
Size:	12,743 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: MMP13_HUMAN, P45452 (See protein sequence)

Recommended Name: Collagenase 3 precursor

Size: 471 amino acids; 53820 Da

Cofactor: Binds 4 calcium ions per subunit

Cofactor: Binds 2 zinc ions per subunit

Subcellular location: Secreted, extracellular space, extracellular matrix (Probable)

6/30 PDB 3D structures from and Proteopedia for MMP13 (see all 30):

1EUB (3D)

1FLS (3D)

1FM1 (3D)

1PEX (3D)

1UC1 (3D)

1XUC (3D)

Explore the universe of human proteins at neXtProt for MMP13: NX_P45452

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_P45452

4/22 DME Specific Peptides for MMP13 (P45452) (see all 22)

GIQSLYG

PRCGVPD

GLLAHAF

NGYIYFF

MMP13 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins: NP_002418.1

ENSEMBL proteins:

ENSP00000260302 ENSP00000339672

Reactome Protein details: P45452
Human Recombinant Protein Products:

	EMD Millipore Purified and/or Recombinant MMP13 Protein
	R&D Systems Recombinant & Natural Proteins for MMP13 (MMP-13)
	Enzo Life Sciences proteins for MMP13
	Browse OriGene full length recombinant human proteins expressed in human HEK293 cells OriGene Protein Over-expression Lysate: MMP13 OriGene Custom Protein Services for MMP13
	GenScript Custom Purified and Recombinant Proteins Services for MMP13
	Novus Biologicals MMP13 Proteins Novus Biologicals MMP13 Lysates
	Browse Sino Biological Recombinant Proteins
	ProSpec Recombinant Protein for MMP13
	Uscn Proteins for MMP13

Gene Ontology (GO): 5/8 cellular component terms (GO ID links to tree view) (see all 8): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005576	extracellular region	TAS	--
GO:0005578	proteinaceous extracellular matrix	IEA	--
GO:0005581	collagen	--	--
GO:0005583	fibrillar collagen	--	--
GO:0005615	extracellular space	TAS	8207000

MMP13 for ontologies About GeneDecksing

MMP13 Antibody Products:

	EMD Millipore Mono- and Polyclonal Antibodies for the study of MMP13
	R&D Systems Antibodies for MMP13 (MMP-13)
	OriGene Antibodies: MMP13 OriGene Custom Antibody Services for MMP13
	GenScript Custom Superior Antibodies Services for MMP13
	Novus Biologicals MMP13 Antibodies
	Abcam antibodies for MMP13
	Uscn Antibodies for MMP13
	ThermoFisher Antibody for MMP13

Assay Products for MMP13:

	Browse Kits and Assays available from EMD Millipore
	OriGene Custom Immunoassay Development Browse OriGene Fluorogenic Cell Assay Kits
	R&D Systems ELISAs for MMP13 (MMP-13) (see all)
	GenScript MMP13-Activity-based Protease Assay for Compound Screening
	Enzo Life Sciences assays for MMP13
	Uscn ELISAs and CLIAs for MMP13

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

MMP13 for domains About GeneDecksing

5/10 InterPro domains/families (see all 10):

IPR024079 MetalloPept_cat_dom

IPR021158 Pept_M10A_Zn_BS

IPR021190 Pept_M10A_matrixin

IPR000585 Hemopexin/matrixin

IPR018486 Hemopexin/matrixin_CS

Graphical View of Domain Structure for InterPro Entry P45452

ProtoNet protein and cluster: P45452

3 Blocks protein families:

IPB000585 Hemopexin repeat

IPB001818 Matrixin

IPB002477 Putative peptidoglycan binding domain 1

UniProtKB/Swiss-Prot: MMP13_HUMAN, P45452

Domain: The conserved cysteine present in the cysteine-switch motif binds the catalytic zinc ion, thus inhibiting the

enzyme. The dissociation of the cysteine from the zinc ion upon the activation-peptide release activates the enzyme

Similarity: Belongs to the peptidase M10A family

Similarity: Contains 4 hemopexin-like domains

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Function Summary:

UniProtKB/Swiss-Prot: MMP13_HUMAN, P45452

Function: Degrades collagen type I. Does not act on gelatin or casein. Could have a role in tumoral process

Genatlas biochemistry entry for MMP13:

matrix metalloproteinase 13,regulator of matrix remodeling component of the MMP cluster,expressed in the synovial

membrane and synovial fibroblasts of patients with rheumatoid arthritis,overexpressed by smooth muscle cells in

abdominal aortic aneurysm

Enzyme Numbers (IUBMB): EC 3.4.24.24² EC 3.4.24.-¹ EC 3.4.24.7² EC 3.4.24.35² EC 3.4.24.65² EC 3.4.24² EC 3.4.24.22²

miRNA Products:		miRTarBase miRNAs that target MMP13: hsa-mir-9 (MIRT000025), hsa-mir-100 (MIRT003420), hsa-mir-27b (MIRT003427), hsa-mir-140-5p (MIRT003961)

		OriGene 3'-UTR Clone: MMP13 Browse MicroRNA Expression Plasmids
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat MMP13
		8/11 QIAGEN miScript miRNA Assays for microRNAs that regulate MMP13 (see all 11):
		hsa-miR-100* hsa-miR-148b hsa-miR-513a-5p hsa-miR-27a hsa-miR-218-1* hsa-miR-1267 hsa-miR-3647-3p hsa-miR-152

		SwitchGear 3'UTR luciferase reporter plasmid: MMP13 3' UTR sequence

Inhib. RNA Products:		Browse for Gene Knock-down Tools from EMD Millipore
		OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for MMP13 (see all 7) OriGene shRNA RFP: MMP13 OriGene siRNA: MMP13
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat MMP13

Gene Editing
Products:

DNA2.0 Custom Protein Engineering Service for MMP13

Clone Products:		Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
		OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for MMP13 (see all 3) OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for MMP13 OriGene custom cloning services � gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
		GenScript: all cDNA clones in your preferred vector: MMP13 (NM_002427)
		Browse Sino Biological Human cDNA Clones
		DNA2.0 Custom Codon Optimized Gene Synthesis Service for MMP13
		Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat MMP13

Cell Line Products:		GenScript Custom overexpressing Cell Line Services for MMP13
		Search LifeMap BioReagents cell lines for MMP13

In Situ Assay
Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for MMP13

Gene Ontology (GO): 5/7 molecular function terms (GO ID links to tree view) (see all 7): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0001968	fibronectin binding	--	--
GO:0004222	metalloendopeptidase activity	IEA	--
GO:0005509	calcium ion binding	IEA	--
GO:0008233	peptidase activity	--	--
GO:0008270	zinc ion binding	IEA	--

MMP13 for ontologies About GeneDecksing

1 GenomeRNAi human phenotype for MMP13:

Increased gamma-H2AX phosphory

Animal Models:
Mouse knock-outs for MMP13: Mmp13^tm1.1Werb Mmp13^tm1Jdar Mmp13^tm1Smk
7 MGI mutant phenotypes (inferred from 4 alleles) (MGI details for Mmp13):

cardiovascular system	cellular	growth/size	homeostasis/metabolism	integument
limbs/digits/tail	skeleton

MMP13 for phenotypes About GeneDecksing

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section

Unified GeneCards pathways - 5/14 super-pathways (see all 14) About this table

See pathways by source

Super-pathway

contained gene-specific pathways

Degradation of the extracellular matrix

	Degradation of the extracellular matrix	1.00			Activation of Matrix Metalloproteinases	0.40
	Degradation of collagen	0.79

Collagen formation

	Collagen formation	1.00			Extracellular matrix organization	0.54
	Assembly of collagen fibrils and other multimeric structures	0.65

Cell adhesion_ECM remodeling

	Cell adhesion ECM remodeling	1.00			Metalloproteases in connective tissue degradation	0.31
	Cell adhesion_ECM remodeling	1.00

G-protein signaling_Ras family GTPases in kinase cascades (scheme)

	Immune response Oncostatin M signaling via MAPK in human cells	0.39			Oncostatin M Signaling Pathway	0.15
	Immune response_Oncostatin M signaling via MAPK in human cells	0.39

Development_Hedgehog and PTH signaling pathways in bone and cartilage development

Development_Hedgehog and PTH signaling pathways in bone and cartilage development

1.00

Development Hedgehog and PTH signaling pathways in bone and cartilage development

0.97

Pathway sources
See GeneCards unified pathways
Show all pathways

5/6 EMD Millipore Pathways for MMP13 (see all 6)

	Development Hedgehog and PTH signaling pathways in bone and cartilage development
	Development Glucocorticoid receptor signaling
	Cell adhesion ECM remodeling
	Immune response Oncostatin M signaling via MAPK in human cells
	Metalloproteases in connective tissue degradation

4 Downloadable PowerPoint Slides of QIAGEN Pathway Central Maps for MMP13

	Inhibition of Matrix Metalloproteinases
	Transendothelial Migration of Leukocytes
	UPA-UPAR Pathway
	Pancreatic Adenocarcinoma

5 GeneGo (Thomson Reuters) Pathways for MMP13

	Development Hedgehog and PTH signaling pathways in bone and cartilage development
	Cell adhesion ECM remodeling
	Cell adhesion Plasmin signaling
	Development Glucocorticoid receptor signaling
	Immune response Oncostatin M signaling via MAPK in human cells

4 BioSystems Pathways for MMP13

	Matrix Metalloproteinases
	AGE/RAGE pathway
	Oncostatin M Signaling Pathway
	Endochondral Ossification

5/8 Reactome Pathways for MMP13 (see all 8)

	Extracellular matrix organization
	Gelatin degradation by MMP1, 2, 3, 7, 8, 9, 12, 13
	Assembly of collagen fibrils and other multimeric structures
	Extracellular matrix organization
	Degradation of the extracellular matrix

MMP13 for pathways About GeneDecksing

Interactions:

SABiosciences Gene Network Central^TM Interacting Genes and Proteins Network for MMP13

STRING Interaction Network Preview (showing 5 interactants - click image to see 12)

5/13 Interacting proteins for MMP13 (P45452³ ENSP00000260302⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 13)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
CCL7	P80098³, ENSP00000200307⁴	I2D: score=1 STRING: ENSP00000200307
LRP1	Q07954³, ENSP00000243077⁴	I2D: score=1 STRING: ENSP00000243077
MMP14	P50281³, ENSP00000308208⁴	I2D: score=1 STRING: ENSP00000308208
ADAMTS5	Q9UNA0³, ENSP00000284987⁴	I2D: score=1 STRING: ENSP00000284987
COL2A1	P02458³, ENSP00000369889⁴	I2D: score=1 STRING: ENSP00000369889

About this table

Gene Ontology (GO): 5/14 biological process terms (GO ID links to tree view) (see all 14): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0001503	ossification	--	--
GO:0001666	response to hypoxia	--	--
GO:0006508	proteolysis	IEA	--
GO:0009612	response to mechanical stimulus	--	--
GO:0022617	extracellular matrix disassembly	TAS	--

MMP13 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

MMP13 for compounds About GeneDecksing

EMD Millipore small molecules for MMP13:
Small Molecule - inhibitor

Enzo Life Sciences drugs & compounds for MMP13

Compounds for MMP13 available from Tocris Bioscience About this table

Compound	Action	CAS #
CP 471474	Broad spectrum MMP inhibitor	[210755-45-6]
Ro 32-3555	Potent, collagenase-selective MMP inhibitor	[190648-49-8]
WAY 170523	Potent and selective inhibitor of MMP-13	[307002-73-9]
Batimastat	Potent, broad spectrum MMP inhibitor	[130370-60-4]

1 HMDB Compound for MMP13 About this table

Compound	Synonyms	CAS #	PubMed Ids
Calcium	Ca (see all 2)	7440-70-2	--

10/14 DrugBank Compounds for MMP13 (see all 14) About this table

Compound	Synonyms	CAS #	Type	Actions	PubMed Ids
WAY-151693	n-hydroxy-2-[(4-methoxy-benzenesulfonyl)-pyridin-3-ylmethyl-amino]-3-methyl-benzamide (see all 2)	--	target	--	17139284 17016423 10592235
1-Methyloxy-4-Sulfone-Benzene	--	--	target	--	17139284 17016423
3-Methylpyridine	--	108-99-6	target	--	17139284 17016423
Hydroxyaminovaline	--	--	target	--	17139284 17016423
Marimastat	--	154039-60-8	target	inhibitor	10852638 10669951
2-{4-[4-(4-Chloro-Phenoxy)-Benzenesulfonyl]-Tetrahydro-Pyran-4-Yl}-N-Hydroxy-Acetamide	--	--	target	--	10592235
4-[4-(4-CHLORO-PHENOXY)-BENZENESULFONYLMETHYL]-TETRAHYDRO-PYRAN-4-CARBOXYLIC ACID HYDROXYAMIDE	--	--	target	--	10592235
4-{[1-METHYL-2,4-DIOXO-6-(3-PHENYLPROP-1-YN-1-YL)-1,4-DIHYDROQUINAZOLIN-3(2H)-YL]METHYL}BENZOIC ACID	--	--	target	--	10592235
5-(2-ETHOXYETHYL)-5-[4-(4-FLUOROPHENOXY)PHENOXY]PYRIMIDINE-2,4,6(1H,3H,5H)-TRIONE	--	--	target	--	10592235
BENZYL 6-BENZYL-5,7-DIOXO-6,7-DIHYDRO-5H-[1,3]THIAZOLO[3,2-C]PYRIMIDINE-2-CARBOXYLATE	--	--	target	--	10592235

10/76 Novoseek chemical compound relationships for MMP13 gene (see all 76) About this table

Compound	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
hydroxamate	66.3	15	10986126 (2), 16603129 (2), 16612565 (1), 19239231 (1) (see all 7)
2-cyano-3,12-dioxoolean-1,9-dien-28-oic acid	66.1	2	11352241 (1), 12932292 (1)
(4-aminophenyl)mercuric acetate	59.5	9	7608162 (2), 17076612 (1)
thps	58.4	1	12437092 (1)
batimastat	55.5	4	10415727 (1), 11774278 (1), 15268899 (1)
sb 203580	51.1	16	19100962 (1), 12009331 (1), 14631115 (1), 19656660 (1) (see all 11)
matrigel	50	6	11774278 (1), 16407850 (1), 20463600 (1), 17322299 (1)
pge2	49	45	15612948 (5), 19998410 (4), 19447216 (3), 18562219 (2) (see all 16)
glycosaminoglycan	47.9	8	9437511 (1), 11817583 (1), 17208315 (1), 17397292 (1) (see all 7)
vegf	45.3	29	19883500 (2), 12810425 (2), 14555274 (2), 18839188 (2) (see all 23)

Search CenterWatch for drugs/clinical trials and news about MMP13

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for MMP13 gene:

NM_002427.3

Unigene Cluster for MMP13:

Matrix metallopeptidase 13 (collagenase 3)

Hs.2936 [show with all ESTs]

Unigene Representative Sequence: NM_002427

2 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000260302(uc001phl.3) ENST00000340273

miRNA Products:		OriGene 3'-UTR Clone: MMP13 Browse OriGene MicroRNA Expression Plasmids
		QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat MMP13
		8/11 QIAGEN miScript miRNA Assays for microRNAs that regulate MMP13 (see all 11):
		hsa-miR-100* hsa-miR-148b hsa-miR-513a-5p hsa-miR-27a hsa-miR-218-1* hsa-miR-1267 hsa-miR-3647-3p hsa-miR-152

		SwitchGear 3'UTR luciferase reporter plasmid: MMP13 3' UTR sequence

Inhib. RNA Products:		Browse for Gene Knock-down Tools from EMD Millipore
		OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for MMP13 (see all 7) OriGene shRNA RFP: MMP13 OriGene siRNA: MMP13
		QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat MMP13

Clone Products:		OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for MMP13 (see all 3) OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for MMP13 OriGene custom cloning services � gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
		GenScript: all cDNA clones in your preferred vector: MMP13 (NM_002427)
		DNA2.0 Custom Codon Optimized Gene Synthesis Service for MMP13
		Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat MMP13

Primer Products:		OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for MMP13 Browse OriGene validated miRNA SYBR primer pairs
		SABiosciences RT² qPCR Primer Assay in human, mouse, rat MMP13
		QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat MMP13
		QIAGEN QuantiFast Probe-based Assays in human, mouse, rat MMP13

Additional cDNA sequence:

AK222748.1 AK292211.1 AK315341.1 AY256443.1 AY256444.1 BC067522.1 BC067523.1 BC074807.2

BC074808.2 X75308.1 X81334.1

2 DOTS entries:

DT.413417 DT.95158006

24/74 AceView cDNA sequences (see all 74):

AX930362 AY256444 AY256443 AA298225 AA926873 AA329956 CA414772 CA414373

BG771388 NM_002427 CA413504 C02454 BP352104 CA412841 BX110082 AA329883

X75308 AA448726 BC067522 N69322 BC074808 AA298256 CA413743 BC074807

GeneLoc Exon Structure

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

MMP13 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: AAATAAAATA

About this image

MMP13 expression in embryonic tissues and stem cells

Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

10/31 LifeMap In Vivo Development Anatomical Compartments/Cells (see all 31)

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Bone

Autopod Growth Plate

Hypertrophic Chondrocytes

Selective marker (cell-identifying gene)

Bone, Cartilage

Bone

Autopod Growth Plate

Terminal Chondrocytes

Bone, Cartilage

Bone

Caudal Endochondral Bones

Terminal Chondrocytes

Bone, Cartilage

Bone

Cervical Vertebrae

Hypertrophic Chondrocytes

Bone, Cartilage

Bone

Cervical Vertebrae

Terminal Chondrocytes

Bone, Cartilage

Bone

Endochondral Facial Bones

Terminal Chondrocytes

Bone, Cartilage

Bone

Lumbar Vertebrae

Hypertrophic Chondrocytes

Bone, Cartilage

Bone

Lumbar Vertebrae

Terminal Chondrocytes

Bone, Cartilage

Bone

Sacral Vertebrae

Hypertrophic Chondrocytes

Bone, Cartilage

Bone

Sacral Vertebrae

Terminal Chondrocytes

Bone, Cartilage

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

Stem Cell Differentiation: 2 LifeMap Cells

Name

Category

PureStem™ mesenchymal progenitor 7SMOO32 (Embryonic Progenitor Cell)

Adipose, Bone, Cartilage

HyStem+TGF?3+GDF5-induced 7SMOO32 cells (HyStem+TGF?3+GDF5 in...)

Bone, Cartilage

See MMP13 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for MMP13

SOURCE GeneReport for Unigene cluster: Hs.2936

UniProtKB/Swiss-Prot: MMP13_HUMAN, P45452

Tissue specificity: Seems to be specific to breast carcinomas

SABiosciences Expression via Pathway-Focused PCR Arrays including MMP13:

Fibrosis in human mouse rat

Extracellular Matrix & Adhesion Molecules in human mouse rat

Tumor Metastasis in human mouse rat

Primer Products:		OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for MMP13 Browse OriGene validated miRNA SYBR primer pairs
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In Situ
Assay Products:

Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for MMP13

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of eukaryotes.

Orthologs for MMP13 gene from 7/18 species (see all 18) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
chicken (Gallus gallus)	Aves	MMP13¹	matrix metallopeptidase 13 (collagenase 3)	73.99(n) 70.79(a)		395683 XM_003640587.1 XP_003640635.1
lizard (Anolis carolinensis)	Reptilia	MMP13⁶	--	54(a)	1 ↔ 1	3(192012999-192021044)
African clawed frog (Xenopus laevis)	Amphibia	gene²	collagenase-3	76.09(n)		U41824.1
zebrafish (Danio rerio)	Actinopterygii	BC049472.1²	--	74.6(n)		BC049472.1
worm (Caenorhabditis elegans)	Secernentea	C31B8.8³	--	37(a)		V(2905685-2909407) --
thale cress (Arabidopsis thaliana)	eudicotyledons	AT1G59970⁶ AT2G45040⁶ (see all 5)	matrix metalloprotease domain-containing protein (see all 5)	28(a) 27(a) (see all 5)	many ↔ many many ↔ many (see all 5)	1(22073534-22074876) 2(18577650-18578914)
rice (Oryza sativa)	Liliopsida	-- -- (see all 4)	matrixin family protein metalloendoproteinase 1 precursor, putative, expre... (see all 4)	8(a) 26(a) (see all 4)	many ↔ many many ↔ many (see all 4)	10(21890877-21896676) 2(30974996-30977090)

ENSEMBL Gene Tree for MMP13 (if available)
TreeFam Gene Tree for MMP13 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

Paralogs for MMP13 gene

MMP20² MMP8² MMP14² MMP9² MMP16² MMP2² MMP25² MMP24²

MMP15² MMP11² MMP3² MMP27² MMP17² MMP10² MMP1²

18/25 SIMAP similar genes for MMP13 using alignment to 5 protein entries: MMP13_HUMAN (see all proteins) (see all similar genes):

AURA2 FAM175A NF2 LINC00596 MMP1 MMP8

GLT8D2 DNAPTP3 MMP3 MMP10 MMP27 MMP7

MMP20 MMP12 MMP26 MMP2 mmp20 MMP14

MMP13 for paralogs About GeneDecksing

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
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SNP ID	Valid	Clinical significance	Chr 11 pos	Sequence	#	AA Chg	Type	More	#	Pop	Total sample
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs17860540^1,2	C	--	98751324(-)	`CTCCAT/CCCTTG`	1	--	int¹		1	NS	178
rs17099791^1,2	C,F,	--	98751549(+)	`TATTTC/GAAACT`	1	--	int¹		8	NA NS WA CSA	328
rs17860538^1,2	C	--	98751577(-)	`TCTTTT/CAGTTT`	1	--	int¹ trp³		1	NS	178
rs17860536^1,2	C,	--	98751695(-)	`TCATGC/GACAGG`	1	--	int¹		2	NS EA	296
rs11602600^1,2	H	--	98751887(+)	`ACCCAG/AAATTT`	1	--	int¹		4	NS EA	420
rs1939529^1,2	C,F,O,A,H,	--	98752366(-)	`TGTCTA/GTATAT`	1	--	int¹		19	NA NS EA WA	1522
rs17860530^1,2	C,F,H	--	98753220(-)	`TGGTCC/TGATGT`	2	S	syn¹ ese³		5	NS NA	4896
rs17860529^1,2	C,F,	--	98753377(-)	`GAATTG/AAAAAG`	1	--	int¹		2	NS NA	294
rs17860528^1,2	C,F,	--	98753406(-)	`TAGAAC/TTTTCA`	1	--	int¹		1	NS	174
rs17860525^1,2	C	--	98753800(-)	`TCATAA/GCATCT`	1	--	int¹		1	NS	170

HapMap Linkage Disequilibrium report for MMP13 (102813721 - 102826463 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for MMP13: --
Human Gene Mutation Database (HGMD): MMP13

SABiosciences Cancer Mutation PCR Assays

QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing MMP13

DNA2.0 Custom Variant and Variant Library Synthesis for MMP13

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

MMP13 for disorders           About GeneDecksing

OMIM gene information: 600108
OMIM disorders: 602111
UniProtKB/Swiss-Prot: MMP13_HUMAN, P45452

Defects in MMP13 are the cause of spondyloepimetaphyseal dysplasia Missouri type (SEMD-MO) [MIM:602111]. A

bone disease characterized by moderate to severe metaphyseal changes, mild epiphyseal involvement, rhizomelic

shortening of the lower limbs with bowing of the femora and/or tibiae, coxa vara, genu varum and pear-shaped vertebrae

in childhood. Epimetaphyseal changes improve with age

Defects in MMP13 are the cause of metaphyseal anadysplasia type 1 (MANDP1) [MIM:602111]. Metaphyseal

anadysplasia consists of an abnormal bone development characterized by severe skeletal changes that, in contrast with

the progressive course of most other skeletal dysplasias, resolve spontaneously with age. Clinical characteristics are

evident from the first months of life and include slight shortness of stature and a mild varus deformity of the legs.

Patients attain a normal stature in adolescence and show improvement or complete resolution of varus deformity of the

legs and rhizomelic micromelia

20/105 diseases for MMP13 (see all 105): About MalaCards

spondyloepimetaphyseal dysplasia, missouri type malignant peripheral nerve sheath tumor metaphyseal anadysplasia osteoarthritis

arthritis metaphyseal anadysplasia 1 periapical granuloma encephalomyelitis

osteochondritis dissecans refractive error squamous cell carcinoma aortic aneurysm

laryngeal squamous cell carcinoma salivary gland cancer abdominal aortic aneurysm vernal keratoconjunctivitis

diverticulitis epidermolysis bullosa localized scleroderma hernia

2 diseases from the University of Copenhagen DISEASES database for MMP13:

Osteoarthritis Rheumatoid arthritis

10/96 Novoseek disease relationships for MMP13 gene (see all 96) About this table

Disease	-log (P-Val)	Hits	PubMed IDs for Articles with Shared Sentences (# sentences)
osteoarthritis	82.4	81	15067375 (3), 15498796 (3), 8730110 (2), 19606871 (2) (see all 48)
chondrosarcoma	71.3	50	9665469 (7), 18554405 (5), 19126648 (3), 19301259 (3) (see all 22)
arthritis	64.1	46	12010565 (3), 15140772 (3), 19248099 (3), 12878172 (2) (see all 21)
rheumatoid arthritis	61.6	46	19379726 (2), 19497915 (2), 9166290 (2), 9259418 (2) (see all 28)
collagen fibril	51.7	7	12192005 (1), 17055235 (1), 17295208 (1), 12747275 (1) (see all 7)
necrosis	51.1	35	9040946 (2), 12687541 (1), 12746902 (1), 12010565 (1) (see all 32)
periapical granuloma	50.6	3	15876293 (2)
tumors	47.9	180	18698413 (7), 19035119 (7), 18373849 (6), 10027405 (5) (see all 76)
metastasis	45.3	41	11802203 (2), 12673424 (2), 9933692 (1), 14667142 (1) (see all 25)
hnscc	45.3	6	16302191 (3), 17334397 (1)

Genetic Association Database (GAD): MMP13
Human Genome Epidemiology (HuGE) Navigator: MMP13 (35 documents)

Export disorders for MMP13 gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
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PubMed articles for MMP13 gene, integrated from 9 sources (see all 911):
(articles sorted by number of sources associating them with MMP13)

Utopia: connect your pdf to the dynamic
world of online information

Molecular cloning and expression of collagenase-3, a novel human matrix metalloproteinase produced by breast carcinomas. (PubMed id 8207000)^{1, 2, 3, 9} Freije J.M.P.... Lopez-Otin C. (1994)
MMP13 promoter polymorphism is associated with atherosclerosis in the abdominal aorta of young black males. (PubMed id 12392760)^{1, 4, 9} Yoon S....Tromp G. (2002)
Mutations in MMP9 and MMP13 determine the mode of inh eritance and the clinical spectrum of metaphyseal anadysplasia. (PubMed id 19615667)^{1, 2, 9} Lausch E....Zabel B. (2009)
Regulatory polymorphisms in extracellular matrix protease genes and susceptibility to rheumatoid arthritis: a case-control study. (PubMed id 16356191)^{1, 4, 9} Rodriguez-Lopez J....Gonzalez A. (2006)
A matrix metalloproteinase gene expressed in human T lymphocytes is identical with collagenase 3 from breast carcinomas. (PubMed id 9562863)^{1, 2, 9} Willmroth F.... Conca W. (1998)
The helping hand of collagenase-3 (MMP-13): 2.7 A crystal structure of its C-terminal haemopexin-like domain. (PubMed id 8969305)^{1, 2, 9} Gomis-Rueth F.-X.... Bode W. (1996)
Genetic analysis of polymorphisms in biologically relevant candidate genes in patients with abdominal aortic aneurysms. (PubMed id 15944607)^{1, 4} Ogata T....Kuivaniemi H. (2005)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{1, 2} Gerhard D.S....Malek J. (2004)
Tumor-derived matrix metalloproteinase-13 (MMP-13) correlates with poor prognoses of invasive breast cancer. (PubMed id 18373849)^{1, 9} Zhang B....Hao X. (2008)
Matrix metalloproteinase-13 is highly expressed in destructive periodontal disease activity. (PubMed id 17076612)^{1, 9} Hernandez M....Gamonal J. (2006)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Disorders
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 4322	HGNC: 7159	AceView: MMP13	Ensembl:ENSG00000137745	euGenes: HUgn4322
ECgene: MMP13	H-InvDB: MMP13

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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Name	Description
PharmGKB entry for MMP13	Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for MMP13	Genetics and Cytogenetics in Oncology and Haematology
NIEHS-SNPs	http://egp.gs.washington.edu/data/mmp13/

Intellectual Property for MMP13 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

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Patent Information for MMP13 gene:
Search GeneIP for patents involving MMP13

GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search

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In Situ Hybridization Assays from
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matrix metallopeptidase 13 (collagenase 3)

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MMP13 Gene

matrix metallopeptidase 13 (collagenase 3)

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