CleftGeneDB-Search

Gene: Mmp9

Basic information

Tag	Content
Uniprot ID	P41245; Q06788; Q80XI8; Q9DC02;
Entrez ID	17395
Genbank protein ID	CAA51314.1; BAB23442.1; CAA81745.1; AAH46991.1; BAE34968.1; BAA02208.1; AAB28942.1; CAA51315.1;
Genbank nucleotide ID	NM_013599.4
Ensembl protein ID	ENSMUSP00000017881
Ensembl nucleotide ID	ENSMUSG00000017737
Gene name	Matrix metalloproteinase-9
Gene symbol	Mmp9
Organism	Mus musculus
NCBI taxa ID	10090
Cleft type
Developmental stage	E12.5, E13.5, E14.5
Data sources	Homology search
Reference
Functional description	Could play a role in bone osteoclastic resorption. Cleaves type IV and type V collagen into large C-terminal three quarter fragments and shorter N-terminal one quarter fragments (By similarity).
Sequence	MSPWQPLLLA LLAFGCSSAA PYQRQPTFVV FPKDLKTSNL TDTQLAEAYL YRYGYTRAAQ 60 MMGEKQSLRP ALLMLQKQLS LPQTGELDSQ TLKAIRTPRC GVPDVGRFQT FKGLKWDHHN 120 ITYWIQNYSE DLPRDMIDDA FARAFAVWGE VAPLTFTRVY GPEADIVIQF GVAEHGDGYP 180 FDGKDGLLAH AFPPGAGVQG DAHFDDDELW SLGKGVVIPT YYGNSNGAPC HFPFTFEGRS 240 YSACTTDGRN DGTPWCSTTA DYDKDGKFGF CPSERLYTEH GNGEGKPCVF PFIFEGRSYS 300 ACTTKGRSDG YRWCATTANY DQDKLYGFCP TRVDATVVGG NSAGELCVFP FVFLGKQYSS 360 CTSDGRRDGR LWCATTSNFD TDKKWGFCPD QGYSLFLVAA HEFGHALGLD HSSVPEALMY 420 PLYSYLEGFP LNKDDIDGIQ YLYGRGSKPD PRPPATTTTE PQPTAPPTMC PTIPPTAYPT 480 VGPTVGPTGA PSPGPTSSPS PGPTGAPSPG PTAPPTAGSS EASTESLSPA DNPCNVDVFD 540 AIAEIQGALH FFKDGWYWKF LNHRGSPLQG PFLTARTWPA LPATLDSAFE DPQTKRVFFF 600 SGRQMWVYTG KTVLGPRSLD KLGLGPEVTH VSGLLPRRLG KALLFSKGRV WRFDLKSQKV 660 DPQSVIRVDK EFSGVPWNSH DIFQYQDKAY FCHGKFFWRV SFQNEVNKVD HEVNQVDDVG 720 YVTYDLLQCP

Abbreviation :
CLO : cleft lip only. CPO : cleft palate only. CLP : cleft lip and palate. CL/P : cleft lip with/without cleft palate.
For humans: CL/P, CLO, CPO, and CLP. For mice: CLO, CLP, and CPO.

Gene expression information

Gene expression during embryonic days (E11.5~E18.5) ~ adult days (Ps) in the lip and palate tissues. (X-axis: days, Y-axis: tissues)

Protein structural annotations

3D structure in PDB database

There is no related protein structure for this gene.

Protein disorder information

Orthologous information

Relation	Gene symbol	Entrez ID	UniProt ID	Developmental stage	Species	Evidence	Details
1:1 ortholog	MMP9		F1P6A2		Canis lupus familiaris	Prediction	More>>
1:1 ortholog	MMP9		A0A452EYC3		Capra hircus	Prediction	More>>
1:1 ortholog	MMP9	4318	P14780		Homo sapiens	Publication	More>>
1:1 ortholog	Mmp9	17395	P41245	E12.5, E13.5, E14.5	Mus musculus	Prediction	More>>
1:1 ortholog	MMP9	458294	H2QKI0		Pan troglodytes	Prediction	More>>
1:1 ortholog	MMP9		A0A287AZD5		Sus scrofa	Prediction	More>>
1:1 ortholog	Mmp9		D3ZYK8		Rattus norvegicus	Prediction	More>>
1:1 ortholog	mmp9		F1QC76		Danio rerio	Prediction	More>>

Identified variants/mutations related to cleft phenotype

Gene symbol	Significant Variants/SNPS	Methods	PubMed ID
MMP9	rs17576A>G	Genotyping	21462296
MMP9	rs6094237A>T	Genotyping	21462296

Other genetic variants/mutations

ID	Variant	Type	Disease	Chromosome\Coordinate	Evidence
rs228710137	p.Lys264Thr	missense variant	-	NC_000068.7:g.164950088A>C	UniProt
rs260975498	p.Arg312His	missense variant	-	NC_000068.7:g.164950412G>A	UniProt
rs28262063	p.Ser359Pro	missense variant	-	NC_000068.7:g.164950902T>C	UniProt
rs28262062	p.Arg367Ser	missense variant	-	NC_000068.7:g.164950928G>T	UniProt
rs28262053	p.Pro514Ala	missense variant	-	NC_000068.7:g.164952629C>G	UniProt
	p.Pro514Ala	Missense	-	-	UniProt
rs13475086	p.Leu639Pro	missense variant	-	NC_000068.7:g.164953375T>C	UniProt
	p.Leu639Pro	Missense	-	-	UniProt
rs235225876	p.Arg649His	missense variant	-	NC_000068.7:g.164953405G>A	UniProt
rs28262043	p.His711Pro	missense variant	-	NC_000068.7:g.164954845A>C	UniProt
	p.His711Pro	Missense	-	-	UniProt

Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO ID	GO Term	Evidence
GO:0001968	fibronectin binding	ISO
GO:0004175	endopeptidase activity	ISO
GO:0004222	metalloendopeptidase activity	ISO
GO:0004222	metalloendopeptidase activity	ISS
GO:0004222	metalloendopeptidase activity	IDA
GO:0004222	metalloendopeptidase activity	IBA
GO:0004252	serine-type endopeptidase activity	ISO
GO:0008233	peptidase activity	ISO
GO:0008233	peptidase activity	IDA
GO:0008237	metallopeptidase activity	ISO
GO:0008237	metallopeptidase activity	IDA
GO:0008270	zinc ion binding	IEA
GO:0042802	identical protein binding	ISO
GO:0044877	protein-containing complex binding	ISO

GO:Biological Process

GO ID	GO Term	Evidence
GO:0001501	skeletal system development	IGI
GO:0001501	skeletal system development	IMP
GO:0001934	positive regulation of protein phosphorylation	ISO
GO:0002687	positive regulation of leukocyte migration	ISO
GO:0006508	proteolysis	ISS
GO:0006508	proteolysis	ISO
GO:0006979	response to oxidative stress	ISO
GO:0007507	heart development	ISO
GO:0007566	embryo implantation	IDA
GO:0007568	aging	ISO
GO:0019087	transformation of host cell by virus	ISO
GO:0030198	extracellular matrix organization	IGI
GO:0030198	extracellular matrix organization	IMP
GO:0030198	extracellular matrix organization	IBA
GO:0030335	positive regulation of cell migration	ISO
GO:0030574	collagen catabolic process	ISO
GO:0030574	collagen catabolic process	IBA
GO:0030574	collagen catabolic process	IDA
GO:0031915	positive regulation of synaptic plasticity	ISO
GO:0034614	cellular response to reactive oxygen species	ISO
GO:0035987	endodermal cell differentiation	IEA
GO:0042493	response to drug	ISO
GO:0043065	positive regulation of apoptotic process	IMP
GO:0043066	negative regulation of apoptotic process	ISO
GO:0043388	positive regulation of DNA binding	ISO
GO:0045742	positive regulation of epidermal growth factor receptor signaling pathway	ISO
GO:0045766	positive regulation of angiogenesis	ISO
GO:0048147	negative regulation of fibroblast proliferation	ISO
GO:0048771	tissue remodeling	ISO
GO:0051549	positive regulation of keratinocyte migration	ISO
GO:0071276	cellular response to cadmium ion	ISO
GO:0071460	cellular response to cell-matrix adhesion	ISO
GO:0090200	positive regulation of release of cytochrome c from mitochondria	ISO
GO:1900122	positive regulation of receptor binding	ISO
GO:1904645	response to amyloid-beta	IDA
GO:1904707	positive regulation of vascular smooth muscle cell proliferation	ISO
GO:2000697	negative regulation of epithelial cell differentiation involved in kidney development	IDA
GO:2001243	negative regulation of intrinsic apoptotic signaling pathway	ISO
GO:2001258	negative regulation of cation channel activity	ISO
GO:2001268	negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway	ISO

GO:Cellular Component

GO ID	GO Term	Evidence
GO:0005615	extracellular space	ISS
GO:0005615	extracellular space	ISO
GO:0005615	extracellular space	IBA
GO:0032991	protein-containing complex	ISO
GO:0062023	collagen-containing extracellular matrix	HDA

Reactome Pathway

Reactome ID	Reactome Term	Evidence
R-MMU-1266738	Developmental Biology	IEA
R-MMU-1433557	Signaling by SCF-KIT	IEA
R-MMU-1442490	Collagen degradation	IEA
R-MMU-1474228	Degradation of the extracellular matrix	IEA
R-MMU-1474244	Extracellular matrix organization	IEA
R-MMU-1474290	Collagen formation	IEA
R-MMU-1592389	Activation of Matrix Metalloproteinases	IEA
R-MMU-162582	Signal Transduction	IEA
R-MMU-168249	Innate Immune System	IEA
R-MMU-168256	Immune System	IEA
R-MMU-2022090	Assembly of collagen fibrils and other multimeric structures	IEA
R-MMU-2682334	EPH-Ephrin signaling	IEA
R-MMU-3928665	EPH-ephrin mediated repulsion of cells	IEA
R-MMU-422475	Axon guidance	IEA
R-MMU-6798695	Neutrophil degranulation	IEA
R-MMU-8939211	ESR-mediated signaling	IEA
R-MMU-9006931	Signaling by Nuclear Receptors	IEA
R-MMU-9006934	Signaling by Receptor Tyrosine Kinases	IEA
R-MMU-9009391	Extra-nuclear estrogen signaling	IEA

Functional annotations

Keywords

Keyword ID	Keyword Term
KW-0106	Calcium
KW-0177	Collagen degradation
KW-1015	Disulfide bond
KW-0272	Extracellular matrix
KW-0325	Glycoprotein
KW-0378	Hydrolase
KW-0479	Metal-binding
KW-0482	Metalloprotease
KW-0621	Polymorphism
KW-0645	Protease
KW-1185	Reference proteome
KW-0677	Repeat
KW-0964	Secreted
KW-0732	Signal
KW-0862	Zinc
KW-0865	Zymogen

Interpro

InterPro ID	InterPro Term
IPR000562	FN_type2_dom
IPR036943	FN_type2_sf
IPR000585	Hemopexin-like_dom
IPR036375	Hemopexin-like_dom_sf
IPR018487	Hemopexin-like_repeat
IPR018486	Hemopexin_CS
IPR013806	Kringle-like
IPR033739	M10A_MMP
IPR024079	MetalloPept_cat_dom_sf
IPR001818	Pept_M10_metallopeptidase
IPR021190	Pept_M10A
IPR021158	Pept_M10A_Zn_BS
IPR006026	Peptidase_Metallo
IPR002477	Peptidoglycan-bd-like
IPR036365	PGBD-like_sf
IPR036366	PGBDSf
IPR006970	PT

PROSITE

PROSITE ID	PROSITE Term
PS00546	CYSTEINE_SWITCH
PS00023	FN2_1
PS51092	FN2_2
PS00024	HEMOPEXIN
PS51642	HEMOPEXIN_2
PS00142	ZINC_PROTEASE

Pfam

Pfam ID	Pfam Term
PF00040	fn2
PF00045	Hemopexin
PF00413	Peptidase_M10
PF01471	PG_binding_1
PF04886	PT

Gene: Mmp9

Basic information

Gene expression information

Gene expression during embryonic days (E11.5~E18.5) ~ adult days (Ps) in the lip and palate tissues. (X-axis: days, Y-axis: tissues)

Protein structural annotations

3D structure in PDB database

There is no related protein structure for this gene.

Protein disorder information

Orthologous information

Identified variants/mutations related to cleft phenotype

Other genetic variants/mutations

Gene Ontology (GO)/biological pathways

GO:Molecular Function

GO:Biological Process

GO:Cellular Component

Reactome Pathway

Functional annotations

Keywords

Interpro

PROSITE

Pfam

Protein-protein interaction

Protein-miRNA interaction