MMP13 (matrix metallopeptidase 13) - Rat Genome Database

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Gene: MMP13 (matrix metallopeptidase 13) Canis lupus familiaris
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Symbol: MMP13
Name: matrix metallopeptidase 13
RGD ID: 12359367
Description: ENCODES a protein that exhibits calcium ion binding (ortholog); calcium-dependent protein binding (ortholog); fibronectin binding (ortholog); INVOLVED IN cellular response to fluid shear stress (ortholog); collagen catabolic process (ortholog); embryonic hindlimb morphogenesis (ortholog); ASSOCIATED WITH alcoholic liver cirrhosis (ortholog); anodontia (ortholog); arteriosclerosis (ortholog); FOUND IN extracellular space (ortholog); intercellular canaliculus (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: collagenase 3; matrix metallopeptidase 13 (collagenase 3); matrix metalloproteinase-13
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1528,793,568 - 28,864,832 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl528,850,522 - 28,864,121 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha528,800,013 - 28,811,179 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0528,904,844 - 28,915,995 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl528,903,544 - 28,915,284 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1528,939,682 - 28,951,055 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0528,819,585 - 28,830,954 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0528,994,055 - 29,005,429 (+)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

References
Additional References at PubMed
PMID:11943478   PMID:18039671   PMID:19291317   PMID:22301074   PMID:28554456   PMID:30032202  


Genomics

Comparative Map Data
MMP13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1528,793,568 - 28,864,832 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl528,850,522 - 28,864,121 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha528,800,013 - 28,811,179 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0528,904,844 - 28,915,995 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl528,903,544 - 28,915,284 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1528,939,682 - 28,951,055 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0528,819,585 - 28,830,954 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0528,994,055 - 29,005,429 (+)NCBIUU_Cfam_GSD_1.0
MMP13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3811102,942,995 - 102,955,732 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl11102,942,995 - 102,955,732 (-)EnsemblGRCh38hg38GRCh38
GRCh3711102,813,724 - 102,826,461 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3611102,318,934 - 102,331,672 (-)NCBINCBI36Build 36hg18NCBI36
Build 3411102,318,933 - 102,331,672NCBI
Celera1199,975,301 - 99,988,043 (-)NCBICelera
Cytogenetic Map11q22.2NCBI
HuRef1198,741,671 - 98,754,423 (-)NCBIHuRef
CHM1_111102,696,655 - 102,709,340 (-)NCBICHM1_1
T2T-CHM13v2.011102,946,765 - 102,959,501 (-)NCBIT2T-CHM13v2.0
Mmp13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3997,272,514 - 7,283,333 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl97,272,514 - 7,283,331 (+)EnsemblGRCm39 Ensembl
GRCm3897,272,514 - 7,283,333 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl97,272,514 - 7,283,331 (+)EnsemblGRCm38mm10GRCm38
MGSCv3797,272,514 - 7,283,333 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3697,272,545 - 7,283,331 (+)NCBIMGSCv36mm8
Celera94,675,357 - 4,686,177 (+)NCBICelera
Cytogenetic Map9A1NCBI
cM Map92.46NCBI
Mmp13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8812,782,829 - 12,793,108 (+)NCBIGRCr8
mRatBN7.284,497,960 - 4,508,239 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl84,497,960 - 4,508,239 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx88,457,570 - 8,467,849 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.086,755,355 - 6,765,634 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.084,757,612 - 4,767,891 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.085,522,739 - 5,533,018 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl85,522,739 - 5,533,018 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.085,527,980 - 5,538,259 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.484,158,887 - 4,169,166 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.184,158,913 - 4,169,165 (+)NCBI
Celera86,061,454 - 6,071,733 (+)NCBICelera
Cytogenetic Map8q11NCBI
Mmp13
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554126,106,994 - 6,118,760 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554126,106,994 - 6,118,760 (-)NCBIChiLan1.0ChiLan1.0
MMP13
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v29103,742,962 - 103,755,946 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan111104,831,140 - 104,844,113 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01197,890,811 - 97,902,778 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.111101,374,960 - 101,387,702 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11101,377,001 - 101,387,679 (-)Ensemblpanpan1.1panPan2
Mmp13
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494786,490,310 - 86,496,608 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365515,040,084 - 5,050,384 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365515,040,084 - 5,050,384 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MMP13
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl933,549,008 - 33,561,162 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1933,549,003 - 33,616,700 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2937,492,665 - 37,504,574 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MMP13
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1194,322,473 - 94,370,665 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl194,322,979 - 94,334,747 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604331,533,765 - 31,547,392 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Mmp13
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249182,228,688 - 2,239,852 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in MMP13
950 total Variants

Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system adipose tissue
High
Medium
Low 4 5 4 8
Below cutoff 1 4 17 3 6 3 1 2 8 10 6

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_005619857 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_022418390 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_022418391 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038475210 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038536351 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038600557 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038665089 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_536598 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AAEX04000005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF149850 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF201729 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF384859 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAHUQ010000061 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAQRD010000089 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAUVH010000371 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  LC028238 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  REHQ01000005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

RefSeq Acc Id: ENSCAFT00000023886   ⟹   ENSCAFP00000022174
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl528,850,522 - 28,864,121 (+)Ensembl
RefSeq Acc Id: ENSCAFT00845001254   ⟹   ENSCAFP00845000958
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl528,903,544 - 28,915,284 (+)Ensembl
RefSeq Acc Id: XM_038475210   ⟹   XP_038331138
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1528,939,682 - 28,951,055 (+)NCBI
RefSeq Acc Id: XM_038536351   ⟹   XP_038392279
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.0528,994,055 - 29,005,429 (+)NCBI
RefSeq Acc Id: XM_038600557   ⟹   XP_038456485
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0528,819,585 - 28,830,954 (+)NCBI
RefSeq Acc Id: XM_038665089   ⟹   XP_038521017
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0528,904,844 - 28,915,995 (+)NCBI
RefSeq Acc Id: XM_536598   ⟹   XP_536598
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1528,793,596 - 28,864,832 (+)NCBI
Dog10K_Boxer_Tasha528,800,013 - 28,811,179 (+)NCBI
Sequence:
RefSeq Acc Id: XP_536598   ⟸   XM_536598
- UniProtKB: A0A8C0K992 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000022174   ⟸   ENSCAFT00000023886
RefSeq Acc Id: XP_038331138   ⟸   XM_038475210
RefSeq Acc Id: XP_038456485   ⟸   XM_038600557
RefSeq Acc Id: XP_038521017   ⟸   XM_038665089
- UniProtKB: A0A8C0K992 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038392279   ⟸   XM_038536351
- UniProtKB: A0A8C0K992 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845000958   ⟸   ENSCAFT00845001254
Protein Domains
Peptidase metallopeptidase

Promoters
RGD ID:13683185
Promoter ID:EPDNEW_C1253
Type:single initiation site
Name:MMP13_1
Description:matrix metallopeptidase 13
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1528,853,694 - 28,853,754EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000015043 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030013444 UniProtKB/TrEMBL
  ENSCAFG00040020399 UniProtKB/TrEMBL
  ENSCAFG00845000761 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000023886.5 UniProtKB/TrEMBL
  ENSCAFT00030024884.1 UniProtKB/TrEMBL
  ENSCAFT00040037746.1 UniProtKB/TrEMBL
  ENSCAFT00845001254 ENTREZGENE
  ENSCAFT00845001254.1 UniProtKB/TrEMBL
Gene3D-CATH 2.110.10.10 UniProtKB/TrEMBL
  3.40.390.10 UniProtKB/TrEMBL
InterPro Hemopexin-like_dom UniProtKB/TrEMBL
  Hemopexin-like_dom_sf UniProtKB/TrEMBL
  Hemopexin-like_repeat UniProtKB/TrEMBL
  Hemopexin_CS UniProtKB/TrEMBL
  M10A_MMP UniProtKB/TrEMBL
  MetalloPept_cat_dom_sf UniProtKB/TrEMBL
  Pept_M10_metallopeptidase UniProtKB/TrEMBL
  Pept_M10A UniProtKB/TrEMBL
  Pept_M10A_Zn_BS UniProtKB/TrEMBL
  Peptidase_Metallo UniProtKB/TrEMBL
  Peptidoglycan-bd-like UniProtKB/TrEMBL
  PGBD-like_sf UniProtKB/TrEMBL
KEGG Report cfa:403763 UniProtKB/TrEMBL
NCBI Gene MMP13 ENTREZGENE
PANTHER MATRIX METALLOPROTEINASE UniProtKB/TrEMBL
  PTHR10201:SF165 UniProtKB/TrEMBL
Pfam Hemopexin UniProtKB/TrEMBL
  Peptidase_M10 UniProtKB/TrEMBL
  PG_binding_1 UniProtKB/TrEMBL
PIRSF Peptidase_M10A_matrix UniProtKB/TrEMBL
PRINTS MATRIXIN UniProtKB/TrEMBL
PROSITE CYSTEINE_SWITCH UniProtKB/TrEMBL
  HEMOPEXIN UniProtKB/TrEMBL
  HEMOPEXIN_2 UniProtKB/TrEMBL
SMART SM00120 UniProtKB/TrEMBL
  ZnMc UniProtKB/TrEMBL
Superfamily-SCOP Metalloproteases ('zincins'), catalytic domain UniProtKB/TrEMBL
  SSF47090 UniProtKB/TrEMBL
  SSF50923 UniProtKB/TrEMBL
UniProt A0A0C6E3R7_CANLF UniProtKB/TrEMBL
  A0A8C0K992 ENTREZGENE
  A0A8C0Z2W1_CANLF UniProtKB/TrEMBL
  A0A8I3MWY2_CANLF UniProtKB/TrEMBL
VGNC ID VGNC:43276 ENTREZGENE