Mmp1b (matrix metallopeptidase 1b (interstitial collagenase)) - Rat Genome Database

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Gene: Mmp1b (matrix metallopeptidase 1b (interstitial collagenase)) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Mmp1b
Name: matrix metallopeptidase 1b (interstitial collagenase)
RGD ID: 1306843
Description: Predicted to enable metalloendopeptidase activity. Predicted to be involved in collagen catabolic process and extracellular matrix organization. Predicted to be located in extracellular matrix. Human ortholog(s) of this gene implicated in several diseases, including artery disease (multiple); female reproductive organ cancer (multiple); intrinsic cardiomyopathy (multiple); obstructive lung disease (multiple); and urinary system cancer (multiple). Orthologous to human MMP1 (matrix metallopeptidase 1).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: interstitial collagenase A-like; interstitial collagenase B; interstitial collagenase B-like; LOC100910997; LOC300338; matrix metalloproteinase 1b (interstitial collagenase)
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.284,598,326 - 4,606,965 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl84,598,391 - 4,606,965 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.085,622,657 - 5,688,762 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl85,623,198 - 5,631,014 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.085,626,460 - 5,691,610 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.484,266,541 - 4,275,115 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.184,266,540 - 4,275,115 (-)NCBI
Celera86,157,657 - 6,204,041 (-)NCBICelera
Cytogenetic Map8q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in Mmp1b
6 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:15
Count of miRNA genes:14
Interacting mature miRNAs:15
Transcripts:ENSRNOT00000011884
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8124597739Rat
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125902202Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8209764047097640Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8209764047097640Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8209764047097640Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8209764047097640Rat


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

nervous system reproductive system
High
Medium
Low 6
Below cutoff 2 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000011884   ⟹   ENSRNOP00000011884
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl84,598,391 - 4,606,965 (-)Ensembl
Rnor_6.0 Ensembl85,623,198 - 5,631,014 (-)Ensembl
RefSeq Acc Id: XM_039082796   ⟹   XP_038938724
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.284,598,326 - 4,606,965 (-)NCBI
Protein Sequences
Protein RefSeqs XP_038938724 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL78536 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: ENSRNOP00000011884   ⟸   ENSRNOT00000011884
RefSeq Acc Id: XP_038938724   ⟸   XM_039082796
- UniProtKB: D3ZRZ2 (UniProtKB/TrEMBL)
Protein Domains
Peptidase metallopeptidase

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZRZ2-F1-model_v2 AlphaFold D3ZRZ2 1-409 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306843 AgrOrtholog
BioCyc Gene G2FUF-31790 BioCyc
Ensembl Genes ENSRNOG00000008881 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000011884 ENTREZGENE
  ENSRNOP00000011884.6 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000011884 ENTREZGENE
  ENSRNOT00000011884.6 UniProtKB/TrEMBL
Gene3D-CATH 2.110.10.10 UniProtKB/TrEMBL
  3.40.390.10 UniProtKB/TrEMBL
InterPro Hemopexin-like_dom_sf UniProtKB/TrEMBL
  Hemopexin/matrixin UniProtKB/TrEMBL
  Hemopexin/matrixin_CS UniProtKB/TrEMBL
  Hemopexin/matrixin_repeat UniProtKB/TrEMBL
  M10A_MMP UniProtKB/TrEMBL
  MetalloPept_cat_dom UniProtKB/TrEMBL
  Pept_M10_metallopeptidase UniProtKB/TrEMBL
  Pept_M10A_matrixin UniProtKB/TrEMBL
  Peptidase_Metallo UniProtKB/TrEMBL
  Peptidoglycan-bd-like UniProtKB/TrEMBL
  PGBD-like_sf UniProtKB/TrEMBL
NCBI Gene 300338 ENTREZGENE
PANTHER INTERSTITIAL COLLAGENASE B UniProtKB/TrEMBL
  MATRIX METALLOPROTEINASE UniProtKB/TrEMBL
Pfam Hemopexin UniProtKB/TrEMBL
  Peptidase_M10 UniProtKB/TrEMBL
  PG_binding_1 UniProtKB/TrEMBL
PhenoGen Mmp1b PhenoGen
PIRSF Peptidase_M10A_matrix UniProtKB/TrEMBL
PRINTS MATRIXIN UniProtKB/TrEMBL
PROSITE HEMOPEXIN UniProtKB/TrEMBL
  HEMOPEXIN_2 UniProtKB/TrEMBL
SMART SM00120 UniProtKB/TrEMBL
  ZnMc UniProtKB/TrEMBL
Superfamily-SCOP Hemopexin UniProtKB/TrEMBL
  Metalloproteases ('zincins'), catalytic domain UniProtKB/TrEMBL
  PGBD_like UniProtKB/TrEMBL
UniProt D3ZRZ2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Mmp1b  matrix metallopeptidase 1b (interstitial collagenase)  LOC100910997  interstitial collagenase B-like  Data Merged 737654 PROVISIONAL
2012-10-05 Mmp1b  matrix metallopeptidase 1b (interstitial collagenase)  Mmp1b  matrix metalloproteinase 1b (interstitial collagenase)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-05 LOC100910997  interstitial collagenase B-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 Mmp1b  matrix metalloproteinase 1b (interstitial collagenase)   Mmp1b_predicted  matrix metalloproteinase 1b (interstitial collagenase) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Mmp1b_predicted  matrix metalloproteinase 1b (interstitial collagenase) (predicted)      Symbol and Name status set to approved 70820 APPROVED