MmuINT0099742 @ mm10
Intron Retention
Gene
ENSMUSG00000017737 | Mmp9
Description
matrix metallopeptidase 9 [Source:MGI Symbol;Acc:MGI:97011]
Coordinates
chr2:164948219-164949064:+
Coord C1 exon
chr2:164948219-164948397
Coord A exon
chr2:164948398-164948834
Coord C2 exon
chr2:164948835-164949064
Length
437 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGAC
5' ss Score
5.41
3' ss Seq
GCCCCTTCCTCCATCCACAGGCA
3' ss Score
11.67
Exon sequences
Seq C1 exon
TGCAAAGGCAGCGTTAGCCAGAAGCTGCGGTCCTCACCATGAGTCCCTGGCAGCCCCTGCTCCTGGCTCTCCTGGCTTTCGGCTGCAGCTCTGCTGCCCCTTACCAGCGCCAGCCGACTTTTGTGGTCTTCCCCAAAGACCTGAAAACCTCCAACCTCACGGACACCCAGCTGGCAGAG
Seq A exon
GTAGACAGATGGCTCGGTGGATAGCTGAGAAGGGCTGGTCAGGAAGATGTCCCCCTCTCCCAAGGAATGGGGCCTCAGATATGCTTTCTGGATTTGGGGGTGATGGGCATGTCTGCCAGGGTTAGGCAGTAGGGGGTAGGTGGTCTGGAGGCTCTGGGCAGATTCGGGTCTGTTGGAGGGACAGATTGGGTTCGGCTTCGAAGGGTTGTGACATGGCGCAGGTTGGCAGTGAACAGTTAAACTCTAGTGGGGCTGAGGGGTAGGCATGGTTTATATCATCTGAGGTCGAGGTGTGATGCTGTCCTCAGGATAGGGGAATTCTAGCTGTGTAGGAAGAACTGGTGTCCTGGCCGTAGAGTCCCTAAGCATGTGGCCCAGAGGTCCAGAGCCAAGGTGCCAGAACTCTGTGATGTCTCTGCCCCTTCCTCCATCCACAG
Seq C2 exon
GCATACTTGTACCGCTATGGTTACACCCGGGCCGCCCAGATGATGGGAGAGAAGCAGTCTCTACGGCCGGCTTTGCTGATGCTTCAGAAGCAGCTCTCCCTGCCCCAGACTGGTGAGCTGGACAGCCAGACACTAAAGGCCATTCGAACACCACGCTGTGGTGTCCCAGACGTGGGTCGATTCCAAACCTTCAAAGGCCTCAAGTGGGACCATCATAACATCACATACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000017737:ENSMUST00000017881:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.004
Domain overlap (PFAM):
C1:
PF0147113=PG_binding_1=PU(14.0=17.0)
A:
NA
C2:
PF0147113=PG_binding_1=PD(82.5=61.0),PF0041319=Peptidase_M10=PU(2.7=11.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCCTCACCATGAGTCCCTG
R:
AAGGTTTGGAATCGACCCACG
Band lengths:
342-779
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types