MmuINT0099749 @ mm10
Intron Retention
Gene
ENSMUSG00000017737 | Mmp9
Description
matrix metallopeptidase 9 [Source:MGI Symbol;Acc:MGI:97011]
Coordinates
chr2:164949947-164950474:+
Coord C1 exon
chr2:164949947-164950120
Coord A exon
chr2:164950121-164950300
Coord C2 exon
chr2:164950301-164950474
Length
180 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
AATACCGTGGGTCTCCTCAGGAC
3' ss Score
6.63
Exon sequences
Seq C1 exon
TGATCCCCACTTACTATGGAAACTCAAATGGTGCCCCATGTCACTTTCCCTTCACCTTCGAGGGACGCTCCTATTCGGCCTGCACCACAGACGGCCGCAACGACGGCACGCCTTGGTGTAGCACAACAGCTGACTACGATAAGGACGGCAAATTTGGTTTCTGCCCTAGTGAGA
Seq A exon
GTGAGTATGCGCTGGGGGTGGGGAGCGGGGCGCCGCCTTGAAGGTTCCAGAATCTTCTTTCCCAGTCTCTCTTTGCCATCAGTGGTGTGGCTACTCGCCCTCTCCCTGGGTCTGGTCCCCTCTGTGAAATGAGACGCATGCTGGGGCCGGGCTTGGCGGTAATACCGTGGGTCTCCTCAG
Seq C2 exon
GACTCTACACGGAGCACGGCAACGGAGAAGGCAAACCCTGTGTGTTCCCGTTCATCTTTGAGGGCCGCTCCTACTCTGCCTGCACCACTAAAGGCCGCTCGGATGGTTACCGCTGGTGCGCCACCACAGCCAACTATGACCAGGATAAACTGTATGGCTTCTGCCCTACCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000017737:ENSMUST00000017881:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0041319=Peptidase_M10=FE(17.6=100),PF0004014=fn2=WD(100=71.2)
A:
NA
C2:
PF0041319=Peptidase_M10=FE(17.6=100),PF0004014=fn2=WD(100=71.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGAAACTCAAATGGTGCCCC
R:
CCTTTAGTGGTGCAGGCAGAG
Band lengths:
252-432
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