MmuINT0099753 @ mm10
Intron Retention
Gene
ENSMUSG00000017737 | Mmp9
Description
matrix metallopeptidase 9 [Source:MGI Symbol;Acc:MGI:97011]
Coordinates
chr2:164952420-164952994:+
Coord C1 exon
chr2:164952420-164952753
Coord A exon
chr2:164952754-164952854
Coord C2 exon
chr2:164952855-164952994
Length
101 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGC
5' ss Score
9.14
3' ss Seq
GATATTTCCTTTCTTCTCAGTTG
3' ss Score
7.88
Exon sequences
Seq C1 exon
GTCGTGGCTCTAAGCCTGACCCAAGGCCTCCAGCCACCACCACAACTGAACCACAGCCGACAGCACCTCCCACTATGTGTCCCACTATACCTCCCACGGCCTATCCCACAGTGGGCCCCACGGTTGGCCCTACAGGCGCCCCCTCACCTGGCCCCACAAGCAGCCCGTCACCTGGCCCTACAGGCGCCCCCTCACCTGGCCCTACAGCGCCCCCTACTGCGGGCTCTTCTGAGGCCTCTACAGAGTCTTTGAGTCCGGCAGACAATCCTTGCAATGTGGATGTTTTTGATGCTATTGCTGAGATCCAGGGCGCTCTGCATTTCTTCAAGGACGG
Seq A exon
GTAAGCAGGGAGGGTGTGTGGGTGAGAGAGGGGGTTTGGAGAGGATCCTGCTTGCGTCTTCCACCAACTTTCTCGGGCCCTGATATTTCCTTTCTTCTCAG
Seq C2 exon
TTGGTACTGGAAGTTCCTGAATCATAGAGGAAGCCCATTACAGGGCCCCTTCCTTACTGCCCGCACGTGGCCAGCCCTGCCTGCAACGCTGGACTCCGCCTTTGAGGATCCGCAGACCAAGAGGGTTTTCTTCTTCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000017737:ENSMUST00000017881:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.821 A=NA C2=0.083
Domain overlap (PFAM):
C1:
PF0041319=Peptidase_M10=PD(0.1=0.0),PF048867=PT=WD(100=30.4),PF048867=PT=WD(100=27.7),PF0004514=Hemopexin=PU(35.6=14.3)
A:
NA
C2:
PF0004514=Hemopexin=PD(62.2=58.3),PF0004514=Hemopexin=PU(40.5=35.4)
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:
CTACTGCGGGCTCTTCTGAGG
R:
TCTTGGTCTGCGGATCCTCAA
Band lengths:
243-344
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