MmuINT0099743 @ mm10
Intron Retention
Gene
ENSMUSG00000017737 | Mmp9
Description
matrix metallopeptidase 9 [Source:MGI Symbol;Acc:MGI:97011]
Coordinates
chr2:164952855-164953414:+
Coord C1 exon
chr2:164952855-164952994
Coord A exon
chr2:164952995-164953263
Coord C2 exon
chr2:164953264-164953414
Length
269 bp
Sequences
Splice sites
5' ss Seq
CTGGTTAGT
5' ss Score
6.32
3' ss Seq
CTGACCCTTCTCTTCCGCAGGAC
3' ss Score
11.85
Exon sequences
Seq C1 exon
TTGGTACTGGAAGTTCCTGAATCATAGAGGAAGCCCATTACAGGGCCCCTTCCTTACTGCCCGCACGTGGCCAGCCCTGCCTGCAACGCTGGACTCCGCCTTTGAGGATCCGCAGACCAAGAGGGTTTTCTTCTTCTCTG
Seq A exon
GTTAGTTTGTGCCCCTCTAGCTCATCGATCCCTCAGTATCCGTCAGCTTAGGACAGACACCTAGTGTAACCCGTGAAACTGCGACTCCAAAAGAGCGCCCCTGCCCAGCTGATAAGATTTGACATTGGGGGGACGGACGGACGGACGGACGGTACTGAATTGCAATTCCCCTTGAGTAGCTCTGATACTTAGCTTCTCTGGCTCCTGCCTCCTGCCCTTCAAAGAGACTGTGCCACACCTTAGTGTCTACTGACCCTTCTCTTCCGCAG
Seq C2 exon
GACGTCAAATGTGGGTGTACACAGGCAAGACCGTGCTGGGCCCCAGGAGTCTGGATAAGTTGGGTCTAGGCCCAGAGGTAACCCACGTCAGCGGGCTTCTCCCGCGTCGTCTCGGGAAGGCTCTGCTGTTCAGCAAGGGGCGTGTCTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000017737:ENSMUST00000017881:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.083 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0004514=Hemopexin=PD(62.2=58.3),PF0004514=Hemopexin=PU(40.5=35.4)
A:
NA
C2:
PF0004514=Hemopexin=PD(57.1=47.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGTACTGGAAGTTCCTGAATCA
R:
GACACGCCCCTTGCTGAAC
Band lengths:
285-554
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