MmuINT0099745 @ mm10
Intron Retention
Gene
ENSMUSG00000017737 | Mmp9
Description
matrix metallopeptidase 9 [Source:MGI Symbol;Acc:MGI:97011]
Coordinates
chr2:164953519-164955850:+
Coord C1 exon
chr2:164953519-164953622
Coord A exon
chr2:164953623-164954772
Coord C2 exon
chr2:164954773-164955850
Length
1150 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TGTGTTCTTGTTTCCCGTAGACA
3' ss Score
11.55
Exon sequences
Seq C1 exon
ATTCGACTTGAAGTCTCAGAAGGTGGATCCCCAGAGCGTCATTCGCGTGGATAAGGAGTTCTCTGGTGTGCCCTGGAACTCACACGACATCTTCCAGTACCAAG
Seq A exon
GTGAGGGCTGCTGAGGCTGGCCGGGAAGGGTCCCTTCGTGAAATGTCTCCCACACTGGACTCCCTCTCTTAGCGACTGGCTAGTTTCTCAGCAGGAGAGAGCAAGCCCTTGGAGATTGAAGGGAATGTTCTAGATAAGAGCCATATAGAGAGCACCCCAAGTTCACACAGCCCGGACCTAAGGTCCGGATTGCTTGCATATCATTCTTTTCCGGGAACTCCAGTAGAGAACGCAGCTCTCTAGAAGGCTCGTTCCTTGATTATTAAACAGTAGCCAAGGGCCTATAATGTGCAGGACTGCCACTAGGGATACGTGGAGAGGCAAGAAAGTGTCTTTGGGCAAGTCACTACCTCTCTTGGGGCCTCAGTTTCCCCATCTGTAAAATGTATTATCTGGAGCTCTGTTAGGCTAATTCAAAGGCTCAAACCTCCCAAATGTATTATTTTTCAGCCATCTCCTTTATACCCTTCCCTCCAACCATACCGGTAACCCAGTAACCTTTAATATATTCTTCAAGAGTGGGGAGGGTTAGGAGAGGAGGGCAGAGGTTCTGACTGTGACCCCAAACGATACGAAGGTAGAAGAAACTCACACGGCCTTGCCTGTGTGTCCAAGTTCTCGTCTCCTCCCCGTTCTCTTGACATCCTCCGTGCTCCACCGAGGCTGGCTGCTCTTTGAACAGATCAAGGTCCTCCATCCCTTAAGGTCTTCGGGCCCGTTGTCCCCTATTTGGAAGACTTCCCACTTAAACTGTCACCGGGCTGCCTCTCTTCAGGCAAAGGAGAAGATTTAATTGGGGCTGGCTTACAGGTCAGAGGCTCAGTCCATTATTTTCATGGTGGGAAACGAGGTGGCACACAGGCAAACGTGGTGTTGGAGAGGTAGCTGAGAGCTCTACCTCAGCAGCAGGCAGCAAGAAGAGAGAGACACTGGGCTTGGCGTGAACATCTGAAATCTCAAAGCCCACCCTAGTGACACAGGTCCTCCAATAAGGCCACACCCCCTCCCACCTCATAAGTGCCACTCCCTATGGGCCTATAGGGTCCATTTTCATTCAAACCACCACAGGTGCTTGTAAAAATCTTGTTCCTTTTGTCAATGATGAGGGAGCAGAGGACTCAGCTTTCTTGTGTGTTCTTGTTTCCCGTAG
Seq C2 exon
ACAAAGCCTATTTCTGCCATGGCAAATTCTTCTGGCGTGTGAGTTTCCAAAATGAGGTGAACAAGGTGGACCATGAGGTGAACCAGGTGGACGACGTGGGCTACGTGACCTACGACCTCCTGCAGTGCCCTTGAACTAGGGCTCCTTCTTTGCTTCAACCGTGCAGTGCAAGTCTCTAGAGACCACCACCACCACCACCACACACAAACCCCATCCGAGGGAAAGGTGCTAGCTGGCCAGGTACAGACTGGTGATCTCTTCTAGAGACTGGGAAGGAGTGGAGGCAGGCAGGGCTCTCTCTGCCCACCGTCCTTTCTTGTTGGACTGTTTCTAATAAACACGGATCCCCAACCTTTTCCAGCTACTTTAGTCAATCAGCTTATCTGTAGTTGCAGATGCATCCGAGCAAGAAGACAACTTTGTAGGGTGGATTCTGACCTTTTATTTTTGTGTGGCGTCTGAGAATTGAATCAGCTGGCTTTTGTGACAGGCACTTCACCGGCTAAACCACCTCTCCCGACTCCAGCCCTTTTATTTATTATGTATGAGGTTATGTTCACATGCATGTATTTAACCCACAGAATGCTTACTGTGTGTCGGGCGCGGCTCCAACCGCTGCATAAATATTAAGGTATTCAGTTGCCCCTACTGGAAGGTATTATGTAACTATTTCTCTCTTACATTGGAGAACACCACCGAGCTATCCACTCATCAAACATTTATTGAGAGCATCCCTAGGGAGCCAGGCTCTCTACTGGGCGTTAGGGACAGAAATGTTGGTTCTTCCTTCAAGGATTGCTCAGAGATTCTCCGTGTCCTGTAAATCTGCTGAAACCAGACCCCAGACTCCTCTCTCTCCCGAGAGTCCAACTCACTCACTGTGGTTGCTGGCAGCTGCAGCATGCGTATACAGCATGTGTGCTAGAGAGGTAGAGGGGGTCTGTGCGTTATGGTTCAGGTCAGACTGTGTCCTCCAGGTGAGATGACCCCTCAGCTGGAACTGATCCAGGAAGGATAACCAAGTGTCTTCCTGGCAGTCTTTTTTAAATAAATGAATAAATGAATATTTACTTATTTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000017737:ENSMUST00000017881:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0004514=Hemopexin=PU(18.9=19.4)
A:
NA
C2:
PF0004514=Hemopexin=PD(78.4=64.4)
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:
GTCTCAGAAGGTGGATCCCCA
R:
CAGTCTGTACCTGGCCAGCTA
Band lengths:
342-1492
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