RnoINT0093260 @ rn6
Intron Retention
Gene
ENSRNOG00000017539 | Mmp9
Description
matrix metallopeptidase 9 [Source:RGD Symbol;Acc:621320]
Coordinates
chr3:161415241-161415762:+
Coord C1 exon
chr3:161415241-161415414
Coord A exon
chr3:161415415-161415588
Coord C2 exon
chr3:161415589-161415762
Length
174 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
TAATAATTGGGTCTCCTCAGATC
3' ss Score
6.57
Exon sequences
Seq C1 exon
TGGTCCCCACTTACTTTGGAAACGCAAATGGTGCCCCATGTCACTTTCCCTTCACCTTCGAGGGACGCTCCTATTTGTCCTGCACCACGGATGGCCGCAACGACGGCAAGCCTTGGTGTGGCACGACAGCTGACTACGACACAGACAGAAAATATGGTTTCTGCCCCAGTGAGA
Seq A exon
GTGAGTATGCACTGGGGGTAGAGAGCGGGGCGCGTCCAGAATCTTCGTTTCCAATCCCTCTGTGCCATTAATGGTATGGTCAGGCTACTCTCCCTATCGCTGGGTCCAGTCTCCTCTGTGAAATGAGAAACGTGCCTGGGGCCAGGCTTGGGAGTAATAATTGGGTCTCCTCAG
Seq C2 exon
ATCTCTACACGGAGCATGGCAACGGAGACGGCAAACCCTGCGTATTTCCATTCATCTTCGAGGGCCACTCCTACTCTGCCTGCACCACTAAAGGTCGCTCGGATGGTTATCGCTGGTGCGCCACCACCGCCAACTATGACCAGGATAAGCTGTATGGCTTCTGTCCTACTCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017539:ENSRNOT00000023965:5
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
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGACGCTCCTATTTGTCCTGC
R:
ATCCTGGTCATAGTTGGCGGT
Band lengths:
258-432
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]