RnoINT0093259 @ rn6
Intron Retention
Gene
ENSRNOG00000017539 | Mmp9
Description
matrix metallopeptidase 9 [Source:RGD Symbol;Acc:621320]
Coordinates
chr3:161415003-161415414:+
Coord C1 exon
chr3:161415003-161415131
Coord A exon
chr3:161415132-161415240
Coord C2 exon
chr3:161415241-161415414
Length
109 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGA
5' ss Score
8.72
3' ss Seq
CTCTAGCCTCCTTTCTACAGTGG
3' ss Score
5.26
Exon sequences
Seq C1 exon
AGCACGGGGACGGGTATCCCTTCGACGGCAAGGATGGTCTACTGGCACACGCCTTTCCCCCTGGCCCCGGCATTCAGGGAGATGCCCACTTCGACGACGACGAGTTGTGGTCGCTGGGCAAAGGCGCCG
Seq A exon
GTGAGATCCAGTATCCGCCCCCACGCCCCGATCCCCGAACCCTGTCCCAATTCCCTTCTCTTACACTGGCCTGTGGCCAGCCGCCCTTACTCTAGCCTCCTTTCTACAG
Seq C2 exon
TGGTCCCCACTTACTTTGGAAACGCAAATGGTGCCCCATGTCACTTTCCCTTCACCTTCGAGGGACGCTCCTATTTGTCCTGCACCACGGATGGCCGCAACGACGGCAAGCCTTGGTGTGGCACGACAGCTGACTACGACACAGACAGAAAATATGGTTTCTGCCCCAGTGAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017539:ENSRNOT00000023965:4
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(13.0=100)
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:
GCAAGGATGGTCTACTGGCAC
R:
GTGTCGTAGTCAGCTGTCGTG
Band lengths:
244-353
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]