RnoINT0093264 @ rn6
Intron Retention
Gene
ENSRNOG00000017539 | Mmp9
Description
matrix metallopeptidase 9 [Source:RGD Symbol;Acc:621320]
Coordinates
chr3:161417378-161417917:+
Coord C1 exon
chr3:161417378-161417663
Coord A exon
chr3:161417664-161417777
Coord C2 exon
chr3:161417778-161417917
Length
114 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGC
5' ss Score
8.19
3' ss Seq
TATATTTTCTTTCTTCTCAGTCG
3' ss Score
8.35
Exon sequences
Seq C1 exon
GTCGTGGCTCTAAACCTGACCCAAGGCCTCCAGCCACCACCGCAGCTGAACCACAGCCGACAGCTCCTCCCACTATGTGTCCCACTGCACCTCCCATGGCCTATCCCACAGGGGGCCCCACAGTCGCCCCTACAGGCGCCCCCTCACCTGGCCCCACAGGTCCCCCTACTGCTGGTCCTTCTGAGGCCCCTACAGAGTCTTCGACTCCAGTAGACAATCCTTGCAATGTGGATGTTTTTGATGCCATTGCTGATATCCAGGGCGCTCTGCATTTCTTCAAGGACGG
Seq A exon
GTGAGCAGGAAGGGTGTGTGGGTGAGAGATGGGGCTTGGAGAGGAATCTCTTTGCATCTTCCACCAACTTCCTAGGGCCAAGATTCAGGGCCATTATATTTTCTTTCTTCTCAG
Seq C2 exon
TCGGTATTGGAAGTTCTCGAATCACGGAGGAAGCCAATTGCAGGGCCCCTTTCTTATTGCCCGCACGTGGCCAGCTTTGCCTGCAAAGTTGAACTCAGCCTTTGAGGATCCGCAGTCCAAGAAGATTTTCTTCTTCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017539:ENSRNOT00000023965:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.781 A=NA C2=0.021
Domain overlap (PFAM):
C1:
PF0041319=Peptidase_M10=PD(0.1=0.0),PF048867=PT=WD(100=37.5),PF0004514=Hemopexin=PU(35.6=16.7)
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
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCTACTGCTGGTCCTTCTGA
R:
TCTTCTTGGACTGCGGATCCT
Band lengths:
248-362
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]