RnoINT0093255 @ rn6
Intron Retention
Gene
ENSRNOG00000017539 | Mmp9
Description
matrix metallopeptidase 9 [Source:RGD Symbol;Acc:621320]
Coordinates
chr3:161418168-161418524:+
Coord C1 exon
chr3:161418168-161418318
Coord A exon
chr3:161418319-161418420
Coord C2 exon
chr3:161418421-161418524
Length
102 bp
Sequences
Splice sites
5' ss Seq
GAAGTAAGC
5' ss Score
6.95
3' ss Seq
ATTTGTTCACCTTCGTGCAGATT
3' ss Score
8.09
Exon sequences
Seq C1 exon
GGCGCAAAATGTGGGTGTACACAGGCCAGTCGGTGCTGGGCCCCAGGAGTCTGGATAAGTTGGGTCTAGGCTCAGAGGTAACCCTGGTCACCGGACTTCTCCCGCGTCGTGGAGGGAAGGCTCTGCTGATCAGCCGGGAACGTATCTGGAA
Seq A exon
GTAAGCACCGCGGCCACCAGTAGGAGGAGCCCTAGCGCCACTCGCCCGCAGCCCTGGGGTGGGGAGCGAGAGGGACTCATACATTTGTTCACCTTCGTGCAG
Seq C2 exon
ATTCGACTTGAAGTCTCAGAAGGTGGATCCCCAGAGCGTTACTCGCTTGGATAACGAGTTCTCTGGCGTGCCCTGGAACTCACACAACGTCTTTCACTACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017539:ENSRNOT00000023965:11
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:
PF0004514=Hemopexin=PD(57.1=47.1)
A:
NA
C2:
PF0004514=Hemopexin=PU(12.5=13.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCGCAAAATGTGGGTGTACAC
R:
AGACGTTGTGTGAGTTCCAGG
Band lengths:
242-344
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]