GgaINT0010377 @ galGal3
Intron Retention
Gene
ENSGALG00000006992 | MMP9
Description
NA
Coordinates
chr20:10531447-10531970:+
Coord C1 exon
chr20:10531447-10531602
Coord A exon
chr20:10531603-10531741
Coord C2 exon
chr20:10531742-10531970
Length
139 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGC
5' ss Score
8.27
3' ss Seq
GCCCCCTCCTGCCCACTCAGGTC
3' ss Score
8.93
Exon sequences
Seq C1 exon
GTTACAGCATCTTCTTGGTGGCTGCCCACGAGTTTGGGCACTCACTGGGGCTGGACCACTCCAGCGTGCGCGAGGCATTGATGTACCCTATGTACAGCTACGTCCAGGACTTCCAGCTGCACGAGGATGATGTCCAGGGCATCCAGTACCTCTATG
Seq A exon
GTGAGCGGTCCCTCTGTAGCTGGCACACCACGGTGGCGCGGTGCCGTGGGGCACCCGGCTGGCAACGCCCTGGGTATGTTCCTGGGACGGGTCTTGCAAGGTGCTCTCTGCAACCTCACGCCCCCTCCTGCCCACTCAG
Seq C2 exon
GTCGTGGCTCTGGCCCTGAGCCCACTCCCCCGGCACCTTTGCCCACCGAGGAGCCCCAGTCCATACCCACCGAAGCTGGCAGTGCCTCCACCACAGAGGAGGAGGAGGAGGAGACACCTGAGCCCACAGCTGAGCCCAGCCCCGTGGACCCCAGCCGGGATGCCTGCATGGAGAAGAACTTCGACGCCATCACTGAGATCAATGGAGAGCTGCACTTCTTCAAGAATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006992:ENSGALT00000039117:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.094 A=NA C2=0.805
Domain overlap (PFAM):
C1:
PF0041319=Peptidase_M10=FE(15.8=100)
A:
NA
C2:
PF0041319=Peptidase_M10=PD(0.1=0.0),PF0004514=Hemopexin=PU(35.6=20.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTACGTCCAGGACTTCCAGCT
R:
CAGTGATGGCGTCGAAGTTCT
Band lengths:
254-393
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]