GgaINT0010375 @ galGal4
Intron Retention
Gene
ENSGALG00000006992 | MMP9
Description
matrix metalloproteinase-9 precursor [Source:RefSeq peptide;Acc:NP_989998]
Coordinates
chr20:10919036-10919498:+
Coord C1 exon
chr20:10919036-10919209
Coord A exon
chr20:10919210-10919324
Coord C2 exon
chr20:10919325-10919498
Length
115 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
CTACTGTTGCTGTGCTGCAGACA
3' ss Score
7.94
Exon sequences
Seq C1 exon
TGCTCTACACCAATGGTGGCAACAGCGATGGGTCTCCCTGCGTCTTCCCCTTCATCTTCGATGGCGCCTCCTATGACACCTGCACCACAGATGGGCGCTCTGACGGCTATCGCTGGTGTGCCACCACGGCCAACTTCGACCAGGACAAGAAATACGGCTTCTGCCCCAACCGAG
Seq A exon
GTGAGAGTGGGGTGGGTGGTGGGGGCCCTGTGGGGTGTGGGGCTGGCGGGGTCCCAGCCGTGGTGCAGGGCGGGCGCAAAGGCATAGCGACAACCCTACTGTTGCTGTGCTGCAG
Seq C2 exon
ACACGGCGGTGATCGGTGGCAACTCCCAAGGGGATCCGTGTGTCTTCCCCTTCACCTTCCTGGGGCAGTCCTACAGCGCGTGCACCAGCCAGGGCCGGCAGGACGGGAAGCTCTGGTGTGCCACCACCAGCAACTATGACACCGACAAGAAGTGGGGCTTCTGCCCAGACAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006992:ENSGALT00000011323:6
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
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCTATGACACCTGCACCACA
R:
CGGTGTCATAGTTGCTGGTGG
Band lengths:
250-365
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]