GgaINT0010378 @ galGal4
Intron Retention
Gene
ENSGALG00000006992 | MMP9
Description
matrix metalloproteinase-9 precursor [Source:RefSeq peptide;Acc:NP_989998]
Coordinates
chr20:10919885-10920380:+
Coord C1 exon
chr20:10919885-10920113
Coord A exon
chr20:10920114-10920240
Coord C2 exon
chr20:10920241-10920380
Length
127 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGC
5' ss Score
7.23
3' ss Seq
GCAGTGGTTTTTCCCTCCAGGAA
3' ss Score
9.55
Exon sequences
Seq C1 exon
GTCGTGGCTCTGGCCCTGAGCCCACTCCCCCGGCACCTTTGCCCACCGAGGAGCCCCAGTCCATACCCACCGAAGCTGGCAGTGCCTCCACCACAGAGGAGGAGGAGGAGGAGACACCTGAGCCCACAGCTGAGCCCAGCCCCGTGGACCCCAGCCGGGATGCCTGCATGGAGAAGAACTTCGACGCCATCACTGAGATCAATGGAGAGCTGCACTTCTTCAAGAATGG
Seq A exon
GTGAGCAGCAGCTCCTGGCTCATCCACAGCAAGTGCCGGGCTGATGGGCGGCAACTCTCCAGGGCTGCCAGGGGGGCACAGAGCTCCGCCTTGTCGAGGTTGTCAGGGCAGTGGTTTTTCCCTCCAG
Seq C2 exon
GAAATACTGGACCCACTCGTCCTTCTGGAAATCAGGCACTCAGGGCGCCTTCTCTATCGCTGACACCTGGCCCGGCCTCCCGGCTGTCATCGACGCGGCGTTCCAAGATGTGCTCACCAAGAGGGTCTTCTTCTTCGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006992:ENSGALT00000011323:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.740 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0041319=Peptidase_M10=PD(0.1=0.0),PF0004514=Hemopexin=PU(35.6=20.8)
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
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGAGGAGGAGGAGGAGGAGA
R:
TGGTGAGCACATCTTGGAACG
Band lengths:
255-382
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]