GgaINT0010378 @ galGal3
Intron Retention
Gene
ENSGALG00000006992 | MMP9
Description
NA
Coordinates
chr20:10531742-10532206:+
Coord C1 exon
chr20:10531742-10531970
Coord A exon
chr20:10531971-10532097
Coord C2 exon
chr20:10532098-10532206
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
GAAATACTGGACCCACTCGTCCTTCTGGAAATCAGGCACTCAGGGCGCCTTCTCTATCGCTGACACCTGGCCCGGCCTCCCGGCTGTCATCGACGCGGCGTTCCAAGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006992:ENSGALT00000039117:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.805 A=NA C2=0.324
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=75.7)
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:
AGTCCATACCCACCGAAGCTG
R:
GCCAGGTGTCAGCGATAGAGA
Band lengths:
243-370
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]