GgaINT0010370 @ galGal3
Intron Retention
Gene
ENSGALG00000006992 | MMP9
Description
NA
Coordinates
chr20:10528554-10529123:+
Coord C1 exon
chr20:10528554-10528690
Coord A exon
chr20:10528691-10528884
Coord C2 exon
chr20:10528885-10529123
Length
194 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
CGGCTGCCTTTCCTCCCCAGAAC
3' ss Score
10.6
Exon sequences
Seq C1 exon
TGGGGCTGCTCCTGGCCCCGCTCACCCTGGCACTGCTGGCTCTCTGCCGCGCCGCCCCACTGCACAGCAAGCCGCAGGCGGTCATCACCTTCCCAGGGGAGCTGCTCAGCGCCCCATCAAACATGGAGCTGGCAGAG
Seq A exon
GTGAGGGCAGTGTGGCCCCAGTGCGGCCCCTTTCCACCGCCCGGCCCCACAGACTTCGTGGGGCTGCAGGCTGGGCTGGGGGCTGCCATCCACCTGGAGGTGCAAGGGCTGGGACCCAGCGGGGATGCAGTGTGGGGAGCTGCCCCTGAGCCCTCTTGCCTCGNTGAGCCCCTCCGGCTGCCTTTCCTCCCCAG
Seq C2 exon
AACTACCTGCTGCGCTTCGGCTACATCCAGGAGGCAGAGGTGAGGAGGAGCAGCAAGCACGTGTCCCTGGCCAAAGCGCTGCGCAGGATGCAGAAGCAGCTGGGGCTGGAGGAGACGGGGGAGCTGGACGCCAGCACCCTGGAGGCCATGCGAGCCCCCCGCTGTGGGGTGCCTGACGTGGGGGGTTTCCTCACCTTCGAGGGGGAGCTCAAATGGGACCACATGGACCTCACGTACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006992:ENSGALT00000039117:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0147113=PG_binding_1=PU(12.1=17.1)
A:
NA
C2:
PF0147113=PG_binding_1=PD(84.5=61.2),PF0041319=Peptidase_M10=PU(2.7=11.2)
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:
TCAAACATGGAGCTGGCAGAG
R:
TGAGGTCCATGTGGTCCCATT
Band lengths:
253-447
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]