GgaINT0010370 @ galGal4
Intron Retention
Gene
ENSGALG00000006992 | MMP9
Description
matrix metalloproteinase-9 precursor [Source:RefSeq peptide;Acc:NP_989998]
Coordinates
chr20:10917368-10917932:+
Coord C1 exon
chr20:10917368-10917499
Coord A exon
chr20:10917500-10917693
Coord C2 exon
chr20:10917694-10917932
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
CTGCTCCTGGCCCCGCTCACCCTGGCACTGCTGGCTCTCTGCCGCGCCGCCCCACTGCACAGCAAGCCGCAGGCGGTCATCACCTTCCCAGGGGAGCTGCTCAGCGCCCCATCAGACATGGAGCTGGCAGAG
Seq A exon
GTGAGGGCAGTGTGGCCCCAGTGCGGCCCCTTTCCACCGCCCGGCCCCACAGACTTCGTGGGGCTGCAGGCTGGGCTGGGGGCTGCCATCCACCTGGAGGTGCAAGGGCTGGGACCCAGCGGGGATGCAGTGTGGGGAGCTGCCCCTGAGCCCTCTTGCCTCGCTGAGCCCCTCCGGCTGCCTTTCCTCCCCAG
Seq C2 exon
AACTACCTGCTGCGCTTCGGCTACATCCAGGAGGCAGAGGTGAGGAGGAGCAGCAAGCACGTGTCCCTGGCCAAAGCGCTGCGCAGGATGCAGAAGCAGCTGGGGCTGGAGGAGACGGGGGAGCTGGACGCCAGCACCCTGGAGGCCATGCGAGCCCCCCGCTGTGGGGTGCCTGACGTGGGGGGTTTCCTCACCTTCGAGGGGGAGCTCAAATGGGACCACATGGACCTCACGTACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006992:ENSGALT00000011323:1
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=15.9)
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
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATCAGACATGGAGCTGGCAG
R:
TGAGGTCCATGTGGTCCCATT
Band lengths:
255-449
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]