GgaINT1018013 @ galGal4
Intron Retention
Gene
ENSGALG00000006992 | MMP9
Description
matrix metalloproteinase-9 precursor [Source:RefSeq peptide;Acc:NP_989998]
Coordinates
chr20:10920241-10920623:+
Coord C1 exon
chr20:10920241-10920380
Coord A exon
chr20:10920381-10920472
Coord C2 exon
chr20:10920473-10920623
Length
92 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGC
5' ss Score
8.19
3' ss Seq
CACCCACATGTTCCACACAGGGA
3' ss Score
6.68
Exon sequences
Seq C1 exon
GAAATACTGGACCCACTCGTCCTTCTGGAAATCAGGCACTCAGGGCGCCTTCTCTATCGCTGACACCTGGCCCGGCCTCCCGGCTGTCATCGACGCGGCGTTCCAAGATGTGCTCACCAAGAGGGTCTTCTTCTTCGCGG
Seq A exon
GTGAGCCCTGCCCTGACCCGGTGTCACAGCACCATGTGTGGGGTGATGCCCGGGGCTCCCAGGGCCAGCTGACACCCACATGTTCCACACAG
Seq C2 exon
GGAGGCAGTTCTGGGTGTTCTCCGGCAAGAACGCAGTGGGTCCCCGTAGGATTGAGAAGTTGGGCATTGGGAAGGAGGCCGGGCGCATCACGGGGGCCCTGCAGCGGGGACGTGGCAAAGTGCTGCTCTTCAGTGGGGAGCACTACTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006992:ENSGALT00000011323:10
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:
PF0004514=Hemopexin=PD(62.2=58.3),PF0004514=Hemopexin=PU(40.5=35.4)
A:
NA
C2:
PF0004514=Hemopexin=PD(57.1=47.1),PF0004514=Hemopexin=PU(45.7=41.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTTCCAAGATGTGCTCACCA
R:
CTGAAGAGCAGCACTTTGCCA
Band lengths:
175-267
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]