GgaINT1018014 @ galGal4
Intron Retention
Gene
ENSGALG00000006992 | MMP9
Description
matrix metalloproteinase-9 precursor [Source:RefSeq peptide;Acc:NP_989998]
Coordinates
chr20:10920473-10920810:+
Coord C1 exon
chr20:10920473-10920623
Coord A exon
chr20:10920624-10920706
Coord C2 exon
chr20:10920707-10920810
Length
83 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
GCGCTTCGCTTTCCCTGCAGGCT
3' ss Score
10.79
Exon sequences
Seq C1 exon
GGAGGCAGTTCTGGGTGTTCTCCGGCAAGAACGCAGTGGGTCCCCGTAGGATTGAGAAGTTGGGCATTGGGAAGGAGGCCGGGCGCATCACGGGGGCCCTGCAGCGGGGACGTGGCAAAGTGCTGCTCTTCAGTGGGGAGCACTACTGGAG
Seq A exon
GTGAGTGGCTCAGGCCAGCAGCCCTGGCACCGTGCTGCAGCAGGTGACTCAATGCAGTCCTGGGCGCTTCGCTTTCCCTGCAG
Seq C2 exon
GCTGGACGTGAAGGTCCAGACGGTGGACAAGGGCTACCCCCGTGACACTGATGATGTCTTTACTGGTGTCCCCCTTGACGCACGTAACGTCTTCCTGTACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006992:ENSGALT00000011323:11
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(57.1=47.1),PF0004514=Hemopexin=PU(45.7=41.2)
A:
NA
C2:
PF0004514=Hemopexin=PD(52.2=66.7),PF0004514=Hemopexin=PU(16.1=13.9)
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:
AAGTTGGGCATTGGGAAGGAG
R:
AGGGGGACACCAGTAAAGACA
Band lengths:
170-253
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]