GgaINT1018015 @ galGal4
Intron Retention
Gene
ENSGALG00000006992 | MMP9
Description
matrix metalloproteinase-9 precursor [Source:RefSeq peptide;Acc:NP_989998]
Coordinates
chr20:10920707-10921453:+
Coord C1 exon
chr20:10920707-10920810
Coord A exon
chr20:10920811-10920953
Coord C2 exon
chr20:10920954-10921453
Length
143 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
TCTCTGCCTCCTTCTCCCAGACA
3' ss Score
10.38
Exon sequences
Seq C1 exon
GCTGGACGTGAAGGTCCAGACGGTGGACAAGGGCTACCCCCGTGACACTGATGATGTCTTTACTGGTGTCCCCCTTGACGCACGTAACGTCTTCCTGTACCAAG
Seq A exon
GTGAGCATGGGCCCACACGGCCGTGCTGTCACCCTGTGCTGCCCTCAGCCCCCACAGGCTGGGCTCCCCCATTCCTCGCCTGGGCAGCAGCTGCATCACCTCGCACTTTCCCACTAACTCACTTCTCTGCCTCCTTCTCCCAG
Seq C2 exon
ACAAGTACCACTTCTGCCGGGACAGCTTCTACTGGAGGATGACCCCACGTTACCAGGTGGACCGCGTGGGATACATCAGATACGACCTCCTGCAGTGCCCCCAGCATTAGGGGCGGAGCAGCTGCTCTGGTGCCACGCTCCTGCCTGCTGCTCCAGCCGGTCCCCCTGCAGCCCAGGAGCGCTGTGGGGCAGCCGTGGGGCAGCTGCGGGGTTGCCCCTGCCGTGCCAGGGCTTGCAGTCTCCCTGGCAGGATGGGGCGTGTGCTCCCGGCCCCCACCAGGGGCTGCCCGTCTGGGGAGCGCGACTCACGCCAGCTCTGCTGCCCGGAGACGTTTGCCCGGCGCAAACTGCACACGGATTTGTAATGACTTTATCTTCTCCTGAGCCAGTAACGCTGGGTCGGCCTCGGCGGGCAGGGACACGGGGCTCTGTGCCTCCCCCGCCTACCGCCGGCTCTGCCAGCCTTCACCTGCACCTTTGTAATAAAGACCGTCCTTTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006992:ENSGALT00000011323:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0004514=Hemopexin=PD(52.2=66.7),PF0004514=Hemopexin=PU(16.1=13.9)
A:
NA
C2:
PF0004514=Hemopexin=PD(80.6=67.6)
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:
GACGTGAAGGTCCAGACGGT
R:
AGGAGCGTGGCACCAGAG
Band lengths:
242-385
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]