GgaINT0010374 @ galGal3
Intron Retention
Gene
ENSGALG00000006992 | MMP9
Description
NA
Coordinates
chr20:10530647-10531066:+
Coord C1 exon
chr20:10530647-10530820
Coord A exon
chr20:10530821-10530892
Coord C2 exon
chr20:10530893-10531066
Length
72 bp
Sequences
Splice sites
5' ss Seq
AGCGTGAGT
5' ss Score
8.2
3' ss Seq
CACCCCTTCTCCCCCTGCAGTGC
3' ss Score
10.62
Exon sequences
Seq C1 exon
AGGTGAAGACCCGCTATGGGAATGCCAACGGGGCCAGCTGCCACTTCCCCTTCATCTTTGAGGGCCGCTCCTACTCCCGGTGCATCACGGAGGGCCGCACGGATGGGATGCTGTGGTGTGCCACCACCGCCAGCTACGATGCCGACAAGACCTACGGCTTCTGCCCCAGCGAGC
Seq A exon
GTGAGTAGCACCGGCTGGAGGCTGCGCAGCCCTGTGGGACTGGGGCCGTTCTCACCCCTTCTCCCCCTGCAG
Seq C2 exon
TGCTCTACACCAATGGTGGCAACAGCGATGGGTCTCCCTGCGTCTTCCCCTTCATCTTCGATGGCGCCTCCTATGACACCTGCACCACAGATGGGCGCTCTGACGGCTATCGCTGGTGTGCCACCACGGCCAACTTCGACCAGGACAAGAAATACGGCTTCTGCCCCAACCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006992:ENSGALT00000039117:5
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:
PF0041319=Peptidase_M10=FE(17.6=100),PF0004014=fn2=WD(100=71.2)
A:
NA
C2:
PF0041319=Peptidase_M10=FE(17.6=100),PF0004014=fn2=WD(100=71.2)
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:
GACAAGACCTACGGCTTCTGC
R:
CTTGTCCTGGTCGAAGTTGGC
Band lengths:
180-252
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]