GgaINT0033659 @ galGal3
Intron Retention
Gene
ENSGALG00000006039 | SNED1
Description
NA
Coordinates
chr9:5939819-5940218:+
Coord C1 exon
chr9:5939819-5939932
Coord A exon
chr9:5939933-5940104
Coord C2 exon
chr9:5940105-5940218
Length
172 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGC
5' ss Score
8.07
3' ss Seq
CTCCCTGCCCTGTGTTACAGAGG
3' ss Score
9.27
Exon sequences
Seq C1 exon
AAGAGTCACCGTGTGAGACCAAGGTGTGCCAGAACGGCGGGACGTGCCAGGTGGCAAACGGGACGGCGGTGTGCACGTGCCAGCCGGGGTACGCAGGAGGAGATTGCGAGACAG
Seq A exon
GTGGGCACTGATGAGCAGCAGGAGCCCGCCTGGCAGGGATGGAGTTGTGTCCCACTTCGGCAAGCTGCATTCCTTCCCCTTCATCCCCACCCAGCCTTATTCCTTGGTCCCCGAGGCCGTAAGTCCACGGTGCTGCGTGTGTCCAACCGGCCCTCCCTGCCCTGTGTTACAG
Seq C2 exon
AGGTGAACGAGTGCGAGTCCAGCCCCTGCCTGAACGGAGGGCACTGTGTTGACCTGGTTGACAACTACACGTGTGTGTGCCTGGAGCCCTTCGTGGGACAGCGCTGTGAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006039:ENSGALT00000009725:7
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:
PF0000822=EGF=WD(100=79.5)
A:
NA
C2:
PF0000822=EGF=WD(100=79.5)
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:
AGAGTCACCGTGTGAGACCAA
R:
CTGTCTCACAGCGCTGTCC
Band lengths:
227-399
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]