GgaINT0033676 @ galGal3
Intron Retention
Gene
ENSGALG00000006039 | SNED1
Description
NA
Coordinates
chr9:5953279-5953771:+
Coord C1 exon
chr9:5953279-5953372
Coord A exon
chr9:5953373-5953492
Coord C2 exon
chr9:5953493-5953771
Length
120 bp
Sequences
Splice sites
5' ss Seq
CGAGTGAGT
5' ss Score
8.49
3' ss Seq
TCCTCTCCCTCTTTTTCCAGGGC
3' ss Score
12.81
Exon sequences
Seq C1 exon
CGGTACATCGTCCATGTCACGACGCTGAGTGGCATGGGGACAGAAGATCACCCCTCGGAGAGTCTGGCCACAGCCCCCTTCCACGTGTGGACGA
Seq A exon
GTGAGTGGGGCTGCATGGTGCTGGCTGGCAGGGCTGTTGCTGGGCTGGGGGCGAGCTCCTGAGAGGCTCGAGGCTGGACGCTGGCGCTGATCCTTTTCTCTCCTCTCCCTCTTTTTCCAG
Seq C2 exon
GGCCTCTCCCCCCTCGCAACCTCACAGCCTCCCGCGTCACCCCCACCTCTGTGTCCGTGACGTGGGAGCAGCCACCCACTGGTGCCGTGGAGGGGTACATCATCAACGTCACCACTGCGCAGAGCGTCAAGAGCCGCTACGTGCCCAACGGGAAGCTGGCGTCCTACACCGTGCGGGACCTGCTGCCCGCACAGCGCTACCGCCTGTCTGTGACAGCTGTGCAGAACACAGAGCAGGGGCAGGTGCACAGCGAGCCCATCCACCTCTACGTCACCACCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006039:ENSGALT00000009725:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.438 A=NA C2=0.330
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(20.9=56.2)
A:
NA
C2:
PF0004116=fn3=WD(100=86.2)
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:
CGGTACATCGTCCATGTCACG
R:
CAGCTTCCCGTTGGGCAC
Band lengths:
252-372
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]