GgaINT0033677 @ galGal4
Intron Retention
Gene
ENSGALG00000006039 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr9:4403992-4404655:+
Coord C1 exon
chr9:4403992-4404270
Coord A exon
chr9:4404271-4404510
Coord C2 exon
chr9:4404511-4404655
Length
240 bp
Sequences
Splice sites
5' ss Seq
CCCGTGAGT
5' ss Score
8.4
3' ss Seq
TAACTCTTTGTGGTCTGCAGTGC
3' ss Score
6.77
Exon sequences
Seq C1 exon
GGCCTCTCCCCCCTCGCAACCTCACAGCCTCCCGCGTCACCCCCACCTCTGTGTCCGTGACGTGGGAGCAGCCACCCACTGGTGCCGTGGAGGGGTACATCATCAACGTCACCACTGCGCAGAGCGTCAAGAGCCGCTACGTGCCCAACGGGAAGCTGGCGTCCTACACCGTGCGGGACCTGCTGCCCGCACAGCGCTACCGCCTGTCTGTGACAGCTGTGCAGAACACAGAGCAGGGGCAGGTGCACAGCGAGCCCATCCACCTCTACGTCACCACCC
Seq A exon
GTGAGTGCCCATCTTTGCCCCCAACGCAGGTGCCTGGGTATGGGATGGGTGCCCCATCGCTGGGAGCCAGCAGGGGGGTCGGTGCGGAATTGCGGCTCGGTGATCCGCTGTTGGGGAAAGGAGCAGCGCACGGCCCAGGTGGCATCGTGTTTCCTTAGCTCTAAATGGCACCCCGGGGACCCCTCACTGCACTGACTGGCTGCCTGCCTCTCTCTAAGCCTAACTCTTTGTGGTCTGCAG
Seq C2 exon
TGCAGAAGGATGGGGCTCCGGAGAGGCGCTGGAGCCAGGCTGGCCATCCCCGTGTCCTGCGCAACAGGCTGCCCCCGGCCTTCCTGCCCGAGCTCCGCTTGCTTGCAGACCATGACACAGCTGAAGAGCCCTCGCCAGCCCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006039:ENSGALT00000009725:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.372 A=NA C2=0.653
Domain overlap (PFAM):
C1:
PF0004116=fn3=WD(100=86.2)
A:
NA
C2:
NO
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:
ATCATCAACGTCACCACTGCG
R:
AGCTGTGTCATGGTCTGCAAG
Band lengths:
303-543
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]