GgaINT0033661 @ galGal4
Intron Retention
Gene
ENSGALG00000006039 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr9:4397117-4397584:+
Coord C1 exon
chr9:4397117-4397242
Coord A exon
chr9:4397243-4397479
Coord C2 exon
chr9:4397480-4397584
Length
237 bp
Sequences
Splice sites
5' ss Seq
ACAGTGAGT
5' ss Score
8.34
3' ss Seq
AATCCCTCCCTCTCTTGCAGAGC
3' ss Score
11.47
Exon sequences
Seq C1 exon
GTGGCCCCCGTGTGCCCAGTGCCTGCCTCTCTAACCCCTGCCAGAACGGGGGCAGCTGCCTGGAGCTGGAGCAGGGCTATGCCTGTGACTGCCCAGAGGGCTACGCCGGGCAGGACTGCCGTGACA
Seq A exon
GTGAGTACCCAGAGTCTCTGTTGGGATGCCACCTTGCTGGGGATGCCCTACTGGAGTGCTTGTGCAACCCCAGGGAGAAGCTGCCCTTGCAGAGTTGGTTCAGGGCTCCAGGACTGAGCTGTGGTCCCTGTCTCCCAGGCAGCTGTGCCCTGGGGCTTCTGGCTGCGGGTCCTGAGCTCCCCCAGTGAGGCTGTCCTGGCACCGCAATACAAGGGGAAATCCCTCCCTCTCTTGCAG
Seq C2 exon
AGCTGACTGAGGGCTGTGAGTGTCGCAATGGTGGCAGCTGCCTGGAGGGGAATGTCACCATCTGCCAGTGCCTGCCAGGGTATTTTGGCCTGCTCTGTGAATTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006039:ENSGALT00000009725:10
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=72.1)
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:
CCCAGTGCCTGCCTCTCTAA
R:
CGAATTCACAGAGCAGGCCAA
Band lengths:
217-454
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]