GgaINT1026036 @ galGal4
Intron Retention
Gene
ENSGALG00000006039 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr9:4405407-4405700:+
Coord C1 exon
chr9:4405407-4405493
Coord A exon
chr9:4405494-4405583
Coord C2 exon
chr9:4405584-4405700
Length
90 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
GCAGTGCACGTTTTTTCCAGGCA
3' ss Score
5.86
Exon sequences
Seq C1 exon
AGCCAGAGGCTCCCGTGAGGCTGGAGAACAGCGAGGAGCCCAGCCGGAGCAGTCTGGCACTGCAGCTGCGAGAGGCATGGAGCAAAA
Seq A exon
GTGAGTCTGGGGTGGCAGGGAGCTGGCGCTGTGGATGTACACAGCTTTGCCAGGGCCCCAGAGCCTGACAGCAGTGCACGTTTTTTCCAG
Seq C2 exon
GCATCAGGCAGAACTGCTCCACAAACCCCTGCAAGAATGGAGGCACCTGTGTAAGCGAGAGCGAATCCTACCATTGCGACTGCATCCCGGGCTTCAAGGGCAGGCACTGTGAGCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006039:ENSGALT00000009725:28
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.500 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0000822=EGF=WD(100=77.5),PF055076=MAGP=PU(31.2=62.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCAGAGGCTCCCGTGAG
R:
AGTCGCAATGGTAGGATTCGC
Band lengths:
167-257
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]