GgaINT1026034 @ galGal4
Intron Retention
Gene
ENSGALG00000006039 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr9:4404511-4404952:+
Coord C1 exon
chr9:4404511-4404655
Coord A exon
chr9:4404656-4404869
Coord C2 exon
chr9:4404870-4404952
Length
214 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGC
5' ss Score
9.88
3' ss Seq
TCACAGCTGTGCTCCCCCAGGTT
3' ss Score
7.44
Exon sequences
Seq C1 exon
TGCAGAAGGATGGGGCTCCGGAGAGGCGCTGGAGCCAGGCTGGCCATCCCCGTGTCCTGCGCAACAGGCTGCCCCCGGCCTTCCTGCCCGAGCTCCGCTTGCTTGCAGACCATGACACAGCTGAAGAGCCCTCGCCAGCCCCCAG
Seq A exon
GTAGGCACCGGCAGGCTGAGCGCAGCCCCTTCCCCCAGCTCTAGGCAAGCCTAGCTCCAGCTGGGCTGTGCCCCTTGCCCGCCCCAGCCTCACTCTGTGAGCTACCTGCAGCACTTGCACTGTGCCACATACCACCTGCAAGCACTTCACTCAGGCTGTCTCCAGCCTTGAGGATCCTGCCCTGTCCCACACCCTCACAGCTGTGCTCCCCCAG
Seq C2 exon
GTTCACTGAGCTGGTGGATGGCAGAAGGAGGATCAGTGCCAGGTTCGGCACTTTGCCAAGCAAATCCATCACCGTGAAGACAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006039:ENSGALT00000009725:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.653 A=NA C2=0.379
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
TGCAGAAGGATGGGGCTCC
R:
GTGTCTTCACGGTGATGGATT
Band lengths:
228-442
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]