GgaINT0033668 @ galGal3
Intron Retention
Gene
ENSGALG00000006039 | SNED1
Description
NA
Coordinates
chr9:5942959-5943310:+
Coord C1 exon
chr9:5942959-5943070
Coord A exon
chr9:5943071-5943196
Coord C2 exon
chr9:5943197-5943310
Length
126 bp
Sequences
Splice sites
5' ss Seq
ACGGTAGGC
5' ss Score
8.81
3' ss Seq
CCCTGCCCAAACTCTTGCAGAGA
3' ss Score
7.84
Exon sequences
Seq C1 exon
GTGGGCTCGCTGGCCAAATACCACTGTGAGCTGGGCTACGTCCTCAGCCAGCACAACAGCCCCCGCGTCTGCCGCTCGCAGGGTGTCTGGAGCGACCCCCCTGAATGTGACG
Seq A exon
GTAGGCAGTGTCAGGAAGTGGCTGAGCCCTGGCCCTGGCTTGAGGCTGTGTCGCTGCTGCATGTGTCCGCGGGACCCTGGTGCTCACTGCTTTCACCTTATCTCCCCCCTGCCCAAACTCTTGCAG
Seq C2 exon
AGATTGATGAGTGCCGGTCTCAGCCCTGCCTGAACGGTGGCCAATGCAAAGACCGCATCGCCGAGTTCCTGTGCGTGTGCGAGCCGGGATACACGGGCCTCCACTGTGAGTTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006039:ENSGALT00000009725:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0000822=EGF=WD(100=79.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGGCCAAATACCACTGTGA
R:
CCAACTCACAGTGGAGGCC
Band lengths:
218-344
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]