GgaINT0033665 @ galGal3
Intron Retention
Gene
ENSGALG00000006039 | SNED1
Description
NA
Coordinates
chr9:5941854-5942170:+
Coord C1 exon
chr9:5941854-5941970
Coord A exon
chr9:5941971-5942043
Coord C2 exon
chr9:5942044-5942170
Length
73 bp
Sequences
Splice sites
5' ss Seq
TAGGTACGG
5' ss Score
7.82
3' ss Seq
TCAGCTTCCGCTGCCCCCAGGTA
3' ss Score
9.41
Exon sequences
Seq C1 exon
CCCGGCCACGGCTCTGCAGCACGGCGCCGTGCCGCAACGGGGGCACATGCAAGGAGGCCGACGGCGAGTACCACTGCGCCTGCCCCTACCGCTTCACCGGCCGCCACTGCGAGATAG
Seq A exon
GTACGGCCCCGGCCTGGCGAGGGGAGGCGGGCGGTGTGTGTGCTTCTCCAGACTCAGCTTCCGCTGCCCCCAG
Seq C2 exon
GTAAACCGGACCCCTGTGCCTCAGGGCCCTGCCAGAACGGGGGCACCTGCTTCCACTACATCGGCAAGTACAAGTGTGACTGTGCCCCGGGCTACGCTGGACGGCACTGCGAGATCGGNACGTGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006039:ENSGALT00000009725:13
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=77.5)
A:
NA
C2:
PF0000822=EGF=WD(100=72.1)
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:
AACGGGGGCACATGCAAG
R:
GGGGCACAGTCACACTTGTAC
Band lengths:
170-243
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]