GgaINT1026033 @ galGal4
Intron Retention
Gene
ENSGALG00000006039 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr9:4403498-4403871:+
Coord C1 exon
chr9:4403498-4403681
Coord A exon
chr9:4403682-4403758
Coord C2 exon
chr9:4403759-4403871
Length
77 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
TCCCCCGCCCGCCTCTGCAGGGA
3' ss Score
9.76
Exon sequences
Seq C1 exon
GACCGCGTCCGGTGGAAGGCTTTGAGATCACGAACGTGACGGCCAGCACCATCACGGTGCAATGGGCTCTCCACCGGCTCAAACACTCCACCGTCAGTAGGGTGCGTGTCTCCATCCGCCAGCCTGGGGACCTGGAAGACCGCACGGTGGAGCTGAACAGCAGCGTGGCCAAGTACACCTTCCT
Seq A exon
GTGAGTGCGGCGGGCGGGCGGTGGGACCGGCTGTGCCCACGAGCCGCCGCGCTCATGTCCCCCGCCCGCCTCTGCAG
Seq C2 exon
GGACCTGCAGCCAGGAGAGCGGTACATCGTCCATGTCACGACGCTGAGTGGCATGGGGACAGAAGATCACCCCTCGGAGAGTCTGGCCACAGCCCCCTTCCACGTGTGGACGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006039:ENSGALT00000009725:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.290 A=NA C2=0.513
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(69.8=96.8)
A:
NA
C2:
PF0004116=fn3=PD(29.1=64.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACACTCCACCGTCAGTAGGG
R:
CTCCGAGGGGTGATCTTCTGT
Band lengths:
182-259
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]