RnoINT0140933 @ rn6
Intron Retention
Gene
ENSRNOG00000023548 | Sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:RGD Symbol;Acc:1566079]
Coordinates
chr9:100421066-100421596:+
Coord C1 exon
chr9:100421066-100421179
Coord A exon
chr9:100421180-100421482
Coord C2 exon
chr9:100421483-100421596
Length
303 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
ACCCTTTGGGTGTTCTCCAGAGG
3' ss Score
7.62
Exon sequences
Seq C1 exon
AGACAGACGAGTGCCAAGCACAGCCCTGCAGAAATGGAGGCTCCTGCAGGGACCTCCCCGGGGCTTTCATCTGCCAGTGCCCTGAAGGTTTTGTTGGAACCCACTGTGAAACAG
Seq A exon
GTAGGGTTCTTTCAGGAGGGTCCCACAGAACCAGGGCTGCTGGGAGATCAGAGGGGAAGCCAGGAGCCATCCTCTTGCTGGACAAGCCACCCAGAGAGAGAAACCCCCAAGGCTGTGGTGACCTGGAGGGAGGAAGGAAACTGGGCGGGGGGTCCCTGAGAGCCCCTCCTACCCACAGGTGTGCCATACCCCTCTCCTGGCCATTGCTCCTTGCCTCCCCCTATCCCGTCTTCCCGCTGTCCTCTCCTCCCTCCCCCAGAGTCCCTCCCTGCAGCTCGGGCCAACCCTTTGGGTGTTCTCCAG
Seq C2 exon
AGGTGGATGCCTGTGCCTCCAGCCCCTGCCAGCACGGAGGCCGGTGTGAGGACGGTGGTGGGGCCTACCTGTGCGTGTGTCCAGAGGGCTTCTTCGGCTACAACTGTGAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023548:ENSRNOT00000022290:18
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:
PF0000822=EGF=WD(100=79.5)
A:
NA
C2:
PF0000822=EGF=WD(100=79.5)
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:
AGACAGACGAGTGCCAAGCA
R:
TCACAGTTGTAGCCGAAGAAGC
Band lengths:
223-526
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]