RnoINT0140937 @ rn6
Intron Retention
Gene
ENSRNOG00000023548 | Sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:RGD Symbol;Acc:1566079]
Coordinates
chr9:100422579-100423279:+
Coord C1 exon
chr9:100422579-100422857
Coord A exon
chr9:100422858-100423095
Coord C2 exon
chr9:100423096-100423279
Length
238 bp
Sequences
Splice sites
5' ss Seq
CCCGTGAGT
5' ss Score
8.4
3' ss Seq
AGCGGCTTGTTGCCCTGCAGGAC
3' ss Score
9.02
Exon sequences
Seq C1 exon
CCCTCAGGGTAGAAAGGGTGGAGGAGAGTGGGGTCTCCATCTCCTGGAGCCCACCCGAGGGCACCACGGCCAGACAGGTGCTGGACGGCTATGCAGTCACCTATGCCTCCTCGGATGGATCGTCCAGGCGCACGGACTTTGTGGACCGGAGCCGCTCCTCTCACCAGCTTCGGGCCCTGGCAGCCGGCCGTGCCTACAACATCTCTGTTTTCTCAGTCAAGAGAAACACTAACAACAAAAATGACATCAGCAGGCCTGCAGCCCTGCTCACCCGCACCC
Seq A exon
GTGAGTTTTTCAAGGTGGCCTGGCCACCACTGCCCAGGAGTGGACCCTGTTCCCTACCCACCCACTTTCAGCAGACAGCTCTGAGGGGGTGGGAGGGGCTGCCTTTCCTACAGGAAAAGATTCGATAACCACAGGGGTGGGTCGGAGAAATGTCGGGTAGAAAGCAGCAGGCACTGGGCTGGGCCGTGAGGAGCAGGTGGCGTAGGTGGCATCAGCTGAGCGGCTTGTTGCCCTGCAG
Seq C2 exon
GACCCCGCCCTATTGAAGACTTCGAGGTCACCAACATTTCAGCCAATGCCATCTCAGTGCAGTGGGCTCTTCATAGGATCCAGCATGCCACTGTCAGCAGGGTTCGAGTGTCTGTCCTCTACCCTGAGGACACTGTGGTCCAGTCCACGGAGGTGGACAGGAGTGTGGACCGCCTCACATTTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023548:ENSRNOT00000022290:21
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.234 A=NA C2=0.032
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(96.4=85.1)
A:
NA
C2:
PF0004116=fn3=PU(71.4=96.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGCAGTCACCTATGCCTCCT
R:
GAGGACAGACACTCGAACCCT
Band lengths:
308-546
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]