RnoINT0140953 @ rn6
Intron Retention
Gene
ENSRNOG00000023548 | Sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:RGD Symbol;Acc:1566079]
Coordinates
chr9:100411520-100412028:+
Coord C1 exon
chr9:100411520-100411645
Coord A exon
chr9:100411646-100411923
Coord C2 exon
chr9:100411924-100412028
Length
278 bp
Sequences
Splice sites
5' ss Seq
AGAGTATGT
5' ss Score
5.66
3' ss Seq
TTCTCCCCACCCCCACACAGGAA
3' ss Score
7.82
Exon sequences
Seq C1 exon
GAAGCTACGTGGTGCCTTCGCCCTGCCTCTCCAACCCCTGCCTGAACGGGGGCACCTGTGTGGATGCTGACCAGGGATACGTGTGCGAATGCCCTGAAGGTTTCATGGGCTTGGACTGCAGAGAGA
Seq A exon
GTATGTTGGCGCTGCTGGGTCTGTGGCCAGGGCTGGAACGGGAGACTGGGGGCCTGCACGTGGCAGCAGAGTTGGGAAGGGTCCTCTCTTGGGTTGTATGTGAAGCAAACTCCGAGAGGGAAAAATAAAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTAGTAGTTTTGTGGGAGGGTGGCCAAGATGGGCCAGGGTTAGGAAAAGGGAGCCACATTCTTTCACCCATGGATGCTTCTCCCCACCCCCACACAG
Seq C2 exon
GAATTCTCAATGACTGCGATTGCCGGAATGGAGGCAGATGCCTGGGTGCCAACACCACCATCTGCCAGTGTCCTCCAGGCTTCTTTGGGCTCCTCTGTGAATTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023548:ENSRNOT00000022290:9
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=72.1)
A:
NA
C2:
PF126612=hEGF=WD(100=36.1)
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:
GAAGCTACGTGGTGCCTTCG
R:
ATTCACAGAGGAGCCCAAAGA
Band lengths:
228-506
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]