RnoINT0140941 @ rn6
Intron Retention
Gene
ENSRNOG00000023548 | Sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:RGD Symbol;Acc:1566079]
Coordinates
chr9:100425675-100425976:+
Coord C1 exon
chr9:100425675-100425819
Coord A exon
chr9:100425820-100425893
Coord C2 exon
chr9:100425894-100425976
Length
74 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAC
5' ss Score
7.29
3' ss Seq
CCGCCTACCCCTGTCTGCAGGTT
3' ss Score
9.25
Exon sequences
Seq C1 exon
CCCCCAGGGATGGCACCGACAGGCGCTGGCACCAGGGAGGACACCACTCACGAATGCTCAGAAATAGGCCGGCCCCTTTGCGCCTGCCAGAACTGCGCCTCCTCAATGACCACGGTGCCCCTGAAACACCAACCCAGCCACCCAG
Seq A exon
GTACACACCCTAGCCCCAGCCCTGGGCTCCCAGTCTACACTCTCAACCCATGACCCGCCTACCCCTGTCTGCAG
Seq C2 exon
GTTCTCAGAGCTTGTAGACGGAAGAGCAAGAGTGAGTGCCAGGTTTGGTGGATTGCCCAGCAGAGCAGTAACTGTGAGATCAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000023548:ENSRNOT00000022290:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.897
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATGCTCAGAAATAGGCCGGC
R:
CACAGTTACTGCTCTGCTGGG
Band lengths:
169-243
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]