RnoINT0036343 @ rn6
Intron Retention
Gene
ENSRNOG00000019527 | Chrnd
Description
cholinergic receptor nicotinic delta subunit [Source:RGD Symbol;Acc:2352]
Coordinates
chr9:94286550-94287000:+
Coord C1 exon
chr9:94286550-94286601
Coord A exon
chr9:94286602-94286854
Coord C2 exon
chr9:94286855-94287000
Length
253 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGG
5' ss Score
8.37
3' ss Seq
CCCTCTCCCAACCCTCCCAGGCA
3' ss Score
8.17
Exon sequences
Seq C1 exon
ATGGCAGGGCCTGTGCCCACACTGGGGCTGCTGGCTGCCCTTGTTGTGTGTG
Seq A exon
GTAAGGGTGGAAATGACTCCCTTCCTGGGGGCCTTCTATGCCCACCTGGGCCCCTCACCGCATGGTGCCCACCCTCACATCATGCCTAATTCCCACTCCCACTCGGCCCTTTCTAACCCTAGATATCCCACTCTCAGGGTGCAGCTGGCTTTCCTCTGCTCTGCTCAGCCCAAGGCTGACCCAGCAGGACCACAGGGAAGCTTCCTTCCTAGGTCCAGTGACCAGCACCCTGTCCCTCTCCCAACCCTCCCAG
Seq C2 exon
GCAGCTGGGGCCTGAATGAGGAACAAAGGCTGATCCAGCACCTGTTTGAGGAAAAAGGCTACAACAAAGAACTTCGGCCGGTGGCTCGAAAGGAGGACATAGTGGATGTCGCCTTAAGTCTGACCCTCTCCAACCTCATCTCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019527:ENSRNOT00000026504:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0293118=Neur_chan_LBD=PU(18.5=83.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGCTGCCCTTGTTGTGTG
R:
GGGAGATGAGGTTGGAGAGGG
Band lengths:
166-419
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]