RnoINT0036349 @ rn6
Intron Retention
Gene
ENSRNOG00000019527 | Chrnd
Description
cholinergic receptor nicotinic delta subunit [Source:RGD Symbol;Acc:2352]
Coordinates
chr9:94288328-94288792:+
Coord C1 exon
chr9:94288328-94288483
Coord A exon
chr9:94288484-94288682
Coord C2 exon
chr9:94288683-94288792
Length
199 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGT
5' ss Score
9.73
3' ss Seq
ACAGCCACTGTTCTCTCCAGTTC
3' ss Score
6.06
Exon sequences
Seq C1 exon
CAATGACGGCTCATTCCAGATTTCTTACGCCTGCAATGTGCTTGTTTCTGACTCGGGCCATGTGACCTGGCTGCCACCCGCCATCTTCCGCTCCTCCTGCCCCATCTCGGTCACCTACTTCCCTTTTGATTGGCAGAACTGCTCCCTCAAATTCAG
Seq A exon
GTGCGTTCACCTGCACCTGAGTGTCTCTCAGTCCAGGGCACCCAGCCATGGACTGGAAGTGGTGAACTGAATGCTTTCAGGCAGAGGCCTTGGTCCCATGCTCAGTCTATAGCCTTCTCCAACTAGCCCTCCCACCCCTGCCACCACCTCCTGCCCGCAGAAGCTCCATCTAGAGACTTACAGCCACTGTTCTCTCCAG
Seq C2 exon
TTCACTCAAGTATACCGCCAAGGAGATCAGACTTAGCCTGAAGCAGGAGGAGGAAGACAACCGCAGTTACCCCATCGAGTGGATCATCATTGACCCTGAGGGTTTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019527:ENSRNOT00000026504:5
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:
PF0293118=Neur_chan_LBD=FE(23.4=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(16.7=100)
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:
TCCAGATTTCTTACGCCTGCA
R:
CCCTCAGGGTCAATGATGATC
Band lengths:
244-443
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]