RnoINT0036344 @ rn6
Intron Retention
Gene
ENSRNOG00000019527 | Chrnd
Description
cholinergic receptor nicotinic delta subunit [Source:RGD Symbol;Acc:2352]
Coordinates
chr9:94293403-94293813:+
Coord C1 exon
chr9:94293403-94293607
Coord A exon
chr9:94293608-94293694
Coord C2 exon
chr9:94293695-94293813
Length
87 bp
Sequences
Splice sites
5' ss Seq
CCCGTGAGT
5' ss Score
8.4
3' ss Seq
CCCCTGGCCCATGTCCACAGGCA
3' ss Score
9.05
Exon sequences
Seq C1 exon
TTCTTCCTGGAGACTCTGCCCAAGCTCCTGCACATGTCCCGCCCAGAAGAAGAAGACCCGGGCCCCAGGGCTCTTATCCGGAGGACCAGCTCTCTGGGATACATCTCCAAGGCAGAGGAGTACTTCTCACTTAAGTCCCGCAGTGACCTCATGTTTGAGAAGCAATCAGAGCGGCATGGGCTGGCCCGGCGCCTCACCACAGCCC
Seq A exon
GTGAGTTCTGGTAGCTGTGGAGCTTGGCCCATGTGTGGGAGGTGGTCAGGGATAGGCATCACGCCTGCCCCTGGCCCATGTCCACAG
Seq C2 exon
GCAAGCCACCAGCAAGCTCTGAGCAGGTCCAACAGGAGCTTTTCAATGAGATGAAGCCAGCCGTGGATGGGGCGAACTTCATCGTCAACCACATGAGGGACCAGAACAGTTACAATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019527:ENSRNOT00000026504:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.246 A=NA C2=0.550
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=FE(28.7=100)
A:
NA
C2:
PF0293211=Neur_chan_memb=FE(16.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTAAGTCCCGCAGTGACCTCA
R:
TGTTCTGGTCCCTCATGTGGT
Band lengths:
183-270
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]