RnoINT0036266 @ rn6
Intron Retention
Gene
ENSRNOG00000018286 | Chrna1
Description
cholinergic receptor nicotinic alpha 1 subunit [Source:RGD Symbol;Acc:69277]
Coordinates
chr3:60454398-60454722:-
Coord C1 exon
chr3:60454577-60454722
Coord A exon
chr3:60454443-60454576
Coord C2 exon
chr3:60454398-60454442
Length
134 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGA
5' ss Score
8.24
3' ss Seq
GGGACCTTCTCTCTTCCCAGGAT
3' ss Score
8.82
Exon sequences
Seq C1 exon
CTGGCACTGTTCTGGGCTCCGAACATGAGACTCGTCTGGTGGCAAAGCTCTTTAAAGACTACAGCAGTGTGGTCCGGCCAGTAGGGGACCACCGTGAGATTGTACAGGTCACTGTGGGACTGCAACTGATCCAGCTTATCAACGTG
Seq A exon
GTAAGACCAGGGCTGGGGGCTCCCTGTGTCATTTATCCTGTGGCACCCACCCTGTGGGACCCCGTCTCACACTGGACTATCTCCCCCTGGCTTCCTTATTCATGCCCTAAAGAAGGGACCTTCTCTCTTCCCAG
Seq C2 exon
GATGAAGTAAATCAGATTGTGACAACCAACGTTCGTCTGAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018286:ENSRNOT00000024706:2
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=PU(18.8=79.6)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(6.7=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:
ACTGTTCTGGGCTCCGAACAT
R:
CTGTTTCAGACGAACGTTGGT
Band lengths:
186-320
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]