RnoINT0036314 @ rn6
Intron Retention
Gene
ENSRNOG00000002484 | Chrna9
Description
cholinergic receptor nicotinic alpha 9 subunit [Source:RGD Symbol;Acc:621534]
Coordinates
chr14:43889641-43890171:-
Coord C1 exon
chr14:43890022-43890171
Coord A exon
chr14:43889787-43890021
Coord C2 exon
chr14:43889641-43889786
Length
235 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
GGGTGCTTCTCTTTGAACAGCCG
3' ss Score
6.22
Exon sequences
Seq C1 exon
GTGGCAGTGAGGGTGTTTTGTGCCCTTCACAGACAGAAGTGGGAGTCCTCGCTGTCTGCCTGACACATTCTACATGTTGGGAAAAGATGAACCGGCCCCATTCCTGCCTCTCCTTTTGCTGGATGTATTTTGCTGCTTCTGGAATCAGAG
Seq A exon
GTGAGAGGCTAGCGCAGTGCTCCATAGGGGCTCCTTAGAGCCTTGGTGAGAGAGACAGGAGGACTGACGTGAGTACATGGCGTGCTTACACCTCTTTCTGACTCTCGATCATCAAGGTAGGTAAGATCAGTCCGCCGCCCCCAAAAAAGAACTCATCCAAAGTTGCCACCCCCCATTTTGACCCCAGAGTTGGTCTTGTTTTGAAATGCCCATCTGGGTGCTTCTCTTTGAACAG
Seq C2 exon
CCGTAGAGACAGCAAATGGGAAATATGCTCAGAAATTGTTCAGCGATCTTTTTGAAGACTACTCCAGTGCTCTGCGTCCAGTCGAGGATACGGACGCGGTGCTGAATGTTACACTGCAGGTCACGCTCTCCCAGATAAAGGACATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000002484:ENSRNOT00000003382:1
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(18.8=79.6)
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
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGCAGTGAGGGTGTTTTGTG
R:
TGTCCTTTATCTGGGAGAGCGT
Band lengths:
293-528
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]