RnoINT0036315 @ rn6
Intron Retention
Gene
ENSRNOG00000002484 | Chrna9
Description
cholinergic receptor nicotinic alpha 9 subunit [Source:RGD Symbol;Acc:621534]
Coordinates
chr14:43888342-43889786:-
Coord C1 exon
chr14:43889641-43889786
Coord A exon
chr14:43888497-43889640
Coord C2 exon
chr14:43888342-43888496
Length
1144 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
CATCTGGATTCGTTGCTTAGGAC
3' ss Score
4.77
Exon sequences
Seq C1 exon
CCGTAGAGACAGCAAATGGGAAATATGCTCAGAAATTGTTCAGCGATCTTTTTGAAGACTACTCCAGTGCTCTGCGTCCAGTCGAGGATACGGACGCGGTGCTGAATGTTACACTGCAGGTCACGCTCTCCCAGATAAAGGACATG
Seq A exon
GTGAGTGGCATTTGGTGGTGACGCTTGGGAGAGAGGCTGACAGTGAAGACAGGAGTTTGCTTCTGAAGAGAGTGTCTTAATGGGCGGGGCCTTGGTCTCCCAAGTGTGAAGTGGGCAGCCCTGGGTACCTGCTGGCAGGAGCAGGGAGAGCCAGGGAAAGGAAGCATCTTACAGAATGAGCTCCTTCTGTCACTTACTAAATGCTGTCACTACTGTTACTATCACCTACAGCTCTGGCCATAAACACTAGCAGTCTAAGGAATGGAAGGAAGACAGTGTGGCATGTGGTCTGATTCTATTCATTAACTGTCTAAAATAGGTCTCTTCATTCAACCAAAGCATTGGTTGCCAAGGGCTGGGAAAGGGACCAGTGACTGCATAATGGCTATGGCCATTTCTAAGTGTGACAGAAATGTCCTTGAGTTAGATAATTGAGATGATTATGCAGGGTGGTAGGTGACTGGAAGCCACCGACAGTTATAAGGTGGCTAAATGATGGGTTATAATATTTTATTCAACTTTAATTATGTGTACATGCCTGTATGTTTGAGCATATTAGTGCAGTGACTGCAGAGGCCAGAAGAGGGCGTCAGAGCCCCTGAGCGAGAATTATAGGAACTGGGGAGCCACCTAACGCAGGTGCTGGAAACTGATCTGAGATACTCTGAAAGAACAGGGCACACTTTAAACTCCAGCCCCATAAAATAGTACTTTGAGGCTATATGGATGTAACCACAAGTTTTAAAAAGGAAGATGGTGTTTCAAGAGGACGTGGCTGGTTCTCTCCATATACATATTTAATTACACAAGCTATCAGATTTGAACGATGTTTTCTTTTGCACCTGGTAGATATTTCCCGGCTTCTGGCTCAAGTGATTATCAGTTGACCCACTTATAGAGAAATCTGAGCAGTTGGCCCAAGGAAAGAGAAAGACTTAAACACAGGTCTCCTTTACAGTTTGTACACTAAATCAAGAAGGCTTTAAATGTGGCCTCGATAACCAATCACCCAGATAGAATTTTCAAAGGTCTCATTTGTGGGTTGAAAATAGATGGGCCCTTTTGAGATTCCTGCTATCAAGAAAAAGTGTCCCAAAGCTGGAAGTGTATACTGGATAAAGTGACATCTGGATTCGTTGCTTAG
Seq C2 exon
GACGAGAGAAACCAGATTCTGACAGCCTATCTATGGATCCGCCAAACCTGGCACGATGCGTACCTCACGTGGGATCGAGACCAGTATGATAGGCTGGACTCCATCAGGATTCCCAGCGATCTGGTGTGGAGGCCGGACATTGTCCTATACAACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000002484:ENSRNOT00000003382:2
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(24.6=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
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGTAGAGACAGCAAATGGGA
R:
CAATGTCCGGCCTCCACAC
Band lengths:
288-1432
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]