DreINT0006781 @ danRer10
Intron Retention
Gene
ENSDARG00000099181 | CHRNA9 (2 of 2)
Description
cholinergic receptor, nicotinic, alpha 9 (neuronal) [Source:HGNC Symbol;Acc:HGNC:14079]
Coordinates
chr14:583890-584680:+
Coord C1 exon
chr14:583890-584072
Coord A exon
chr14:584073-584328
Coord C2 exon
chr14:584329-584680
Length
256 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCAA
5' ss Score
2.83
3' ss Seq
GAACGTCTTCTCTGCTTCAGGTG
3' ss Score
9.61
Exon sequences
Seq C1 exon
AGGGCGGATGATGATTTCTCAGGCCCGGTGGACACTAATGTCGTTCTGCGCTACACCGGTGAGATCACGTGGGACGCTCCGGCCATCACCAAGAGCTCCTGTGTGGTGGACGTTTCCTACTTTCCCTTCGACAGCCAGCAGTGCAACCTCACGTTCGGCTCCTGGACATACAACGGCAACCAG
Seq A exon
GTGCAACACATCTGACAACAGCTGAACTTATTCTCTCCTCTGGCTGCCGTCATCAGTCTCACACTAATGTTTTCCTTCTTCTAAGAAGTCTTGATAACAGCATCCTGGAGCTTTTCAGTTATTATTTCAGCTAATAGGATTGTAGAATAATGACGTGTTGTTCTCTCCTAGTTTCCCAACTATGACCACTTCTGCTGCAGAGAAACACACTCCATCATGATATATACTGAATTACTGAACGTCTTCTCTGCTTCAG
Seq C2 exon
GTGGACATCGCGATGGGCAGTGTCAGCGGCGACCTCTCGGACTTCGTGGAGAACGTGGAGTGGGAATGCCACGGGATGCCGGCTACCAAAAACGTGATCATGTACGGCTGCTGCTCGGACCCGTACCCCGACATCACCTACACTGTGCTGCTGCAGCGCCGCAGCTCCTTCTACATCATCAACCTGCTGCTGCCCTGCTTCCTCATCTCCTTCCTGGCGCCGCTCAGCTTCTACCTGCCCGCAGACTCCGGGGAGAAGGTCTCGCTGGGGGTCACCGTGCTGCTGGCGCTGACTGTGTTCCAGATGATGGTGGCGGAGAGCATGCCTCCCTCTGAGAGTGTTCCTCTCATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000099181:ENSDART00000158505:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.049 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PU(51.7=98.4),PF0244212=L1R_F9L=PU(72.2=85.2)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(46.6=45.8),PF0244212=L1R_F9L=PD(25.0=15.3),PF0293211=Neur_chan_memb=PU(23.7=47.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATGTCGTTCTGCGCTACACC
R:
GCACAGTGTAGGTGATGTCGG
Band lengths:
295-551
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]