RnoINT0036316 @ rn6
Intron Retention
Gene
ENSRNOG00000002484 | Chrna9
Description
cholinergic receptor nicotinic alpha 9 subunit [Source:RGD Symbol;Acc:621534]
Coordinates
chr14:43885309-43888496:-
Coord C1 exon
chr14:43888342-43888496
Coord A exon
chr14:43885842-43888341
Coord C2 exon
chr14:43885309-43885841
Length
2500 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
TGTCTTCATTTGATCTCCAGGGC
3' ss Score
8.97
Exon sequences
Seq C1 exon
GACGAGAGAAACCAGATTCTGACAGCCTATCTATGGATCCGCCAAACCTGGCACGATGCGTACCTCACGTGGGATCGAGACCAGTATGATAGGCTGGACTCCATCAGGATTCCCAGCGATCTGGTGTGGAGGCCGGACATTGTCCTATACAACAA
Seq A exon
GTAAGTGCTATTCGACTAGAGGATTCTCTGGACTTAACCTACTGATTTAGGAGAAACTTAGAGCTCATGTCAAGGGGACATTTAAAACACACGTGGAGTGTGAACCTAAGTCCTTATTCAAATCTCAGATGATCAGAGCACCAGGTCCTAAAAGCCTAGAGTTGGAAGAAGACCATCAAACTCTATATTCCCCCCTCTCAGGCGCAAAATTGGAGGTAGGCTCCTAGGCATTAAGCACAGACTGGCTGACTTGAGGAAGAGACGCCTGTCAGCTCACATTTTTGGAAGCTGAGAATGTAACTTTAAGTGTAGATTTGTGGGTTGGGGATTTAGCTCAGTGGTAGCTGGGGGGGGTGTAGATTTGTTTCTCCGTGTGCTGGGGGCAGGGACCTGTTCCTCACCCCTCCCCCAGCTTCTGTTGTTTGCTGTCTTTTGTCTCTGGAGTTGTAGAAGCATCGTTTTGACCCTTGCCTTCATCTTCACTTGGGGTTCTCTTTGGCAAGCCCTGTGCCAGAATCTCCGTGCCCAAATCCCCACTCTTGTAGGAGAATCTCGAAACAGGCTGAGGTGGCCACCCTGTCCCAGGGTGAGCTACATCTCCACTCAGTGTATCTATAATAACTTCCTCCCCCTCCCTCTCCCCCTTGTCCCCCTCCCCTCCTCTTCCTCCTCTCCCTCCTCTTCTTCCTCTCCCCTCCCCCTCCTCCTCCTCTTCTCGTGTGATTTTATTTGTTGTTCCCACTTTGTTTTGAAAGGCAGAATCTGCTAAACTGGAGCTCCCTTGGATCTGACAATCTTCCTGCTTCAGCCTCCCAAGATCTCCACCACTCTAACAGCTCTGTTCCTCAGGTTGCCGAAAAGCTAGGAGTTCTATGTGAGAATTTTCTGGAGATGCAATCGAATTTGCTCATGATCCAGAGATCATATAACAGGAATGCTACTATGGTTAGATAGGGTGGGCCGCCTGGCATCTGTCCTGTGGGTTTCAGACTCTAGAGCAGAGGAGAGGTGCGTCTTGGGAATGTTTGGGCTCTTCTCAGAACAAAGCGCCTTGCGCACATAGGTATGGTTCATGTTTCTCAGACTGTGAAGTTTAGGTGAATCACCTAGAGATCTTGAAAACACTCAGGTTTGAATTTAGCAGCCATAGCGTGGGCCTGCAGTTTTGCATTCCCACAAGCTCCAGAGAGCAGCTCTAGAAAGCAGCAGATGTCACTGGCCCAGTGAGTATTCTCCAGAAGGAGCCAGATCTCTTGCCCAACTCAAGCTCAATGTCTCCACCTCTTTTCTGTCGTCATGGGAGTTCCTCTGCCTTTATTCTGGAACCTAAGCTCCTATGGATTGAGAGGTGTTCTGCTATTGTTCAGATAAAAATGGGGGTTTGGGGATTTAGCTCAGTGGTAGAGCGCTTGCCTAGCAAGCGCAAGGCCCTGGGTTCGGTCCCCAGCTCCGAAAAAAAGGAAAAAAAAAAAAAGGGACCTACTGGGGAGGGGCTCCCTAGGTAGGAGCTCCCTGGGCAGAGTCTCCTGGTGGTCATGAAGAGCCCTTGAAAAGGCAACGTGGTGGGTGGCAACCTTGAGTGTACCACGCCTTACTCAGAGCCCATCTAAAGGTCCTGACTGGCTTTTCACTCCTCATTCTAAGTGAGGAGAATGTTCCATGTGCCTTCCAAGCAAGCTAACATTTAAGAGCTAGGCTTTATTACTCTAATCTACCCTTCTCCTCCTCCTCTTCTCTCCCTCCTACCCTTTACTCTTCTCCCTCCCTCCCCTCTCTCTACCACCACTCTCAGCCACAGAGTGTGATAGGGTGAGCTCTGAGAGTTCTGTTGACATAGATGATCTCTCAAAGTTTTGGGTAGATTCCACCAATTCTCCCCGAGGAACAAACAGAACAAAGGGGGCTCCTGCTTCAGTTAAGCACCGAAGTGACCAGTGCTACCAAACCGCTTCTTTGTGAGCATACACAGCCTCTAAGTTTAATCTACCCCAGTGACTATGATGGAGAAGCAGGCTGTGCTCTCATGAGCCCGTGGTAACAGTGCCACCTGGAGGAAGATGGATTCCCTAGAAGAAAATGGAATCAGGAGGGACAGAGGCTGACAAAGTAAGAGAGGATGTCCTGAGAAATGGCGAACATCCGTAGGATTACAGATGAATGACTTTTTCCTCTGTGCTTTTCAAATGAACACACACTTCTGATGACAACAACGGAACCAGAGATGCAGATTTTAGCCTTGGCAGGCTCCCCTCATTCCTGCTGTTCAGTAGCATTGGCATAGGCTGGTGGGAACATGGAGCAGAGCTGCTTTAAGGATGTTATGGGACGTGGCCAGACCAGTCGCAGGAGGTGGAGGAGAAGGGTGTGTCGGAAGTGATCCAAACTCACAGAGAATGGGGACCCACTGCCAAAGGTGCTGAAGTGACAGACACAGGGCAGCGAGCGGTCCAGGGGTTAAGTTGGTAAGCTTCCTCAGCACGTGTCTTCATTTGATCTCCAG
Seq C2 exon
GGCTGACGATGAGTCTTCAGAGCCTGTGAACACCAATGTGGTGCTGCGATATGATGGGCTCATCACCTGGGACTCACCGGCCATCACCAAAAGCTCCTGTGTGGTGGATGTCACCTACTTCCCTTTTGACAGCCAGCAGTGCAACCTGACCTTTGGCTCCTGGACCTACAATGGAAACCAGGTGGACATATTCAATGCCCTGGACAGCGGTGACCTCTCTGACTTCATTGAAGATGTGGAATGGGAGGTCCATGGCATGCCTGCTGTAAAGAACGTCATCTCCTATGGCTGCTGCTCCGAGCCTTACCCAGATGTCACCTTCACTCTCCTTCTGAAGAGGAGGTCCTCCTTCTACATCGTCAACCTCCTCATCCCTTGCGTCCTCATATCGTTCCTCGCTCCGTTGAGTTTCTATCTCCCAGCAGCCTCTGGGGAGAAGGTCTCTCTGGGAGTGACCATCCTATTGGCCATGACTGTGTTTCAGCTAATGGTGGCAGAGATCATGCCAGCCTCAGAAAATGTCCCTCTGATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000002484:ENSRNOT00000003382:3
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=FE(24.6=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(55.6=64.2),PF0293211=Neur_chan_memb=PU(24.1=31.3)
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
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]