RnoINT0036317 @ rn6
Intron Retention
Gene
ENSRNOG00000002484 | Chrna9
Description
cholinergic receptor nicotinic alpha 9 subunit [Source:RGD Symbol;Acc:621534]
Coordinates
chr14:43883458-43885841:-
Coord C1 exon
chr14:43885309-43885841
Coord A exon
chr14:43884399-43885308
Coord C2 exon
chr14:43883458-43884398
Length
910 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGT
5' ss Score
8.83
3' ss Seq
TGGTGCTCCTTTTATTCCAGGAA
3' ss Score
8.69
Exon sequences
Seq C1 exon
GGCTGACGATGAGTCTTCAGAGCCTGTGAACACCAATGTGGTGCTGCGATATGATGGGCTCATCACCTGGGACTCACCGGCCATCACCAAAAGCTCCTGTGTGGTGGATGTCACCTACTTCCCTTTTGACAGCCAGCAGTGCAACCTGACCTTTGGCTCCTGGACCTACAATGGAAACCAGGTGGACATATTCAATGCCCTGGACAGCGGTGACCTCTCTGACTTCATTGAAGATGTGGAATGGGAGGTCCATGGCATGCCTGCTGTAAAGAACGTCATCTCCTATGGCTGCTGCTCCGAGCCTTACCCAGATGTCACCTTCACTCTCCTTCTGAAGAGGAGGTCCTCCTTCTACATCGTCAACCTCCTCATCCCTTGCGTCCTCATATCGTTCCTCGCTCCGTTGAGTTTCTATCTCCCAGCAGCCTCTGGGGAGAAGGTCTCTCTGGGAGTGACCATCCTATTGGCCATGACTGTGTTTCAGCTAATGGTGGCAGAGATCATGCCAGCCTCAGAAAATGTCCCTCTGATAG
Seq A exon
GTGAGTGTATACTTGGAGCTTAGCTTTGTGGCAGTTGTGATGGTGTATGTATGCCTCAGGCTAAAGCAGTTGAAACCGTTGGCCCCCTGGTTTTTTAAAACCCATCCAGTGCCTGCTGATGGCCTCTCTGCTTATAGTGATGGTTGTTGGAATTAAATGGTTCTTACGATGTCCAGGTTCACAAAAGAACACTTGTTTATATTTATCTGTTTCTGGATTTTGAGACAGTTTTACAGTGTAGCCCAAGTTGGCCTCAAACTTATTTAGCCAAGGAAGAAGTGGATCTTCTGTTTCTCCTTTCCTCCCCCTCTCGAGTGCTGAGACTGTAGGTTTGTTCCACCAAACCCAATTTACTTGGTACTGGGGATCAAATCCAGAGCTTCATGCATGCCGGACAAGCCTGTGCTCAGCAGTGACGTCTGTTCACAGTGTTAGGTCTTTCTCCTCAGAAGGACGCATAGCAGCTGTGTCAGGAAGCTGGTATCTCAAGTCAGACCTCTACCCTCCCTGCATAACGGAAGCCTCACCCACTTACCAAAACAGAGGTTCCTATGCCCAAAGGGTTTGCTTTAGCAGCCTGTCTCAGAATTAAGTGTTTTAGCTATAGTCTAGGTTTGTACAGAGAAATTTATGGTGCCATTTCTGCTATACACAAACGTAACTGTACCTTTGTAAGTTGGACACTCACTACACTTGTTTTATAGAACACAAAGTTCAACATGATACTTGGCTTTGGTTCTGAGTCTAGTTGGGATAATGATGCTGGACTTCAAACTTAGAAAGTCAGATTCCAAAGTCTCTTTTGGTGACCACCAGGGTGACCAGTTTCTTCAGAATGGTGTCTGATTCTTTCTCATCGAATATGAAGAGATAATAAAAATGAACTTATCTGGTGCTCCTTTTATTCCAG
Seq C2 exon
GAAAATACTACATAGCTACCATGGCCTTGATCACTGCCTCCACAGCCCTTACCATCATGGTGATGAATATTCACTTCTGTGGAGCTGAGGCGCGGCCAGTGCCACACTGGGCCAAGGTGGTCATCCTGAAGTACATGTCCAGGATCTTGTTTGTCTACGATGTGGGTGAGAGCTGCCTTAGTCCCCGCCACAGCCAGGAGCCAGAACAAGTCACGAAGGTTTATAGCAAACTCCCAGAATCCAACCTGAAAACGTCCAGAAACAAAGACCTTTCCAGAAAGAAGGAAGTAAGAAAACTCTTAAAGAATGACCTGGGGTACCAGGGTGGGATCCCCCAGAATACTGACAGTTATTGTGCACGCTATGAAGCACTGACGAAAAATATCGAATACATTGCCAAGTGCCTCAAGGACCACAAGGCCACCAACTCCAAGGGCAGCGAGTGGAAGAAGGTCGCCAAAGTCATAGACCGTTTCTTCATGTGGATTTTCTTTGCTATGGTGTTTGTCATGACCGTCTTGATCATAGCAAGAGCAGATTAGCAGGAAAGAGGAGTGGGCTGGTAGGCATTTAGAGATTTGGGGAAAACCCAATAAAATCACCTGAGATCTGCCCCAGCGTGTGAGTTCAGCTGCTGTTCATACATAATTTAGGGGATAGGTTGCGTATGCTTTTATTCCTAACTTCAATCAATATCCTAGTTACATGTCAGGTTAAATCAAGCAGGAGATGCAAGGTTTCAAGGGTAAAGGGCTGGAGGAAGAGAGTTAGAAAGGACCCTTTCACAGGCTCCCATGAAGGGGAGTGGTGGCCTTCAGTTTATGTAATTATCTCTTTATTATTGTAGACAACAAAGCACAGTGTATTCCTGCTTTAAGATTTAAAGCAAGAAAAGACAAAACAAATTCATTCTCTTAGTCCTTAATAAAACTTTTTTTTTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000002484:ENSRNOT00000003382:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.022
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(55.6=64.2),PF0293211=Neur_chan_memb=PU(24.1=31.3)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(75.4=96.7)
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:
TCCCTTGCGTCCTCATATCGT
R:
TAAGGCAGCTCTCACCCACAT
Band lengths:
342-1252
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]