RnoINT0036269 @ rn6
Intron Retention
Gene
ENSRNOG00000018286 | Chrna1
Description
cholinergic receptor nicotinic alpha 1 subunit [Source:RGD Symbol;Acc:69277]
Coordinates
chr3:60450631-60451549:-
Coord C1 exon
chr3:60451354-60451549
Coord A exon
chr3:60450869-60451353
Coord C2 exon
chr3:60450631-60450868
Length
485 bp
Sequences
Splice sites
5' ss Seq
CCGGTAGGT
5' ss Score
9.39
3' ss Seq
AACCTTGTTTTGATTCTCAGGAA
3' ss Score
7.67
Exon sequences
Seq C1 exon
TGCAGATGGAGACTTTGCCATTGTCAAATTCACCAAGGTGCTCCTGGACTACACCGGTCACATCACCTGGACCCCTCCAGCCATCTTTAAAAGCTACTGTGAGATCATTGTCACCCACTTTCCCTTCGATGAGCAGAACTGCAGCATGAAGCTGGGCACTTGGACCTATGACGGCTCTGTGGTGGCCATCAATCCG
Seq A exon
GTAGGTAGTAGCCTGCTGGGCTACGGCTGGTCTCAGAACTAGGGTCACTAGGTGTCCAAGTCAGCCTCTAGACAATCACAGGCTCCTGGCACCGCTCCAAACTAGAGAAGCATCTAGTCGTATGGCTTTCAGTTGAATGCCAAGGTTCTTGAGGCACTGCCCAAGAGAGCTAAGTAAGAGCTTAAATAAATTCTCTTTGCTATGTGCTGTCTCGATAAGTCTGATAAAATGAATCTTGGGTGTGGCTCGGGAGTGGGAGGGACAGTGTTTTAAAGTCTCCTGTAGGTTTGCGTGTAGAGCCGAAATGAGTAAGCCTAACTTACCATATGACGTGTTCTATAGAAAATCAACCTATCACCCCAAAGCAGAGTTGGTCCAACATCCCTCTTGGCAAAGTGACCCTCCGTACGGGACATGGCTACCATGTCTCTGCCCTTCCTTGGGGTGGAACAGCAGGAGTCTGCAAACCTTGTTTTGATTCTCAG
Seq C2 exon
GAAAGTGACCAGCCCGACCTGAGTAACTTCATGGAGAGCGGAGAGTGGGTGATCAAGGAAGCCCGGGGCTGGAAGCACTGGGTGTTTTACTCCTGCTGCCCCAACACCCCTTATCTGGACATCACCTACCACTTCGTCATGCAGCGTCTGCCTCTCTACTTCATTGTCAACGTCATCATTCCCTGCCTGCTCTTCTCCTTCTTAACCAGTCTGGTGTTCTACCTGCCCACAGACTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018286:ENSRNOT00000024706:5
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(31.2=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(24.0=62.5),PF0293211=Neur_chan_memb=PU(15.3=27.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGACTACACCGGTCACATCA
R:
GAGCAGGCAGGGAATGATGAC
Band lengths:
344-829
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]