RnoINT0036278 @ rn6
Intron Retention
Gene
ENSRNOG00000017424 | Chrna2
Description
cholinergic receptor nicotinic alpha 2 subunit [Source:RGD Symbol;Acc:621533]
Coordinates
chr15:42816194-42817424:+
Coord C1 exon
chr15:42816194-42816336
Coord A exon
chr15:42816337-42817272
Coord C2 exon
chr15:42817273-42817424
Length
936 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TTTCTGTCTGTATCCCACAGTGT
3' ss Score
10.43
Exon sequences
Seq C1 exon
TTGCAGAGAGACAGTGCCTCAAAGAAGCCAGCTCTTGGTAGTCCAAGGGAAACCAGGACCCTCTGAAGCCATGACCCTTTCCCATTCTGCTCTCCAGTTCTGGACACATCTTTATCTCTGGTGTCTCCTTCTGGTGCCAGCAG
Seq A exon
GTGAGTGGGTACCACTACTACCACAGGCCACATAATGGACTCTCCTGAAGGCCAGCTCACTTCATTTTCAAGAGTACCTGGGACACTTAAGGTCATTGGCTGTGTGCCAGCACCACAGGGTGAAGATGAGAGGATGTTTCAACTCTAGTATTAGCAGCTTTGTTGCCTTTGAAAGTCCCAAGTTTTAGTATTCCTGATCTCCAAATGCAAACAGCATCCTAGACCACTCAAGCTTACTGTGGGGATGAAGGAAGCTTACACACAGCACACAGGTGAGGGCAGATAGGTGGGTACACAGTAGCTATGGTCATTGCAGTATCTTCTATCCCAATGGTTGCTGGGATTTTCTGGGTTTTTTTTTTTTAAGGTTGTTCTTTGCCTGCTCAGACAGCAGGGCCTCTGAGTGAAGAAGCTATTATGCAAAGCACAATGGAAAGGACATGATAAATTCCAGCAGACAGTTTTGCAGAGCTTTGCACAGCTGAAGAGAACTGGTCACAGCTGGTGATTTAAGAACTCAGGGTGGGACCCTGCGTGGGAGATGTTCTCGTGGGTGGAAAGGGGGAAAAAAACCTCACTATCAGCCAGGTTCATAGCAGTGGGTGAAGCCTCTCTTAGCCATCTCCCATCCCCACCCTATACTGCTCGAGGCTCTCTGGTTCTGGCTGAGACTGGTTTCTAGGTCTGAGCAAGAAAGCTCAGCTGTGGCAACCCTCATTCCCTGACTTTAAAATCAGGAAAACACCAGGAGTGTTTGCTGTTTGCCCTGTGTGTTATTATGTAAACAGAGTGGCATATTGGTTAAGCACCGATCTTCATTGATCTATGGAATCCTCAATGAGGTTTGAGATGGGCTTCCTACGTACATCCCTGTACTGAGGCCACACGATGTTGAACGCAGACTCTTTTTTTCCCTTTTCTGTCTGTATCCCACAG
Seq C2 exon
TGTTGACCCAGCAAGGCTCACACACCCATGCTGAGGACCGCCTGTTCAAACACCTGTTTGGAGGCTACAATCGCTGGGCACGGCCAGTGCCCAACACTTCTGATGTGGTCATCGTGCGCTTTGGATTATCCATTGCTCAGCTCATAGATGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017424:ENSRNOT00000023475:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0293118=Neur_chan_LBD=PU(18.8=76.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCAGAGAGACAGTGCCTCAA
R:
CACATCTATGAGCTGAGCAATGGA
Band lengths:
294-1230
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]