RnoINT0036354 @ rn6
Intron Retention
Gene
ENSRNOG00000003777 | Chrne
Description
cholinergic receptor nicotinic epsilon subunit [Source:RGD Symbol;Acc:2353]
Coordinates
chr10:57242822-57243435:-
Coord C1 exon
chr10:57243193-57243435
Coord A exon
chr10:57242965-57243192
Coord C2 exon
chr10:57242822-57242964
Length
228 bp
Sequences
Splice sites
5' ss Seq
TTGGTAGGG
5' ss Score
4.44
3' ss Seq
CCTTCCTTCTTGAATCATAGGCA
3' ss Score
7.88
Exon sequences
Seq C1 exon
GGATGCTGGGATGGGGTGGGGCAAGGGACACAGGATGAGGCAGCTGCCTCTTCCACCCCCACAGCAGGGGCAGAGGATTAGGTGACAGTCCCTAAACCTAGTCCGGAACTAGCACCCTCCTCCCCTTCACACAGGCACCTTGGCCTGCTCCCTCAAGCTTGTCAAAGCTCAGAATAACCTGAGAACCAGACATCAGGATGACAATGGCTCTGCTTGGGACCCTGCTTCTCCTGGCACTCTTTG
Seq A exon
GTAGGGACAAGGGTGAGGGGAGCCAGGTGGATCCATATGTCAACATGAGGGGGGGAGGGAAAGGACTGAGTTGGAGACTGAGACAGTACTTGGTCCCCAGGTACAATAATGTCGGTTTGGGAGAAATCCAGAAATACAAACCCAGGAGGGTGCACTGGCCTGAGGGGCAGAGAGAAGCCTTTCAGGCTGCTGCTTCATGTGCAGTGGCCCTTCCTTCTTGAATCATAG
Seq C2 exon
GCAGAAGCCAAGGCAAGAATGAAGAGCTGAGCCTGTATCACCATCTCTTCGACAATTATGACCCAGAATGCCGGCCAGTTAGGAGACCTGAGGACACTGTCACCATCACCCTCAAGGTCACCCTAACCAACCTCATCTCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000003777:ENSRNOT00000005050:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0293118=Neur_chan_LBD=PU(18.0=81.2)
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:
AAGGGACACAGGATGAGGCAG
R:
GCCGGCATTCTGGGTCATAAT
Band lengths:
296-524
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]