RnoINT0036288 @ rn6
Intron Retention
Gene
ENSRNOG00000011202 | Chrna4
Description
cholinergic receptor nicotinic alpha 4 subunit [Source:RGD Symbol;Acc:2346]
Coordinates
chr3:176546327-176547965:-
Coord C1 exon
chr3:176547895-176547965
Coord A exon
chr3:176546479-176547894
Coord C2 exon
chr3:176546327-176546478
Length
1416 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
ACCTTCCGCCTCCCCCACAGCTA
3' ss Score
9.68
Exon sequences
Seq C1 exon
GGGCCCCGGGGCGCCGCCGCCGCTGCTGCTACTGCCGCTGCTGCTGCTCCTAGGGACCGGCCTCTTGCCTG
Seq A exon
GTAAGTTTCGAAACGCGAAACGGGCCCTTTTCTCCCGGGTCCTGGCAGCTGGGACTCCGGGGCTCCGGGAGAGGAGGCCCCGGGCTGCGGTGCCAAGCCGCGGGTGCGCGCAACGGGATAGCCACAGAGACTCCTCCACCCACTACAGCTCTGATGTCCTGCGGTGCTAGCTGAGCCAGAGAAGAGGGAATCAGCCTCCAAGTGCTGGGAGAGGGGGTTTGAGTGGAGGCGGGGGTAGGGGGTGGGGGAGGGTGGTCTGCCTGCATTTCGGAGCTGGAACCAGAATCTACAACTAGGATAGAGGTGGAGTCCACCTAGGAGGGAGGTTCCATCCTGCCAAATCTCGCCTTCAGACCGCCCCCATGTCTGCCCCTGTTTTTAGGGATCTGCCCCGGCCCCTGGAGCTCCCACCCTATCCTTTCTGCTCCCAGGCTTCCTCCACCTCTCTTCCTCTCAGCAGACACATCTAACCCTAACCCGTGCTGGGGCTTCCTGCAGTTGTTTAATCCTGGCCTTCTCACTGAGCAAAGTGGCTTCCCTAACTGGTTGGTTCAAGATACCAGGATGGATGAGGTTGAGGGAGGAGGAGGCTGGGGGGGACCTCTAGGAGTCCCCTCCTGAGGAGTTCCTGTGTCTCTCAGGTGAGCAAGATCCAGTAGACAGCAAAGGCTCCCCTTTTTCTTCCCAACCCCCTCTTTTGATGCAGCAGCCCAGCAAATGGAGGTAGGGAGGCCCCCTAGCCACGTGGGGGGGGGCAGGTGGAGAGGACACAGATGGGCTGCTGGCTGGTGGGATGAGGGACCACCCTCTTCATGAAGCAGTGTGGTGCTTATCCACGGCATCTTGTATCCATCTATGAACACAGGGTGCTGGTGGCCCTGAGGGTCTGCAGTCATTGTCAGGGTGTACACTAGAAGCCCAGGCAGCAGGACCACTCCTGTGGACAGTGGCTCAAGCTCCTGCAGCCAGGAGAAGTGGTGCCTGGCCCTCTTTCATTAGTGCGTCCGTCTGTCACCCCCCTTCCTCTATCCTAGCTGCCCCATACACCTTCTGCCACCACCACCCCCTCCCTGCTGTCACTTCATGTCCTTTGTCTCCGGTCACTGGAGATAGGGCACTTCCATCCGAAGTGATTGTCTGCGGGGGAGCTCTACACAATTAATTCAGTGTTCACTGTGTCACTTGTCTTGTTTTCCTGGTGGAGTGCGGGAGGGCCTGACCCATTCTTGGGACCTTGGAAAGGCTTCCTTGAGGGGAAGGGTAGGGGTGCAGGTGAACAAGGCAGCATGCCCAGGACCCCAAGGCGACGTCTACCAGGAATCAGAAGAAAGGGCTCTGATGGCATGGGGCCTGGTGTGGAGCTGGAGGGGCAGCCTCTGTGGTCATCTGAGCTTAAACCTTCCGCCTCCCCCACAG
Seq C2 exon
CTAGCAGCCACATAGAGACCCGGGCCCATGCGGAGGAGCGGCTCCTGAAGAGACTCTTCTCCGGCTACAACAAGTGGTCTCGGCCAGTAGCCAATATCTCAGATGTGGTCCTCGTCCGCTTTGGCTTGTCCATTGCTCAGCTCATTGACGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000011202:ENSRNOT00000009041:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.012 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0293118=Neur_chan_LBD=PU(18.8=75.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGCTACTGCCGCTGCTG
R:
CACGTCAATGAGCTGAGCAATG
Band lengths:
198-1614
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]