RnoINT0036270 @ rn6
Intron Retention
Gene
ENSRNOG00000018286 | Chrna1
Description
cholinergic receptor nicotinic alpha 1 subunit [Source:RGD Symbol;Acc:69277]
Coordinates
chr3:60448181-60450868:-
Coord C1 exon
chr3:60450631-60450868
Coord A exon
chr3:60448405-60450630
Coord C2 exon
chr3:60448181-60448404
Length
2226 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TTTTCCCTTTGTCTTTCTAGGGG
3' ss Score
12.44
Exon sequences
Seq C1 exon
GAAAGTGACCAGCCCGACCTGAGTAACTTCATGGAGAGCGGAGAGTGGGTGATCAAGGAAGCCCGGGGCTGGAAGCACTGGGTGTTTTACTCCTGCTGCCCCAACACCCCTTATCTGGACATCACCTACCACTTCGTCATGCAGCGTCTGCCTCTCTACTTCATTGTCAACGTCATCATTCCCTGCCTGCTCTTCTCCTTCTTAACCAGTCTGGTGTTCTACCTGCCCACAGACTCAG
Seq A exon
GTGAGGGCGGTTGTCATGGCTGTAACTGCTGTGAGGCTCAGGCTGCTAGTCTAGGGACAGCCAGGTAAGTGTGTGCTCACAGAGGTGCAGGGACCCAAGTCATCATTGCTGTGTGCAGGCCACCAACAGACAGGTGCTGGGTGGCTGAGGGACCTCAGCGGAGCTCACCACTCAGGAACCAAACTCGGGTCCTCTCTCGAAGAACAACAAGTGCCCTTAACTAACACTGAGCCGTCTCTCAGCGTGAATGAGGCTCTTCGTCTGCTTGTATGTCTATGCACTACGCGTGTGTGCTTGGTGCTAATGGAGGCCAAATTAGGGCACAGTGTCCCTGGAATGACAGTTAGAGATGCTCGTGAGCTGCAGTGTGGATCCTGGGAATGGAGCAGCCAATGCCCCTGACTTCTGAGCCTTCTCTTTTGCCCCCTCCATTTCTTTTGAACAAATAAGTACAAATAAATATTTTCTTTTTTAAAAAAGATTTACTTATTTATTATAAATAAATAAATACACTGTACACTGTAGCTGCCTCAGACACATCAGAAGAGGGCATCATATCCCATTACAAATGGTTGTGAGCCACCATGTGGTTGCTGGGATTTGAACTCAGGACCTCTGGAAGAGCAGTCAGTGCTCTTAACCTCTGAGCCATCGCTCCAGCTCCAAATAAATATTTTGAACTTCCTAATCATGAAACTTCTGAAAGCAAGAGAAGACACTGCTAGAGCAATACAGATCTAACTGGCCGCTATAAATACTGAACAGTCTATGCCTGTAAATACTAAATGCTTGTGAGTACTCTGAGCTTGGCAGATGTTAGTTATTCTAGTATTATTGGACAGACAATGGCAAATAGCTTGATAACTTTAATGTTGAGAGTCTTGGCTCTTTCTTTCGGAGGTAGAATTGAGGATTCCTTGCTTATCTTTCCTATGTATCCCCCAGTTTTAGTCGCTCCACGGGGTCACAAAGTCACTGTTCAAGGATGTCCATGGGTCCTGAATTCCAAGGATGCTCAAGTCCCTCATCTAAAATGGCATTGTAGTCACATGGAACTTTAGGATATCCTTTGATACTTAAAATTGTTTCTTGACACACTGTAAAGACTATACAAAAATAGTTATCACGTTGTTTTGTTTGAGGGACAGTGGCAGGAGAATCTACATATATTCAAGACAGATACAATTTAATTTTTCTGAATATTTTCGGTCTGAGTTTGGTTGAATTCTTGCAAAATCTGCAGTTACGGAAGGCTGTCTGCCTACTTATAGCCTGGTAAGGTATTCAAGGCTACAGTAACAGCAGAAAAGGCAACACAAGAGAACTCCCTAGGGACCCCAGCAAGAGCGGCCCAAGGTTCTCTGTTGCGCCCTACAAAGACGACCCAGTGCCAGTCAGCCTGACCTTCCTGCAGCCTGCTCAGCCAGGACCCCTGAGACTCGGGGCCCACAGGGAAAAAAAAAACAGAGGATTTGGGGGAATCCCTTACCATGAGAACCAAACCAAGCCAAGAACTGATTTGAGAAGACAAACTTTTTAGATGAAAGTAAGAGGAGGTCAGGAGGTTGTGAGTCCCTGGGCGAGCTGCAGTCAGCATCTGGATAGCGGATTCTTTATATATATATATGTATATAGTTTTGGCCTAGCAGCTTCACATTGAAAGAAAGGTATTTTCTGGGCTGCCCCGCCATCTTCTGGGTAACAAAATGACCAGGGGTGAGGTTTATTCAAACTTCCACCCTGGCTCTAGCTTGCCAACCCAGAATCCCTCTTGTTTTCCTGAGTCCCAACAACAAAAAAGGAAGAGTCTAGGGCATGAAACCAAGTTGCCATTCGCTGCTTGGCAGCTGTAACGGAAACCCTGGCCACTTGATGCTGTCAGGGCCCTGCGGTCTCCGGGAAAGGATCCCCAGATTGTCCTTTGAGAACATGCTGGTTACATTCCTTCACCTTGGGTTTTGGTGGCTGATGAGTGTGGAGGGACTGTTTGATGGAATGGCACAGGTGGATGCTTGAAGCAACAGCAGCCTGTTTCTGTGTAGCTCTGGCAGAAGACACTACTCCATGCCCTCACACAGTCTTCTGGTACATGTCTGCGTCCACCCCACACCCGTACTGTGACACTAGTATACAATATGCTTGTTCTGCCTCAATCCAAAGTTACATTGTAACGTCCTGGGGTTTCAGGAGCAGAAGCGTTGTTACATTTTCCCTTTGTCTTTCTAG
Seq C2 exon
GGGAGAAGATGACGCTGAGCATCTCTGTCTTACTGTCCCTGACTGTGTTCCTTCTCGTCATTGTGGAGCTGATCCCTTCCACCTCTAGCGCTGTACCCCTGATCGGGAAGTACATGTTGTTTACCATGGTCTTTGTCATTGCGTCCATAATAATCACCGTCATTGTCATCAACACACACCACCGTTCGCCCAGCACCCACATCATGCCCGAGTGGGTGCGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018286:ENSRNOT00000024706:6
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=PD(24.0=62.5),PF0293211=Neur_chan_memb=PU(15.3=27.5)
A:
NA
C2:
PF0293211=Neur_chan_memb=FE(51.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]