RnoINT0036268 @ rn6
Intron Retention
Gene
ENSRNOG00000018286 | Chrna1
Description
cholinergic receptor nicotinic alpha 1 subunit [Source:RGD Symbol;Acc:69277]
Coordinates
chr3:60451354-60453253:-
Coord C1 exon
chr3:60453144-60453253
Coord A exon
chr3:60451550-60453143
Coord C2 exon
chr3:60451354-60451549
Length
1594 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGC
5' ss Score
7.47
3' ss Seq
CTCTCTTATCCCGACCACAGTGC
3' ss Score
7.05
Exon sequences
Seq C1 exon
CAATGGGTTGATTACAACTTGAAATGGAATCCAGATGACTATGGAGGAGTGAAAAAAATTCACATCCCCTCGGAAAAGATCTGGCGGCCGGACGTTGTTCTCTATAACAA
Seq A exon
GTAAGCAAAACCATGCAGGGTGGGCCAGCGTCCCCTCAGAAGGACTGCCACAGGCGCTTCCCCACCCTTCGCATTAAATAACCCTTAAAACCAGAACCACGTTGACAGGCGAGGAACGCCATATGGCGTCCCATGTTATGAATAGAAACAATTATGGAAGCCAAATTGAATCAGGGCTGTGGGTGGGGACATTAATCCCGGAGAGCTGCGATGGTGCGATGGTGCGTGTGGAGACACCCGGACTTCCCGTCTCTGAGTCCCTTGGAATCAAATACCTCTCCCTCCCCTCCCCGCCCCAGGGGTCTCAACTCCCCGGGGTGTTATTCATCACATCCTGAATGCCATCCCACCATCAGTGCCCGGATGTCTCCCTTGCCATCCACTGGGCCCTGCAACAGACTGTGCGTTGTGAAATTATAATGTGATTCACGACACTTGGCTTAATGACACGTTCATTATCATATGCCCTTCATTTGTCAGGGAATATTCATTTCAAAGAGCATCCTTCCAAGGCGGGAACAGGAGCATGCGCAGTCAGCTAACTGGGGATTTGCAGTCTGATCTGTGCTTTACAGCAGATGTTGCTGGGGCTGGCAGAGGTTGTAGATGAAAATGGCGCCCTCTGGCGGCCCTTCCAGCATCTAGCACACAGCTAGAGCTGGGATTGCAGGGTGAGCCAAATTCCCCATTGTTGGTGGAGAGAGATGTTGATAGATGCAGTGTCTTGTCTTTACTGAGAACCCCACCGCTTTAGTTCTCTCCACAGACTGCACCTCCGTGGCTAGAGAAAAGGGCTGGGGAAGCAGCTCAGTGGCAGAGGATTTGTTTAACGTGTGAAGCCATTATATTGAATTCTGAGAACTAGAGAAAATGGACTTTTTAAAAAATCTGTTTCCGGTTTCTGAAAGGGGTTCCAGCTATGTGGCTGTGCTGGATTTTCAGACTCACATGGCCCCCCTGGATGCCTGGTGCTAAAGACCACACTTAAGGAGTGAGGAGCTCTGTGCCTTTCTCTCTCAGCTATAGGGTTTGCCCCCCTGCTAGTCAGAAGGCATCTGAGTTTGTGACTTGTCCCATCAGGTTCTAAACATCAGCCCCCCCCACACACACACACAATATTCAGCTGCTAGGAGTGTTTATTTTAAATTTCTGGTCTTTCCAGCCAACTCTGAAAGCACAGAGTTGGAGTCTGACATTGCAAGTGTCTCTGGGGACAGGAAAGGGAAGGCTGAGGTGCATCGGGTCTGTGTCATTTGTTTCTCTGTGAAGCCTGTAGATTCTCACATTCATCCTCCGAGACGCTGACTTGGACCTTGGTCCGCGCTCAGAAAAACTTTGCTTTCTCTCATTGATTCATTGATTCATTGATAGATTGGGCTTTACTGTGTAGCCCAGGTGACTGAGGAATCACTTGCCTCAGCTTCTAGAGTGCTGGAACCACAGAAACACATCATCCCACTTGGCTACTGCTTAGGACTGTGTGGTTTTCTTGACCATGACCCAAGTGAGCATTGGTGTAAGTCAAATTTGGGGAGCACCGCCATGGGTTGGAATGCAACATTGGCGCCATTTTCCTCTCTTATCCCGACCACAG
Seq C2 exon
TGCAGATGGAGACTTTGCCATTGTCAAATTCACCAAGGTGCTCCTGGACTACACCGGTCACATCACCTGGACCCCTCCAGCCATCTTTAAAAGCTACTGTGAGATCATTGTCACCCACTTTCCCTTCGATGAGCAGAACTGCAGCATGAAGCTGGGCACTTGGACCTATGACGGCTCTGTGGTGGCCATCAATCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018286:ENSRNOT00000024706:4
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(17.3=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(31.2=100)
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:
TGATTACAACTTGAAATGGAATCCA
R:
GGATTGATGGCCACCACAGAG
Band lengths:
297-1891
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]