RnoINT0036265 @ rn6
Intron Retention
Gene
ENSRNOG00000018286 | Chrna1
Description
cholinergic receptor nicotinic alpha 1 subunit [Source:RGD Symbol;Acc:69277]
Coordinates
chr3:60454577-60460724:-
Coord C1 exon
chr3:60460621-60460724
Coord A exon
chr3:60454723-60460620
Coord C2 exon
chr3:60454577-60454722
Length
5898 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGT
5' ss Score
10.91
3' ss Seq
ATGTGTCATTTCCTGCACAGCTG
3' ss Score
8.52
Exon sequences
Seq C1 exon
TGCAGCCAGAGTGCCAGGGAGTGGGACAGGCTGCTGGAGGCCACACCAGCGTCCACAGCCCATGGAGCTCACCGCTGTCCTCCTGCTGCTGGGCCTCTGCTCCG
Seq A exon
GTAAGTCCCAGGGAGGGGGCTCTCCTTTGAGGGTGAAACACTAATGTGCCCCATGTCCCATACCAAGGTCTTGTTTCTTTAAAGGGAACACAGGACACGGCTATACCAGCCAGAGGCTTCTCTACCAGTCACAGCTTGGTGTTGGCTCGGATGGAATCTTGAGGATAGATTTTTAGTTTGTTTCCCCAGAATGGGAGCTGCCTGGTCAAAAGCCACGAGCAAGAGATCCTGGTCGCTCTGGCGTTGCCTGGTCCCAAGCTCAGTCATGTGAACGTGATAGCCCACTTGTACAATCAGAGCCACTGGTAGACTATGCTACCGTTCTCATCTACCTTCATGTTCAGACTAGTGAAGGCAGGTCCAGCACACAGCCATAGGGCTGCATGTGCCAAAACGATCTAGCCATAGATACATACAAGGGCATAAACTTATTTAAACTTCGTTATTTTATTTTTGATATTATTATTATTATTATTATTATTATTATTATTATTTGTAGCTAGATTGCATAGTTTGGGTGTGAACTGTGTAGACAACGATGGGCCTTTTGTCACTGGAGAATTTGTCTGAGAATGAAGAGGTTTGATTGACAGCTACAGGTGCCTGGAAACCTGTTAACAATGTAACCAAACTGTCTCTACAAAGAAACTGTTTTGTCATGTCTAGGTTTTTAAAGTCAGAGATTCGTTTTTTTTTTTTAAGTCCATATAAATCCATGGCCGCTGCACTCCCACTCCACCCCACTTTGTAAGGATCTTACTACTATGTAGGTTTTATGTTTGAGTTGGACTCACGAAACCTTGCACAGCCCTTGACCTACTCTCTACTCTGGAATGTGTCCCATCACAGCCGCTGAAACGCTATCCTGAGCCCCAGACTTCCGGTAGAGGGAAACAGGAGATGTGTGTTGATTACTTCCGATGAACTTACTGGTCATATCATTCCACTGAGGAGCATGGTGGCTTAAAGCCTGCAACTCCCCTCGCTCTAACATTGCTCCGACAAACACAGGCCTTCCAGGCAAAAGCAAAGAGCACACACNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTACACACACATATACACACACACACTCACACACATACATTCACACACTCACACACTCACACACATATATACACACGCACACACTCATACACACTCACACACATTTATTTTCAATAGCAGAGTTAGAGGAAGTGTCTAAACTCAGATGGATTAAATGCTGTGAAATTTAAAGTTGATCCAACCAAAGCAGGCATGTGCATGCACGTATTTACAAGCATCACACTTGGTGAAAACTTGTTTTAAAAAATTTTAAAGAATTTTTTTATTTTATGTGTATGAATGTTTTGCCTGCATGTATATGCACCACATGTGTGCCCAGTGACTACAGAGGTCAGAAGAGGGCCTCAGATTCCCTAGAGTTACAGATACGCATGAGCCACCATGTGGGTACTGGGAACAGAATCTAGGTCCTGTGCAAGAGCAACAAGTGCTCTTAACTTCTGAGCCAGCCCTCCAAGCCCCTCAGTGAAAGTTCTTATGTGATAGATAGGCTTCTAAATATTACCTACAAGACCTCTTAGAACAACACAGTTCACGTGCAGCTAGTAAGAGTCAGTGTTGTGTGTTTTGATCCCATGTGCAGTCTGTAGTAAGCAGAGGAAGCCCTGAGCAGGTGAAATCATGGGTGAGTATGTGTGTTAACATGGGCATGGCCAGGTCAAGAACCCCAAAAGCCTCAGACCCATGGAGGAATAGAAAAGCCTTCCTGGTGGGGTAAGACTCCAAGGAAGATGGCAAAGCCATCATGTGTGGATATTGGAAGGATGTGTAGAGAATGTCCACCATAGTTTTCTGGCCCCTGGGTGTTATGGACGGATGACTGACTGTTCCCCTACAGAACTGTCCCACCGAGATAGCTAACCTTGTCCCCTTGACCCAACTGTATATAAACCCTGCATCCTTGCTTATCTCTATGCACTAATCCTTCCTCCATGTTCAATCTATTTAATAAACACATTGAGCTTCCTGGGCTCTGAGGTTTCTCTACCCGAGAGACCAGGCCATGGGATCATGGCTTTTCTGTGTGTCCATGTGTCTGTCTATGTTTCTTCTCTCAGCTTCTTCGCTGTCCCAGTCAGGTCCTTTTCTGGAGCCACGCAGAGAATGAGACGGCAGTCCATAGAAATTTAGAATTATAAACTGAAGTCCAGCACCCTAAATTTGTTTATTATAAGGAAACCGAAGGGAAAAGATATAAACTGGCCTGCAGGGTGTGATCACTTAAGAACTTAAGAACTCCCACACCCAGGCCTAAAACAATCTGAAATCACCCAGGTAGAGACAGAGCATGAGGTTGGAGTAAGATTTACACAAGGCGACTCACTACAGTTCAGAATTCTTTCCCTCAAAACCAGGGTCCAGTTCCCTGTGTACAAATGCAAAGCGGGTTCAGTCAGCAAAGCACTGGCATTACAAACACAGGACCTTAGTTCAATTCCCACAACCCATATTTAGAAAACCAGGCATGGTGACAATGTCTGTAATCCTGACAATGTGTAAGGAAAGGCAGAAAGGTCCCTAGTGCTTCCTGGCCATCTAGCCTAGCCTACATAGTAAATTTTAGGCTAATGACAGCCTGTCTCCAAAAAGATGTGGATCCCTGAGAAATGACATCTGAGGTTGTCTTCTGGCTTGTACATGCAGGTGCACACATACGTGCTTGCACACACACATGTCTTAGTTAAGGTTTTACTGCTGTGAACAGACACCATAACCAAGGCAACTCTTATAAAGGACAGCATTTAATTGGGGCTGTCTTACAGGTTCAGAGGTTCAGTCCATTATCATCAAGGCAGGAACATGGCAGCATCCAGACAGGCTTGGTACAGGTAGAGCTGAGAGTTCTACATCTTCTCCCAAAGGAAGCCAGGAACAGACTGAGCATCCTCAGGCAGCTAGGAGGAAGATCTCCAAGTCCACCCCCCACAGTGACACACTTCCTCCCACAAGGCCACACCTTCTAATAGTGCCACTCCCTGGGACGAGCATATGCCAACCATCACAGCACACATGCAAACACACAGTTACGCACATGTAATATGATCTAGAAAGCTCATTTTACACACAGTCACATACACATAATATGATGTAGAACATGCACTTTGAACATGTGGACTCTTAGCAACAGTCCTTCGGTCAGGGTCACTTTCCCCGTGCCTACTGAACACACCCCAGTTGTTCTGGTTACGTGGCACCTTTCACAAACTTCTCCTACCATCCACTCAGGAACCTCAGCCATGCCACTGCCACCTTTCTCAGGGCACATAAATTCCCAATGGGCTGATAGCTATTGATGTCAATGACAAATGTCACTCACCCTGTGAACAGAGAGAAGCCAATTCATGCCAGGTTCACCTTCAAATATTGTAGCATTTCTAATACAGTGTTTGCATGCAGATATTCAACAGACAAGTGTGGTGGGTTAAGTGTCATCACTGTTGGAGTCAAGAGCATTGCTATGCTTTGGCTACAAAGGGCAATGTTGACATGCCTTGTTGTCTATGTAGAACCTTCCTCTTTAACGAAAGAGAGCTTACTGGCTGTGCTGACTCCAGCACTCCAAGCCATATTGGAGCTAGAAAGGGGATTGCAGAATTCTTCCTTGGAGTCTTGGAAAATTCTATGACATCGACTTGCTTACTCATTCTCTTGCTTACTCATTACTCAGCTCTATGGGCTGTTTCCTCGCAATGGATTGCAGTAATGTTTCTGTAAACCCTGTTGGGGAAACATTGTATCTCCTCACCTTGCCCATTGAAACAACTCTAAGAAGTAGAGAATGAGGTGGCAATTCCTCATGAAGGGAACCAGGCCCCTTGCCATGGGCAAGGGCTGGAGGTGAGTGTCTCCAGCATGCTGGCACACCTATTTCCCCTGTCCTCCTCCCTTAGTGAACCATTAGGCCAGATGCACAGCTTTTCTGGAACACACTGCTGACCCTCTTGCTTTCTATGTGTTCCTCCTGTGCAAAATCTGGGTCTCTGCACAACACCCCTTCTTGAGAGTCAGCAGCTTGCCAGCAGTTTGGGGAAGTCCTATGAGAAAGTTTTTTAGTACTGTTGGAAGTTTTGAGGTTCAGACAACTTAGGAAGCTAGATTTGAGATGTGGCTAGGTCAGGGTTCATGGGGTTCACAGCAAAGATGTTTAAGCTATGCTGAAAGATTTGCGAAAGCTCAAATCTAAATAGAGATTACATTCTACCTTTAGGAATGAGATAAATTGTCTGTAACTCTGCCTCTGGGGATCTAAGAGGTCACAGCTAAGCATTGAGCCTCAGTGTTTTCATCTGTGAAGCTGGGGTTAAAATAAAAATCACCCACCGAATCATTCTAACTATTTGGGAGGATTACAGATGGTCATGGGACTTAACTTACCAGGTAGTTGAGTAGCGTTAGTCATTTTATAAAAATCTAAGGTCTGGGTGAGAAATAACACTTCCGAGCAAGAGGGAACACATCTCATGAATCCAACATTTCTTAGCCCATGGGTGACCAATGGGTAATGGTGACCTCAGCAACAGCTTTCAAACAGAGAGTATCTGGTTACATAAATCAGGGTGAATGGCTCGTGTGTCTGCTCTTAGAAAAGCAGCCTCTGTTTTTGTCAGGCTGGAGTTATAGACACCCTTATAAGGTGCATGATGGATTTGGGAGGGGTTTTCGCCTAGGGATAAGAGTATACGAAGTTGTGAGATTGCAGCCAGCCCACACCACACTCATAAAATTAGGAGTTGGGGTCACCACATGGAATTTGAAGGTTCTGTTAGCTGAATGACCTTGGGCAAGTCCTGCACTTTCCGAAGGTCAGGTCAGAGTAGTCACTTTGCCTCAGCAGCCTCAGGGGGTGACACCTAGGAGAGCCAAGAAGGGAACTATGTTCTGAAGAGAAGTCCTAGCCCCAAGTCATCAGAGCACAGGTTGGTTTGTTCTTTCTGTTTTAATCGGTACGTGACTGTAACAGCTGAGATTTGTAAAAACTGAGAAAACATACACATCACATAAATTTGATTATTTTAACCATTCAAAGTACACAGTTCAGTGGGAATATCACCATCACATAGTTCTGATACTCTTGTCTCCAAAGGCCACACTGAACCCATTAAGTGGCCCGGTTCTCCAAGTCACACTTAGAACCACCATCTTCCCACCTCTGTAGACTTACTACCCTTTTATATCTGGCTTTTCACACTAGCTTAATGATGGTATCAAGGTGCGTACATGTTTCGACAGCATCCTCACTTCCTTCCCCTTTTATGACTTAATACTACTCCATTGTTGTATACACCCTAATGCATCCATCCACGTACTTGCTGGCGGCACTTTGAGTGTTGTACGCAGTGCTGTTATCCTTTGGATGTGTCCAGGAGTGCACTTGCTGGGTCATATGGTAACAGTGCGTGAGGTTTCAACGTTTCCATAACTTCACCAAACTTATTACTTTCCTTTTGCTCACCATGGCCAGCCTAGGGACTGTAAAACAGCAACTACTTTTAATTGCTAATGACAGTGTGAAATGGGACACCAGTCAGTCCAGCCATGTCCAGGCTCTGAAACACCTAGCCTTCCTGTGGCTTTTTCATGTGTGTGGTGTCTTGCCAAATGTGATGTAAGGTGACCTATCCAGAGAACAAGTGTTGACCGTCGCTGAGTATGGGACCGCACCAGCAACTGTGTTCGGGAGGGGACTCTGTTTCCCATTAGCTGGCTGTGCCTCTAACCCTGGTGAGACTGCGTGCAAGGTGGAGAACTACATCTGACGGTAAATGTGTCATTTCCTGCACAG
Seq C2 exon
CTGGCACTGTTCTGGGCTCCGAACATGAGACTCGTCTGGTGGCAAAGCTCTTTAAAGACTACAGCAGTGTGGTCCGGCCAGTAGGGGACCACCGTGAGATTGTACAGGTCACTGTGGGACTGCAACTGATCCAGCTTATCAACGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018286:ENSRNOT00000024706:1
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(18.8=79.6)
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:
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]