RnoINT0036287 @ rn6
Intron Retention
Gene
ENSRNOG00000013829 | Chrna3
Description
cholinergic receptor nicotinic alpha 3 subunit [Source:RGD Symbol;Acc:2345]
Coordinates
chr8:59592403-59597375:-
Coord C1 exon
chr8:59596364-59597375
Coord A exon
chr8:59594136-59596363
Coord C2 exon
chr8:59592403-59594135
Length
2228 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAT
5' ss Score
8.39
3' ss Seq
TATTGCCTTTTGTTTTCCAGATT
3' ss Score
10.59
Exon sequences
Seq C1 exon
CGCTGATGGGGATTTCCAGGTGGATGACAAGACCAAAGCTCTACTCAAGTACACAGGAGAAGTGACTTGGATCCCGCCGGCCATCTTTAAGAGCTCATGCAAAATCGACGTGACCTACTTCCCATTCGACTACCAAAACTGCACCATGAAGTTCGGCTCCTGGTCCTACGACAAGGCAAAGATCGACCTGGTCCTCATCGGCTCCTCCATGAACCTCAAGGACTACTGGGAGAGTGGCGAGTGGGCTATCATTAAAGCCCCGGGCTACAAACATGAAATCAAGTACAACTGCTGTGAGGAGATCTACCAAGACATCACGTACTCGCTGTACATCCGTCGCCTGCCGCTGTTCTACACCATCAACCTCATCATCCCCTGCCTGCTCATCTCCTTCCTCACTGTGCTTGTCTTCTACCTGCCCTCCGACTGTGGGGAGAAGGTGACACTCTGCATCTCTGTGCTCCTCTCCCTGACTGTCTTTCTCCTGGTGATCACCGAGACCATTCCTTCCACCTCGCTGGTCATCCCCCTGATTGGGGAGTACCTCCTCTTCACTATGATTTTTGTCACCTTGTCCATTGTCATCACAGTCTTTGTGCTCAATGTGCACTATAGAACTCCAACCACACACACCATGCCCACTTGGGTCAAGGCCGTGTTCTTGAACCTGCTCCCCAGGGTCATGTTTATGACTAGGCCGACCAGTGGTGAGGGGGACACTCCTAAGACGAGGACCTTCTACGGCGCTGAGCTCTCAAACCTGAACTGCTTCAGCCGTGCAGACTCCAAAAGCTGCAAGGAAGGCTACCCCTGCCAAGATGGGACCTGTGGCTACTGCCACCACCGTAGGGTAAAAATCTCAAATTTCAGTGCCAACCTCACAAGAAGCTCCAGTTCTGAGTCTGTCGACGCTGTGTTGTCCCTCTCTGCCCTGTCACCAGAAATCAAAGAAGCCATCCAAAGTGTGAAGTACATTGCCGAAAACATGAAAGCACAGAATGTAGCCAAAGAG
Seq A exon
GTAAATAACGGTTTTCATAATGGCAGCCTTGTGCGGTGATACACAGGGCAGAGCTTAGAAAGTTAGACTCAGGGGCTCGAGAGACTGCCCATCGATTAAGAGGGCTTGGTGCTCTTGGGAAGCCACATCAGATGGCCCACAGTGCCCATAACTCTAGTTCTGTGGAATCCAACACCCTTCTTTGGCCTCCTCAGATAAACACACACACACACACACACACACACACACACACACACACACACACGGATGGGGTGGGGAGACAGAGAAAGAGACAGAGAGACAAAGAAGGAGGAAGAGGCAGGGAGGGAGGGAGGGAGAGAGATTGATTAGCCTCTTGAGTCAGAAACTGTCTTCAGACCAGTTACATGCCCTTGGATACATTAGTTACCTCACTTGTGGTCCAAGCTGGCCTTGAACTCACTATTATACTCTCGGCTCCCTCCGTAGTGGGATTCCAGGACTGTGTCATCACATTTTGTCTCAGATGTATACAGGCATAAGGGCCATTTCTTAAATCAACATTGATATTAAAAATACTGATCGCCAATGAGTCTGCTGAAGCAACCTCTTAAGACTGCACTGATTGTCCCCATTTTTCAGATGAGGACATTGAAACCGAGGGCGATGCAATCTGCTCAGACTAGAAAGGAGCAGAGCTGGATTAAGACTAAAGTTCGTCACCCTTTTCAACAGGCTGTCTCCTAGAGCTGTGTGGGTGCTACTTAGCCTATAGAGTGATGTAAGACTCAGGTTGTGGAACTGAAGTGCTTACGGACAAGTCTGAGGAATTCAAATAGAGTAACCTAAGTCAAACAGGGCATTATGATTCTAACTTTACCACAAGTGTGACTTCATGGTGCCACTGAAAGGACACAGTTACTCAAGCTTATAATGGTGAAACGAAAACCACATCTCCCAGGCCATTTCGTGTGCTTAATTGAATTATAAAATTACACACTGCTTCTTCATTATGTGATCATTGCTTCAAGATCAATTGACTCCTGGGCTCTCTCTCAACCCAATTGTGGTTTCTCTGCTTTCTGAATTGTCTGGGAGTTTAATTACCATAGATTCTCCTTCCTGTTTCAAGCCTAAATTGAAGCTCATTATATACAATTATTCTTTCTTCCATTTTTGGCCGTACTATCAGCCATTGTGTCTGCTCTTCAGCCTGTCTGGTCATACAACTGAGGTTGTCATTTGTTAGGTGGGCATTTTAAAGGGGAGTGGTGACAAGGAAAATGTCAGGCTTGCCCGGTGGGCTTATTTCATATTTGGAACGGATGTTACACGGAAATTAGAGTCTAAAACAAGTATTAGTACCAATGAACAAGCACTTTGAAACAATGTCAAATGATTTCGGTTTAAAGTCACCATTCTAACAAAGGCTCCAGATCTTCCTATAGAAGTATATGAGCTTTAATAATTGGAATTCAATGTAGAAAAATAGATTTTGTGCACACACACACACACACACACACACACACAACTTCTGAGTGGTGGTACATACTTGCAATCACCGATCTCAGGAGGCGGTGACGTGGTGATCAACAATTTGAGCCCCACCTAACCTGTGTAGACATGAAGACCAGACCTTACCTTGAAAGAAAAATGTATTCTCGTTAGAAACAGAGCTAACATAGCACATATTTTCCATCTGTTCCTCCATACATGAAATTTGAGGTTGGTAGATATATTAGTACTTTTTTTTTTACTGCTGTGACCATATGCCTATAAGAAGCAACTGAAGGGAGGGTTTATTTGGACTTAACCACTCCAGGGAAATGGTCCAGCATGCAGTCATGGTGGCAGGAGTGTGAGGCAGCTGGTCACACTGCGTCCGCAGTCATGAAGCAGAGAGACGAGGGCCACCATTCAACTTACTCACTCACTTGTATTCATCTAGGACCCTAGCACAGGGAAGGATGCCACCCACAGTTAGGGTAGGTCTTTCCTCCTTTATCAGTCTAATCTAGTCAGTCTCTCATGGTCACCTCCAGAGGCTAACCTAGTGAGATAATCTCTCCTGAGCATGCCCAGTGGTTTGTCTTCTAGGTGACTGTAGATCCTGTCAACCATCACCGTAAATTTCCTCAGATCATATCAATAAGAAAAAAAATTTCTTAAATATTAAGTAAAATGGCTTCTGTACCTTAACAAGATTTAATACTAAAAATTGACCCTTCTCCCCCATGTTCCATTTTCTTTTATTGCCTTTTGTTTTCCAG
Seq C2 exon
ATTCAAGATGATTGGAAGTACGTTGCCATGGTGATTGATCGCATCTTTCTCTGGGTTTTCATCCTGGTGTGCATTTTAGGAACGGCGGGATTATTTCTGCAACCCTTGATGGCCAGAGATGACACATAGACTGTGCACTGTTCATCGAGGCTCACCTGTGCTGACGCAAGGGCACTTCCTCAATAGCACTATACTTTATCTGATCACTGGCTTGGAGTTTGCTATTTCAAGGGTTATTTTCAACTCATCTTGATTTTTCGTAAAAAAGAAATGTGGGAGACAAATGTCTAGTTATTTATCATGGGTAAATGAACATTTCACTACCCCTGTGATTGAAACTTTAGGTAGAAAAATTTTCTGTTCATAAATATTAACTCCATTAGTGCAGGATCTCCATAGAACTCATTTGCTCAGCCCATAAACTTCTTGAAATCGTAGTGTATTCAGCAGCGCCTGTTACTTCCGTTCTTTACTATCTTTCCATGTTGGCATTTGTGTTGCTGCAAAACCCCACATATCATACCCCGAGAAATGACACCTGGTCTCACACTCACTGTTAGTAAACTACTCTAGTCTGTTCAAGTTCCTAATTCAGAAAAAAAAAATCCCATAGAGCCCCGCAAGACTTTAATCCCAGCACTCAAGTAGAGTTAGAGGCAGGCGGGATCTCTGTGAATTCCAGGCCAGCCTGGTCTAGACAGTGAGTTCCAGCCCGATCAGGACTGCATAGTGAGACCCCGTCTCAAAACAACAAAACCCCCACAAACTGGACAGCTAAACTCAAAGTTATTTCTCACAGTTTAGGAGCCTGGGAAGTCTAAAATCAAGGGGCCAGCAAGACTGTCTGGGGAGGAGTCTTCCTCATAAAACATACCTTCCAGTGTGTCTCCAAGTGGCTGAAAGGGCTAGACTCTCTGGAATCTTTTACAAAAGCACTAATTCCATTTGTTGTCAAGGCATGACCTCATGATCTAATAACGTCCCAAACAGAGTTGCATGGTAGGTTCACACATGAGCTGCAGGGAGCCATCCAGACTCTAGGATGAGCCGTCAGATCAGGGCTTCGCTACCTTAGCACTAGGGTTTGGGCTCCAGAGTCGGGCTGGGGATATGAGATGTGTGGACTTCAGCAGCTGATGGTTCCTTCCCACTAGGACGCCAATCACAAGCCTGTGTGTCTCGGCTGTCAGAGCACCCAGAATGTAGGATGTTGTCAAAATTGATTATGCTCGAGAAGCTATTTGAACAAATTGAGTTTCCCATATTACATTTCCGAATCTGAACCACAGCCCCTAGAGACAGTCCACAGAGACCATTTGAGTATTCTTGCTAGGTTTTTTTTTCCATGCAAATGTACAACCTGACAATTGCAATTCACTGTGGCTTGTATTTCAGTAAGTCAAGAGGAAGAGGATTCTATGAAATTTGTTGGCTTACAAATATCTTAACAGTGATTGAGATATAAGAGACGAGGGATATATACAAACTAAGACAGCTAACAGCAATTTACATTGAACTAGATTCTATCAGTGTCCCTCATATCATAAGCACCTGAGATAATAAACTTTAAAAGAGGAAATGTGTATTTTAATATATTCTCAATTCTCATCGAGAATTTCATACGTATTTTGATCATACTCATCCCCTCCTCCTACCTCTACCCAGACCCACCCCCCTTCTTGACTCATTCAACTTTGCGTCCTTTAAAAATAATATACATTTATCAAGACCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000013829:ENSRNOT00000019307:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.006 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(55.6=34.0),PF0293211=Neur_chan_memb=PU(86.7=63.6)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(12.5=72.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
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]