BtaINT0038370 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015252 | CHRNA9
Description
Bos taurus cholinergic receptor, nicotinic, alpha 9 (CHRNA9), mRNA. [Source:RefSeq mRNA;Acc:NM_001192546]
Coordinates
chr6:60972479-60980272:+
Coord C1 exon
chr6:60972479-60972633
Coord A exon
chr6:60972634-60979739
Coord C2 exon
chr6:60979740-60980272
Length
7106 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
TTTCCTCCTCTGACCTCCAGGGC
3' ss Score
10.41
Exon sequences
Seq C1 exon
GATGAGAGAAACCAAATTCTGACTGCCTATTTGTGGATCCGCCAAATCTGGCATGATGCGTATCTCACATGGGATCGAGACCAATATGATGGACTGGACTCCATCAGGATCCCCAGCGACCTGGTGTGGAGACCGGATATTGTCCTATATAACAA
Seq A exon
GTAAGTGCAAGTCAGTAGCTTCTCAGGAATGAACTTGATTAGGCAGAACGTAAACATAATGTGGCCTCCCTGCTGGCTCAGTTGGTAATGCAGGAGACCCAGGTTTAATCCCTGGGTAGGGAAAATCCCCTGGAGAAGGAAATGGCAATCCACTCCAGTATTCTTGCCTGGAAGATCCCATGGACCGAGGAGCCTGGCAGGCTACAGTCCCTGGGGTCACAAAGAGTCCGACATGATTTTAGCAAGTAAACCACCACCAACCACCAAACATAATGGAAGAGGAAAGTTTGAAACATGCATGAAGTTAAGTCAATTCATGTTCCTAGATCCTGAACTGATAGTTAGAAAACCTCAGATAATAAAATAATAATGGTCATAAAAATCTTAGAGCTACATTCTCCCTTTCAGGTGAGAAACTGTATTGGAAGTCCTGTTAGTTTTCTAGGGCTACTGTAGCAAAGTACTACAAGCTGGGTGGCTTAAACCACAGGAACTGTTGTCTCACAGTTCTGGAGGCTAGAAGTATAAGATAAAGGTATTGGCAAAGTTAGTTCCTTCTGAGGCGGTGAGGAAAATCTGTTCCCTGTCTCTGCCCTAGATTCTTGGGTGGTTGCTGGCAATCTTTGCTCTCTTGACTTGTACAAGCATCACCCCAATCTCTGCCTTCTTCTTCACATGGCATCCTGTTCCCTGTGTCCATATTTCCCCTTGCATTGAAGACACCAGTCATGTTGAATTAGATGCTCACCCTACACCAATATGACCTCGTCTTTTTTAAAAAATTAAAGATAATTTTATTGTGCTTTTCTTAACACAAAAAAATTACAGACTTACTGTTTAAAAAAGATAAAGTTGTCTAAATTAAGGCACTAAGACAGAAGTAAAAATTACTCATAATCCCACAGAATATGACCTCTTCTTTTAAATACATTTAACTACTAATTACAGCTGCAATGACTGTTCCAAATAAGGTCACATTCTGAAGTGCCGGGGTAGGATTCAACACATGAAATTTTTGCAGATGCAATTCAGCCCATGACAGTGGTGCTTCCTTGTCAATGATCATGTATGGAAAATACATGTTACTGTTAAGATTAAGGGGCTTTCCAGGTGGTGCAGTGGTAAATCTGCCTGCCAGTGCAGGAGATGCAAGAGACAGGGGTTCAATTCCTGGCTTAGGAAGTTCCCCTAGAGTAGAAAATGGCAACCCCCTCCAGTATTCTTGCCTGGAAAATTCCACGGACAGAAGAGCCTGGCGGGCTACAGTCCATGGGGTCACAAACTGTTAGGCACAACTGAGCTACTGAGTACATTAAGATTTAATCAGAATGGACCAGCTAAAAGCTGGCCCATGGATTTTGGACTTTGTATAGAGTGAAAGATGAACTGGACCATAAGATCACCAGTTGGCCTTTTCCTGGTCTGAGAGCAAGGGGTCTTAGTGAGTGGGCAGGTAAGGCTTCAGTTTCTAAAATTGTAAAGTGGGCATGAATCACCTGAGGAGCCTGCTAAAATACAGATTCTCATTCAGTAGGTCTGGGGTAGAGTTGGTCGTTCTGCATTTCTCTGAGCTCCAGACGGTAGTGCTGCTGGCCCATGGACCACACTTTGAGAATGAACCAGATCACTCTGTCACAACTCAGGCTCAGCTGCTCCACCTGTTGTCAAAGGGGCTCTCTCTCTTTTTATTCTGGAACTCAAGTCTCTCAGAGTTAGGAAAATTCCTCTTTGAGCAGAGAGAGATGAATGAGGAGCAACTTGGACAGGGGGACTCTCCTGGGGACTCAGCCATCTGTTGGGCGTGAGTTTCCCTTCAGGATGCCACACTGCTTGGTTGCAGCCTGGATTTTAGTTTCAGTCCCTACTCAGCTTGTCCAAGGGTCACAACCTTGTGAATCATACCTCTGATCCTGCTGACTATTCCCCACTCTGAGTGGCCAGAGGTATCTTCTGTATGCCTTCCTAAGCAAGGTAACATCCAAGTGCTAAGTCTCTTTCAGTCATGCCTGACTCTTTGCGACCCCATGGGCTGTAGCCCACCAGGTTCCTCTGTCCATGGGATTCTCCAGGCAAGAATATGGGAGTGGGTTGCCATTTCCTTCTCCAAGTACTGGTGCTTTATTACCATGGTTCACACCCTGCCCCCGCCTCTCCTCCCCAGCACACACACAAATACACACATGTAGAAGGCAAGAGAATGGGCCAGGATGTCCATCACCTCCTCCTGGAGAAGAATCAGAGGATATACTTTACATAGAACACTTAAAGCATTCTGTAAGTTCAGAATTCTCCCTGAAAAAAACAGAATGCTGGTTCTCCTTTTCCTCTTGCTTTGATTGACTGAAGCAGTGACCAGCTCTTATTGAAAGTCTTCTTTGTGAGCTGGCATGGTGACCTAAGTTAAGCCTGCCCCAGACCTCCTTTATCAGAGAAGCCAGTTAATCACTAATGAGCTCACACAAACCTGTGGTGGCTTTGGTAAATTTTGTCCCCATTCTCCATCCTTCCCCTCCCTGCCCAGATCACTGGCCTCCTTGAGATGTGTGAGTTCTGGTCCCCACACAGACCTTTCCCACTATAATGGTTCATCAATTCTTTTCTGTTCGTCTGGGTTAACTCTTTAGTCTTCTTTGCTCTGCTCTTACAGTTCTGTTTTGAATCCTCTTTTCTCCTGTGTATTCTCCTTCTCAGTAACATCAGAGTTTTACTATCAATATTTAGAGGAAACCCTAAATGTAGCTGTGATTGGATGTCATTTGCATCCCTTTGAGCAGCTGAAATGAGAATGGAAGAGAGTTAGAGTATCAGGCAAAGGAGGATCTCCAGTGATAGCTATTGCCCTGACCCTGGTCCTTCTAGCTGAATCCCTGGACCTGTAGAATCTTCTGATCTCAGATATAATATCAGTACTTCTCAGAAACCAGTACCAAACCTTGTAGACCCCGGAATGGGCTTCCTGAGTGGTGGTAGGGAGAATAAAGAGGGGTGTAGGACAGGTGATGCAGTCGTGTGTGATAAACATAGTTTGGGCAGGAAGATGCTGAACATCTAGATTCACCATTGGTGCCTGAGTCCATGGGGTAGATTATCTGGGGACTGAGTGAGCAGGATGGTGGTGTGCCTGGAAGCTATTTCGTGTGAGGAGCAGTCGAATTGATTGATGCTTAGTTAGAAAGAGAGAGGTCCTTAGGAAGACTTGATGGCTATCATAGGCAATCAGAGAGAAAATAAGGTGGAGGGAAAAGAGGAAATTCCTCCAGAGGACAAAACCCAAAACAACAAGTAGAAGTTAAAGGGTTTTAAAAATTGCATTTTAATTCAATTAAAAGAAAAACTAATAATTTGAATAATGAGTTTTCCTAAGAGGTAGTGAGCTCTATAACAATATAATGATTCAAGCAGATATTGGCTATTAGCAGTTCAGTAAATGAATAAATAAATTGAGGCTCGAAGTTCTGGTGGGGTTGTTTAGTATAGGTCTGTGGCCAATATAATGGTTGGTGTAAGAGACTGCAAGGATTCCTGACATTTTTAAACTAGGTAAAGAGTGGATTACAGAAATTTCAGATGTGTGTTTATTATGAGATAGTTTTAATGGTTGGATTTTAACGAACAGGTTTAACACTTGGATTTTAGACCTAATGAGAAATTAGGTACCCTGCTGAAATCAGAAGATTTGTCTATAATTTAGCTTTAAGTTCTGCTTACATAGCTTAGATGAAAGAAAGTGTAGGAAAACTTTCAGATGAGGTTGGATATACATATGTCAAATTTGTTCAAATTTTACACTTTAAATGTATGCAGTTTATTGTATGCCAATCAATAAAACTCTTTAAAAAGAAAAAAAAAAGATGAGATTAGTAGTAAAGGAGGGAGAAGAGGAAAAGGTTTGGAGAAAAATGTATGGATTTATTGTGAGACCTGTTCAGTTTGGAAGACCAAAGGAACATTCGCACGGAGATGGTCAACAAAGAGATTGCAAAGGCCAGTTTAAAGCCTGGAAAGAAGGTCAGGGATAGAGCTATCAAAACCCCTTTAAGCCCTTATAGAACTGCTCAAGGAGATCTGGAAGCACTGGTGGGCCATAGGAAACCATTGCACGTGCTGAGCTGTAAAATGATGTGATCAGAGAAACCAGGGAAATAAAACAAAGTACTGGTCATGAAGCAATTAATAGTAATGTCTTCAAACTCCTCCTGAGTAGCTGGGGTGATGTTTTCAGACAGTGGGCTCCTTTACCCTCTGGCTTTTGGTTGGGTTGGCCCAATGAGAAACATTGTGAGCAGTTGGAGGAAGAAAAGAGAGTAAGGTTGGGGCATGTATTCCCTTGCTCCCTTCCTAGAGTTATTATCTTTGGCTGGCTGTATCCTTTGACAGAAGGCATGTCTTCTATGGGAGAAGGAGATGGCATCCCACTCCAGTGTTCTTGCCTGGAGAATCCCAGGGACAGAGGAGCCTGGTGGGCTGCTGTCTATGGGGTCGCACAGAGTCGGACACGACTGACGTGATTTAGCAGCAGCAGCAGCAGCAGCAGCAGCATGTCTCCTATCGTGGTGACCCTCTTCTGCCACTCTTCCCTCCAGGTATTGGTAATTGCACCTTCCCTTCATTTCTTCAGGCTCAGGAACGGTAATAACTCTGCTGTTACTAGTCCTAAAGTGGTTGCCCTATACTTATCTTAGTAGAGTCCTTTTATTAAATCCTCCTCAAGCTACCTAATTTGAATGTGCCATCCATTTCCTGCAAGGACCATGACTAATAGAATCGTTCTAGCTCCAAATATATTCTCTCTGACTCCCAGATCTCTTGTACCAACGTAGGATAGGTGAGTGATGCTCCAGTTCTCAATTCTTGGATAGCTAATTATATATACTTTTTATTTTTACAAAGGGTAGGTTCTGGCATTTTCAAAAATGCCATTTTGTTGTCTTCACAAGACCCACATTAAAGATCCCCTCTTTAGACCTGCATTAAAAAGTGAGCACCACAATTCAGCTGCAGTGCTTTGATTAGAGTGGACACAATCAGACCATTGCATTGTGGTACCTAAAGGTTAATAAGTAGGAAAAAACTTGTAAAACATGTCAGTTCTTAGATCTAATACATCATCTTCTAGCAATTTAACCTAAGGAAAGAGTCAGTGGATAAATGCAACAGTTTGACCACGGGGATGTTCACTGTTGCATTGTTTGTAAATGTGAAAAATAGAAACAACCATAATGCAGAATATCAGTGAGCTGGTTAAATTACTATGGCACATCTCTAAAAAGGAGTATAATTGAATATCATTTAACCATGAAAATAATGTTGCAGAAGATTATGGACAGATGAACACCTACATTTTAAAATTGTCTCAGTCTTGTTTTTGGTAAACTAACTTTTTTATTTCAAGATAATTTTACAGAAAAGTTGGAAAGATGGTACAGAGTTCCTGTATACTTTTCACACAGTTTTCCTTAACGTCATGTCTTACATAACCATAATACATATGCCAAAACTGATATAATACTATTAGTGGTGCTATTGGTAAAGAATCTGCCTGTTGATGCAGGAGACACAAGAGATGCAGGTTTGATCTCTGGGTCAGGAAGATCCCCTGTTGTAAGAAATGGCAACCCACTCCAGTATTCTTGACTGGAGAATTCCATGGGCAGAGGAGCCTGGTGGATTACAATCCATGAGGCCACAAAGAGTTGGGCAGGTCAGAACGACTGAGCACACAATTAAACTACAGGTTTTATTTGGACTTCACCAGCTTTTCCACTAATGTCCTATTTTCTGTTTCAGGATCTAATCCAGCATATCACATTACATTTATCGATAATATAGTTTATAGGGAAAAAATTGTAAGGAACAATCAGAAAAATATGCATTAAATATTAACAGAAATGTATCAGTTAAGGCTGAAAGCATTGAAAACTGACTTTGTCAAAAAAGGAATTTGTAGGAAGGATATGCTCAGCTCACTGAATTAAAGGAGAAAAATCATTGATAGGGCCTTGGAAAGAACAGACTAGGACTACTCCATAGTTCAAGACAAGGGGCTATTGAATTTTTAAAAAAATTTTAAGTAATTGATTTTTCTAGGAATCCATCATCAGATTGACTCTTTTTGGTCTTTGGGTCACCCTGCTTAATATTTAAACTCCAGGAAGTGTGAATCAGTTGGACCTAGCTCAGGTCACAAGCCAGCCCCTGGCCAGGGGAGCCTAGGGTACCTTGATCATTTCATCTGCCTTACAATGGTGGTGGAGAAAGTCATTCCCCAAAGCGAAATAGAAATTTTGTACCCCCAAAATGCCAGCCATAAATGTTGATAAAGCAAAAACAAGATATATCTAGAATAAATTATCTTTTAGATTATAGATGAATAATTTTTTCCTCTGTGTTTTTCAGATGTTCTACAATAAACATGTAAAATTCTTCCAACAGCAACAAAGAGCTACTTTAATATTCTTGTGCCCAAAGTTAACAAAAACATTTAAGCAGAGCCTCTCTGTCAGATTTTAGCCTCGTTTACTTTTTGTCTGGGTGTTTGAATCATTATACCTGGACCAAGAGAATGGCATTGGGAATGGAGAGGAAGGGATAATAGGCAGAGATGCTTATTTGTTTAATTTTGGTTGCCCTGGGCTGCATGTGGGCTCTCTTCTTGCGGTGAGCGGGGTCTACTCTTCGTTGGGGTGCACTGGCTTCTCACTGCGGTGGCTTCTTCTGCTGTGGATCACGAGTTCTGTGTGCACAGGCCCAGTAGTTGTGGGGCATGGGCTTAGTTGCCTCGCAGTATGTGGGATCTTCCCAGTCCAGGGATTGAACACGTGTCCCCTGCATTGGCAGGTGGATTCTTAACCACTGGACCACTAAGAAAGTCTGGCAGAGGTGCTTTAAAGGAAAAATCCAAGAGAACTTGGCCCTGACTAGTTACAGGAGGTGGAGAAGAAGGGCAAATTAGAGTTGATTTTGGACTTGCAAGCCAGTGTACCGAGAATGGTGGTCCATTGCCAAAGACACTGAAGTGATGGGAAAAGGGCAGTGAGCTGTCTGGGTTAAAGAACTTGGTGAGTTGTCCTGGTAAGCAGCTCTCATTTTCCTCCTCTGACCTCCAG
Seq C2 exon
GGCTGACGATGAGTCTTCTGAGCCCGTGAACACCAATGTGGTCCTGCGGTATGACGGCCTGATCACTTGGGATGCACCAGCCATCACCAAAAGCTCCTGTGTGGTGGACGTCACCTACTTCCCCTTTGATAATCAGCAGTGCAACCTGACCTTTGGCTCCTGGACCTACAATGGCAATCAGGTGGATATCTTCAATGCCCTGGACAGTGGAGACCTCTCCGACTTCATTGAAGACGTGGAGTGGGAGGTGCACGGCATGCCTGCTGTGAAGAACGTCATCTCCTACGGCTGCTGCTCTGAGCCTTACCCGGATGTGACGTTCACTCTCCTTCTGAAGAGGAGATCCTCCTTCTACATCGTCAACCTCCTCATCCCATGCGTCCTCATATCTTTCCTGGCTCCCTTGAGTTTCTATCTCCCAGCAGCCTCTGGGGAAAAGGTCTCCCTGGGAGTGACCATACTGTTGGCCATGACTGTATTTCAGCTCATGGTGGCAGAGATCATGCCAGCCTCAGAAAATGTCCCTCTGATCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015252:ENSBTAT00000039651:3
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(24.6=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(55.6=64.2),PF0293211=Neur_chan_memb=PU(24.1=31.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
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]