BtaINT0038371 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015252 | CHRNA9
Description
Bos taurus cholinergic receptor, nicotinic, alpha 9 (CHRNA9), mRNA. [Source:RefSeq mRNA;Acc:NM_001192546]
Coordinates
chr6:60979740-60984421:+
Coord C1 exon
chr6:60979740-60980272
Coord A exon
chr6:60980273-60983879
Coord C2 exon
chr6:60983880-60984421
Length
3607 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
GGTTGCTGTTATTTTCCCAGGCA
3' ss Score
7.2
Exon sequences
Seq C1 exon
GGCTGACGATGAGTCTTCTGAGCCCGTGAACACCAATGTGGTCCTGCGGTATGACGGCCTGATCACTTGGGATGCACCAGCCATCACCAAAAGCTCCTGTGTGGTGGACGTCACCTACTTCCCCTTTGATAATCAGCAGTGCAACCTGACCTTTGGCTCCTGGACCTACAATGGCAATCAGGTGGATATCTTCAATGCCCTGGACAGTGGAGACCTCTCCGACTTCATTGAAGACGTGGAGTGGGAGGTGCACGGCATGCCTGCTGTGAAGAACGTCATCTCCTACGGCTGCTGCTCTGAGCCTTACCCGGATGTGACGTTCACTCTCCTTCTGAAGAGGAGATCCTCCTTCTACATCGTCAACCTCCTCATCCCATGCGTCCTCATATCTTTCCTGGCTCCCTTGAGTTTCTATCTCCCAGCAGCCTCTGGGGAAAAGGTCTCCCTGGGAGTGACCATACTGTTGGCCATGACTGTATTTCAGCTCATGGTGGCAGAGATCATGCCAGCCTCAGAAAATGTCCCTCTGATCG
Seq A exon
GTGAGTTCCTCTTATACTTTTGAGTCAGCTTTCTGGTGAATGTGGCTGTATCTGTGCCTTTAAACTCATAGCAATTAAGTCAACTACAAACTCAACACAAGCTCATTTAGTGTCTTCAGTTGGCATCTCTGAATGTGGCTGTTCAAGACAAAGCTGGGCTCGAGGTCTCCAGGTTTACCCAAAAGAGGAATGAGAGCTGTGTGGTTTAGAGCAGTGGTCCTTGAAGTATGGTCCCTGGACCCACAGCATCAGCCTCAATTTGGATATACAGATTGTCAGGGCCCACCCTAGACCTGCTGACTAGGGTGGAGGTAAAGCCTGCAAACTGTTTTCACAAGCTTTCTGGGTGATTCTGATGAGCTTTTTGTTAAAGTCAAAAAACCACTGGCTTTTAGGCTAAGGCCTTGATTTTGAAGTTAAAGAAATCTGCATTTGAACTCTGACTTCACCATTCCTTCCTTGATCAACCTTAAGCAATTTACTTGCTCTTTGAGTCTCTACTTCATCATCTTCAGAATTTGTGTAATTGCTACCTCACTGTGCATTGCTTAGCACAGAGCCTGGCATATGGTGAGGACTGAACCAACAGTGACTGTTAGTATCTTATCACATCACAAGGGGTTTCTTCTTGGGAAAAATGGTAAACACGATGGAAATGATGAGCTAGATTTTTAAGCCTGCCATCTACCCTTGATAGAATAATTCTCAACCTTTATTAGGTATAATAGGTGTGAGAGACTTAAAAATGCAGGTAACTGGTGGTCCAGTAGTTAAGACTCTGTGCTTCTACTGCAGGGGTGCAGGTTTGATCCCAGGGCAGGAAAGTTCCACCTGCCATGAGGCTCAGCCAAAGGAAAGAAAAAGAAAAAAATACAGGTTCTCACAGCAAAAGAGGTTTTTAAAAAGCAGTCTTGGACAAGATTTGGGAATCTGAGGTGATTCTAAAGTAGATCACATTCTCAAACATCTGCAATAATGAAATGTTCCTCCAAGGGTACTGTGGCTGCCATCACTGCCTTTCTTTTCCTTCCCTCTCTTGTTGTGAGATCCCTCCTAATACCTTTAATACCTACTTCCTGCCACCAAGGATAACACCCAGATCCACCACCTCTGCCTCAGTGACTCATGTTGTAATAGATGCTTTCAAGAATCAGAAGCTAGATCTCGTTTTTAGTTCTGTAAAGCAATCAGTAGGGGGAAATTTCAGAACACCAAGAGACTTAGTGACCAATATAAAAGAGATATTATACTGCCTTTTCTCTCCTGAATGTAGTATTAGCCATATGAATAACATTCAGATGTTATTACGTTGGTTTCTCTGTTTGGAGATTTCTTCCTTGTCATGTTTCTCCAGGCAAGTCACACACACACACACACACACACACAAGCCACACACACACACACACAGACTTGCACTTGCACTCGCACTCATGCACATCTTTTTGAGAAATAGTCACAGAAAGTTCTCTCCTTTCTCATCACCACTAATAAAGAGGAAACGGTGTGTTGGTTCTTTCATTACTTCTCCTAAGGCAGAAATGATTGACAGTGATGACATCCAATCATAACCCTGTTTGAGGCAGGATCAGTAGGCAGATCCTGCTCTCTGCTTTACCAGCTAAAGTCAACAGCAAGCTGGCTCAGTTTCTGAAGCAAGGTATCTCAGAACATGACTCATAAATTTTATAAGCATTGCTTTTCCTGTGATAATATGAAATGTATCTTTTTAGGAAGGGTACACATAGATCTTTCTTGAGAGTATTTAATAGTCACAACTTGTTATTTGTAGCACCTATGAAATAGAGTTCCAGTTTTAAGAAATGTATTTACATTTCCTGCATTAAGTATAGCATTTGATCCAGGCTTTTGACCCATAGCCTTTGCAATGTTAAGAAATATTTTATTTTTAGTTTACTCAGAGCTTTTAACAAATAATAAACAGATGATGAATATTACCAAATGTATTGTTTTCATCTGTAAAGACAATCATGTGTGTTTTTTCTTTTCCTGTATTAGTGTTGTAAATTACAGTTTTCTGTTGTTGAACTAAATCCTTCTTTATCATGATGAGTTATCAATTAAAGACACCATAGATTTAGTTAGCCAGTAATTTTTATAGGAGTTTCTCAAATGTATCTATAAATGAAATGGCCTTAAAATTTCCTTTCTTGTTTCTTTTAGAGTCAAGGCTAAATTTATTTCATGAAATGAACCAGTTAGGCAGTATTCCCTCTTTTCTATTTTTGAAACAACTTGCATTAAGATATGAGTTATCTGTTCCTTAAAAATTCAGTGAAACTCACCTGTAAAACCTTTTGGTTCTAGAGCTTTTTGGAAGATGGGTGGGTAGAGGTATTTAATTCCTATTTCTATTCAAGCATTCTTTCTTCTTAGACTAAATTTGACATCTTCTAGATGATAAAGAGTCTGCCTGCAATGTGGGAGACCCAGGTTTGATCCCTGGTTTGGGAAGATCTCCTAGAGAAGGAAATGGCAACCCACTCTAGTATTCTTGCCTGGAAAATCCCATGAACGAAAGAGCCTGGAGGGCTACAGTCCCTGGGGTCACGAAGAGTCAGTCACGACTGAGCAGCTAACACATGTATTTATAGAAATTTCATCTAGGTTTTTGAATGTATTATCATATAGCTACTTGTAATGTTATTTTATTGTTTTCTAAATTTCTATCCTCTTATTTTTTCTATTGCATCCTTTTTCTCTCTCCTACCACTATTCCATGAATGGCCTTATCAAATGTTTATCAGTTGTATAGCTCTTTTCAAATAACTTGTTTTTGTTCATTTTCTAGGTTCTTTGTTCTGTATTTCGAAAATTTGTTAACTTATCTTTATTGTTTCCTTCCTTAATTTTCCTTTTTCATGACTATTTGCTTTTTGCAATCACATATTAAAGACTAATAAAGACACAATATCCCCTTTCTTCGCCAGTAAGAGTGAGATTCCATATTAACAAGGTTTAATGACAATTCTGGGAACTGACCAAGATCATTCATTGTTTATTTGTTTTGCTGAATGTCGAAGTTTTTCACATAGTGATAGCAAAAACTTACAAATCTTTTAACTCAAGGAAGAGGACAGTGCTAAAAACTTTTCCTGTCTTTTTTCAATTAAGCTTCACCTTAGTCTTGTGAGTTAGATATGAATATTATAGTCATTCTATAGAGAAGAAAGCTGAGGCTTACCAGAATTATATAACTCCCTGTAGGTCACAAGTCTACTGAATGACAGAGCTGAGATTTGAACTCAGTTTTATTCAAAAGTCTATATTAGTCACTATTAATGTGTACAACTTCCAGTTGTTTCTTCGTGAGTCAAATATGAGGACAGTTTTCCCCCCTAAATATATATTTATTTATTTGGCTGCTTCGAGTCTTAGCTGTGGCACGTGGGATATTTCATTGCAGCACATGGATTTTCTAATTGAAGTTCATGAGCTTAGCTTCTTCGCTAAATGTGGGATCTTAGTTCCCCAACCGGGGATAAAAACCACGTCCTGTGCATTGCTAGATGGATTCTTAACTGCTGAACCACCAGCGAAGTCCCTTGAAGACAGTTTTAAGCTAACTTGGTTGCTGTTATTTTCCCAG
Seq C2 exon
GCAAATACTACATAGCCACGATGGCCTTGATCACAGCCTCCACTGCCTTGACCATTATGGTGATGAATATCCACTTCTGCGGGGCTGAGGCCCGGCCAGTGCCACCCTGGGCCCGGGTGGTCATCCTGAAATACATGTCCAGGATCTTGTTTGTCTACGACGTGGGTGAGAGCTGCCTGAGCCCCCACCAAGACAGGGAGCGAGACCGTCTTACGAAGGTTTATGACAAACTTCCAGAGCCCAATCTGAAAACATCCAGAAATAAAGACCCTTCCAGAAAGAAGGAAGTGAACAAACTCTTAAAGAATGACTTGAGGTACCCGGGTGAGAACCTGGAGGATGGTGACAGCTACTGTGCACGGTACAGAGTGTTGACGAGAAATATTGAATACATCGCCAAGTGCCTCAAAGACCACAAGGCCACCAATTCCAAGGGGAGTGAATGGAAAAAGGTTGCAAAAGTCATAGACCGATTTTTCATGTGGATTTTTTTCATTATGGTCTTTGTGATGACTATTTTGATCATAGCAAGAGCAGATTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015252:ENSBTAT00000039651:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.072
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(55.6=64.2),PF0293211=Neur_chan_memb=PU(24.1=31.3)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(75.4=96.7)
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]