BtaINT0038347 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003130 | CHRNA3
Description
Bos taurus cholinergic receptor, nicotinic, alpha 3 (neuronal) (CHRNA3), mRNA. [Source:RefSeq mRNA;Acc:NM_174719]
Coordinates
chr21:31500106-31506342:-
Coord C1 exon
chr21:31505331-31506342
Coord A exon
chr21:31500235-31505330
Coord C2 exon
chr21:31500106-31500234
Length
5096 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGG
5' ss Score
10.28
3' ss Seq
TTTTTGTTTTTGTCTTTCAGATT
3' ss Score
12.91
Exon sequences
Seq C1 exon
TGCTGTTGGGGATTTCCAAGTGGACGACAAGACCAAAGCTTTACTCAAGTACACGGGGGAAGTGACTTGGATCCCCCCAGCCATCTTTAAGAGCTCATGCAAAATCGACGTGACCTACTTCCCGTTTGATTACCAGAACTGCACCATGAAGTTCGGTTCCTGGTCCTACGACAAGGCAAAAATCGACCTGGTCCTGATCGGCTCCTCCATGAACCTCAAGGACTACTGGGAGAGCGGCGAGTGGGCCATCATCAAAGCCCCTGGCTACAAGCACGACATCAAGTACAACTGCTGCGAGGAGATCTACCCGGACATCACCTACTCGCTCTACATCCGGCGCCTGCCCCTGTTCTACACCATCAACCTCATCATCCCCTGCCTGCTCATCTCCTTCCTGACTGTGCTCGTCTTCTACCTGCCTTCCGACTGCGGTGAGAAGGTGACCCTCTGCATCTCGGTGCTCCTCTCCTTGACCGTGTTTCTCCTGGTGATCACCGAGACCATCCCGTCCACCTCACTGGTGATTCCCCTGATCGGCGAGTACCTGCTCTTCACCATGATCTTTGTAACCTTGTCCATCGTCATCACCGTCTTCGTGCTCAACGTGCACTACAGGACCCCGACCACCCACACGATGCCCGCATGGGTGAAGACCATATTCTTGAACTTGCTTCCCAGGGTCATGTTCATGACCAGGCCAGCAAGCAACGAGGGCAACACTCAGAGGCCAAGACCCTTCTATAGCGCTGAGCTCTCAAACCTGAATTGCTTCAGCCGCATAGAGTCCAAGGTCTGCAAGGAAGGCTACCCCTGCCAGGACGGGCTGTGCGGCTACTGCCACCATCGCAGGGCAAAAATCTCCAATTTCAGTGCCAACCTCACGAGAAGCTCCAGTTCTGAGTCTGTTGACGCTGTGCTGTCCCTCTCTGCTCTGTCACCGGAAATCAAAGAAGCTATCCAAAGTGTCAAGTATATTGCTGAAAATATGAAAGCACAAAATGAAGCCAAAGAG
Seq A exon
GTAAGGCTGTGTCTGTTATTACATTAGCATTCACTCATTCAACAAACATTTATTGGTTCTTTGTGGACAAGGCTTAGGGTGGGGTTAAGGAATTAGACTTAACTCACTGGCATCAGTGAGCTGTTTTCAGACCTGCTCTTCCATGTACCAGTTACATATCCCTGGATGTGTTGCCTCACTTGTGTGAGCCTGTCTTGTCTTCTGTAAAATGGGATGATAAAGGTTGTATGTAGTGCCTTGCATTTAGCTCCTGGGCTGCCAGCCGTTTAGGCCATAGGAACTCCTAATGCCAAGAGAGAATGGATTAGGAGGTAGGCTGGAAGAGGGAATGAGACCAGATGACCTACAATTAGTATTGATTAGCTGAGCTGACGTTTTAAACTTGACTGATTGTGTCCCCCTATCCCCCTGTAGGTGTAATTTACATAAGGTACACGTGTCTTAAGTGTGCATACAGTTCAGTGAATTATTACATTATGTGTACACTCGTGGAACCATGATCTAGATAAAGACATAGAACATTTCCAGTGCCCAGAAAGCTCCCTCGTGCCCCTCGCAGTCAGTACCCCACTCCCTCCCTCCTTAGTAGCCGCTGAGCCTGGCCTCTTTTCCATTAATTTTACCTATTCTTTAGAAAATGTTTTAAAACTTATTGGCTGCACTAGCTTTTAGTTGTGGCATACAGGATCTAGTTCCCTGACCAAGGATTGAACCTGGGCCCCCTGCATTGGGAGAGTGGACTCTTAGTCACTGGACTACCAGGCAAGTCCCTGATTTTACTTACTCTTGAAATTCATATAAGTAGCATTGCATAACCTCTTTCATATTTGACTTATTTCTTTCAACAAAATGTACAAAACGTCTGAGGTTCATCCTTTGGGCTTGTTACTGCTGTGTAGTATTCTGCAATAAGACAACACCGCCTTCTGTTTATTAATTCCATCTACAATTGTTGGGTGTTTCCAGGTTGGGGCTATTGTGAATAAAGCGGCTCTAAATGTTCTTATACATATCTTTGGGTGAATACATACGTTCGTTTCTCCTGGATACACACCTAAGGACGGCACTGCTGGCTCACTGCAGAGATGTATTTTCCACTTAAGTGGATACTGTCAGGTTTCCAAAATGTTTAAGCCGATTGACACACCCACTGGCGACGTTTGCGAGTCCCCAGCTGCCGCCTCTCCTCGCCAGCGGGGTGAAGTGGCATCACTTGATGTTTTAATTAGCATGTCCTGGTTGAGTAATGAATGGGTCTCCTTTTCATATGCTTATGGGCCATTTGGATATCTTCTTTTGTGAAATATCTATTCACACGCTTGCCCATGGTTTTTTCATTGGGTGGACTTCTATTTTGTCCAAAAATCTTATTTTAGAACTAGTGATAGGTATTAATGATGGGGAAGCGTTACGTGTTTGGCTGCTCCCACTCTGTTTACCCCCAAGGTTATTATGCTCTGCCTTAAGTTGCTTATTAGCAGAGAGCTAATTACTAGATAATTTCATTTCCTGATGCCCTGGAGGTAATTAATGTTGGTAGGGAATGTCTAGATCCCCTCTTTCAGCTGTGAATGGCATATTAATAGGAGTGGATGAGACAGGAGGGAGACAGAGACAGTGGCCCTATCTCCTCACCCCACCCATCCGAGCAACTCTGTGCCCATCTTGTGACTGTAACAATGCGCAGCCGCCCGATGATGTCAGAAATTTAGCCAAAAGGCCAGGCCTGCCTTCAGATTCTGTTGAAGCAATTGTTGGACATTGAGTACATGATTAGTGAAAACCTCTTGTTGGTCTAACACTAAGCACTTTTGCAGATACTCTCTAACATTTATCTACTTTTAAAATCATCACTTCTTTGGAGTGATAATTGGGTGGACTTCTATTTCCTCCAAAAATCTTCGGTTAGAAATAGTGATAGGTATTAATGATGGAGAAGCTTTACACTTATGTGTTTGGCTGCTCGCAACTAGAGGCACATGGTTCATCTCATGAGGCAGCCACTGCTCACCTCTGGTCATCTGGTGATGTGGTCCCATTGTTTTTCCAGAGAATGCAGAAATCTGGACCACAGGGCAGTGGATTGCTGTTTGTGAAAGGGTGGCAGGTGTTAGAATAAAGATGCCTACTCAGTGCTCTGGGGAGTTGGGCTGTCGGAAAGATTCCTTTTTCTATCTTACTGTGTGACTGACACACTGCTGTGTACATAATTTCCCAGAGATGTTTTAATTTCCTAATTCCCCGGCTCCAACTTGGCTGGTTTTACCTGTCCTGACCTCCTAGGAATTCAAACCAAACAGGCCCAGTTCTCCCAGAGCCATCTCGTGAGGGTGCTGGGAGCCCGTGAATGACTGTCCCTGGACACACCAGGCCCCACAGGGACAGGAGTGTCACCGTGTCCCCTGCCTTGGCTCTTCTCGAGCTGTGTTGGTGCCCCTTACTTGCTCACACTTGTGAGGAGTTTCACTAACACTCTAAATTCAGAGTTAAGGTAGGATTGGGTTCCAAATTAGAAAACTAGTCAGGGAGCTTGTGGGTCTCCTGTTAATACTTTCGTTTGACGGTTTTGACAGCTGATCCTTCAAGACTGGTTCCATTGCATGAGTTGCTCTTGAGGTCTTGGAGGCGTGCACAGATCAGAGCCATGACCTTCTGAGCTCATAAGCCTGAGGCACTTGTTTGGTTGAGATATAGATACAGAGATATATCTATAGATGTATGTATATCTGTTACTTCATTCATTCCAACCAGAGTCTGACTTTTGATCAACGATTTATTTATATGTATTGTAATTACTGATTTCCGAGGGTTAAATTTCGGGCATCTTATTTCATGTTTTGCATTTACTTTTTTTTTTGCCCCGGTTCTTGTCGTGCTTTAGAAACATGAAACTTCTTTTGCTGATTGAAAGCCGTGTGCTCTCTTTTTATTCTTCTGTCACCTTGTCCCTCAAGATCTCCTCCTCGTCCCTTTCACTCCGCTGTGGTGGTTTCATCTTTGATGTGGGGAGTGAGGCGGGACGTCTCAGGCCCCGCCAGTCAGTGGGCACCTTTTCTCCTCTCTCTTCCTGGCTCCACTTTGCTCACAAGTGGCCCCACCTGCCTGTCTGGGCCAGGAGTAGCAGGCTGGAAGGAGGCACAGGGTTGGGGGAGAAGAGCACAATCAATCCCTCTCCAGTTCTTCCTTCTAACAAGACCCTCCTCCTCCAACCCCACGCTCATGCTCACACTCACCAAGCCACACCCGTGCGTGTTTCTGACCGTCTTTACTGCAGTCTCTTTTCTGGGATATCTCCGGGGATGGGCTGAGGGATGACACCAGGCACTTGGGCCAGGTTACCATTCTGCCTAACACGCATCTACCTGTTCACGCATCATCGGTGCCAAAGTTTCCAGAGAACAGCCAATAGCATTGTGCCGAAATACCCAGAGTCAGACATACAGTTAATTTTCCCCCAGATCTCTTTGCAGCACTCTTTGTATTATGTGTAAGACCCGAGTTCACTCTTTCTTCACCAGGCTAAACCATGTGAAATGCTGTCAGAGGGAGATTTATAATGCCTCATTTTTAAAATCAGCATGAATATCAATTGGTATTATTCATTAAGGACCCTGTGCCAGGCACGTATTTCATTTAATCTTCGTAACAACTCTCTGAAGTAGGTACTGTTCTTATCCCTGATTTACCAATGAGGAAACTGAGGCTAAGCGAGGTCACATATTTGAACCAGATTCTCACACCTAGAAAGCAGCAGAGCTGGGAATTGTAACAAGTCTTGCTTTTTCCACCCCACTGCTTCCTAGAGCCTTAGGAGGTTTAGCCAGTAGCGGGGTTAGTAGAAATTACAGGGTCTATTTTATACTTGAAGCTTTTACAAACCAGTCTTAGGGATTTGAATAAAGTACCTTGTGGCAAACAGGGCATTATAGTTCTAATCCTTTGACTTCTCAGTGTCATCGAGAGGATGCATTGACTCAAGTTCCTAATGGTGAAATAGAATCTTGGTCTCCCAGCCCCATCTCAGTCCACTTAATTAAATTACAAAATCACATGCTGCCTCTTTATTATGTGATTATTTCTTAAAAAATCAGTTGATTCATGGGTTCTCTTTTTCTCAATCCAATTATGGTTTCCTTGCTTTCTGAGTTGTCTAGGAGTATAATTAATGTGCAGTTCTCCTTCCTATTTCAAGCCAGAATTTGAAGCTCTATTATATACAATTAGACTCGCTCTTTCTTCCATCTTTTACTTTATTGTCAGCAATTGTTTCTGACTTTGAACCTGTCCTATAATTATACAGAATTCCCTGATACTTTGGCCTTATAATTGAAGATGATAGTTGGCTAGTTGGGTATTGTGGACAGGGGGACTGTGTGAGAGAAAGAGTGATGAGGGGCTTGCCCTGGTGTGCTTGTTTCATTTTTGAAACAGATGTTAAAAGGAAATTAGAATCTAAAACTGGATAAGAGCTAGTACTTTGAAATAATGGTAAATGATGTTGGATTGCTTTAGCTATTCTAACAAGGGCCCAGAATCCTCCCACAGAAGTATAAGTCAAATAACTGGTTTAACTAACTTTATAAATTAGAATTCAATTTGGGGGGGTGGGGGAAATGGGTTATGTATATATTAAGAAATTTCTTATTTATGGGAGTTCCCTGGCGGTCCAGTGGTTAAGGCTTCACCTTCCAGGGCAGGGGGTGCAGGTTCGATCTCTGGTCAGGGACCTAAGACCCCACATGCCTCCCGGCCAGAAAACCAAAACATAAAACGGAAGCAATATTGTAACAAATCCAATAAAAACTTTAAAAATGGTTCCCATCAAAAAAAATCTTTAAAAAAAGAAATTTCTGATTTTAAAGCATTTAATATGACACTTTATTCTTGTTTCTCTAGTACATAAAGAGAAATGTGAGAAGGGAGATTTCCTCAGACTACATTAATTAGGAAAAAAAAGTTTTCTTGCATGTTGGCAGCAGAATGGTTTCTTCTCCTCTTGAAACCCATTTATTAAATATTTGTTGAAAATATGTTCAGTTTGCCTTTTCCTTCCTGCTTTATTTTTTCCTCTCATGATTTTTGTTTTTGTCTTTCAG
Seq C2 exon
ATTCAAGACGATTGGAAATATGTTGCCATGGTGATTGATCGTATTTTTCTGTGGGTTTTTATCCTGGTGTGCATTTTAGGGACGGCAGGATTGTTTCTACAACCCTTGATGACCAGGGACGACGCGTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003130:ENSBTAT00000004070:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.005 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
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]