BtaINT0038346 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003130 | CHRNA3
Description
Bos taurus cholinergic receptor, nicotinic, alpha 3 (neuronal) (CHRNA3), mRNA. [Source:RefSeq mRNA;Acc:NM_174719]
Coordinates
chr21:31505331-31511513:-
Coord C1 exon
chr21:31511404-31511513
Coord A exon
chr21:31506343-31511403
Coord C2 exon
chr21:31505331-31506342
Length
5061 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGG
5' ss Score
7.66
3' ss Seq
CCTCCCGTTTGTTTTCACAGTGC
3' ss Score
9.61
Exon sequences
Seq C1 exon
ATCTGGAACGACTACAAGCTGAAGTGGAACCCGTCCGACTACGACGGGGCCGAGTTCATGCGCGTCCCTGCGCAGAAGATCTGGAAGCCAGACATTGTACTGTACAACAA
Seq A exon
GTAAGGTGCCGGGTGGCCCCGACCCTCTTGGGGCTGTCAGCCTGGACCGGGGTCCTTGGCCTTCTGTGCTTTACAGCCTAGGCGTCCTGAGACCTTTGCCAAGAGGGCTTCATTCATCTGATTCATTCCACAGGTGTTTATTGGGCATCTCCTATATGCCAGGTGTTACGTGGTGCCTGAGAGCCCTCTTCCCTTTCCTCATGCTAAAAACTCATCTTTAAGTCAGAATCATATCCCGTTGTTGTTGAGATAAGGTGGCACAAAACATTAATAACCACCACTCCTCTTGCCTCTAGGAGTTTGCCAGACATCAGGGAAGCCAGGCATGAGTTATAATATCAAAACATACAGTGAGAGAGAGGAAGGGCAAAGAAGGAGATACATGGGAGTGGGCATTGGTCACCAAGGCAGGAGCTGAACCTCCCTGAAAGTCAGGTCCCACCAGGCCCTATGGTTAGGGCATGGGAAAGCTTCATTCTTCTACTCAACTAACTGATGCTCCCCTCCCAGCCTGATGCTGTACGTACGCCTTTGCCCACCAGTGGCAGGAAGCCCTGCTTCTTTCTCACTTTCAAAGGTTCTTTTCCAGCTGGTCTGAACCTGTACATCCTGGCACCTCCAAAACCAGCCTCTCTTTACATGCCAACCTGACACTTTGCGCATTTAACCTCTGTTCAGTTCAGTTCAGTCGCTCAGTCGTGTCTGACTCGTTGCGACCCCATGAATCACAGCACGCCAGGTCTCCCTGTCCATCACCTACTCCCAGAGTTCACTCAGACTCATGTCCGTCCAGTCAGTGATGCCATCCAGCCATCTCAGACACACAGAATTTTAATGGATATTTTACAGTATGTACTAGTTTATTCTCTGGGTATTGCAAAACTTCATGTTTGCACCTGTGCTTATCTCTGGAGTTATAGTGTCTTGAAAAAAGCAGTGAGCATTTTTCAGCAAAACACTTGATATAGAATTAGTCGAATCTGATTTTAAAGTGTTCTATGTTTAGGTATGTCTGCCAGATTAGTACAAATTAATATGTTTTACTATTAGTATTGGGACTAGAGGAGCTGAATCCCACTTTCTAGTCATGGGCTAAAAGAACTAAAAGAAGGAGTCCTTTATCCATTCCAAAGATGCTCCATGTTTTATTTATTGCTTTCCCAAGAAAAGACAGCATTCATATTTCTTTCATGCAACTTGTAAATTGGCACTTAAAGAACTGGGACAGGGGATAAATTAACTGGTTTGCAGAATGTGAGGCATCCTACGAATCTCCTGGTCCAGAGGCTCTTAGGGAGCTGGGCAGGGTGGTGAGAATTTTTCCTGAGATAGAATTAAAGTGGGCACAGCTTTTAATCTTATGATTTGAAAGTCATAGCTGTTTTCTTGCTGGCAGTCTTGGGTGAACAGCTGGGGTGCTTTAGGGATGTATGCTTTTAACAGTAATGAGAGATGTAGTGAAATGTTTCAAAGCAGATGTGGAGAGGAACAAATATCAAAAGGAATTTCCTTGGAATCTGAAGCTGAAAATAACATTTAGAGAAAATCATCCAGCTCCTCTCTCCTAACTAAAACTTCAGTTTCTCTAAACCTCAGGTGAAAGTTTCATCTCAACACACTAGAAACACCTTTTACCTTCTTATGCCAGTTTCTTCTATGGTTTTTTGTTTTCTGAAGTTCGTTCTCTAGTAGAATCCTCAGAAATTGTTCATGGACACCATATACCCTAAGTTCTCACACGTTCAGAACTCACAGTACCCTTTTTAGGTAATATTTTTGTCATTTTGCTGATATAAAATCCTTGGTTCACATTTTCCTTCCATGAAAATCTTAAAAATGCTGACTCATGTTCTAGTATGAAGTATTGCTGTCAAAAACGATTGCCAATCTAATTTTCTTTTTCTTGTATAATCTGGTGACTTTGGGGAGAGAAAAGGGACTCTATTAATAAGTGTGCCTGGACCACAGAAATAAACCAGGGCTATCCTGAAACATTAGGATGCATAGTCAGCTGGGATGCATACCCAGCTTTTTCTTGAGTAACCCAAAGATATTTTTCATTTACCTTTAAAATCTAGTTGTTTCACTCTGTATCATATACATAATAAGACTTCTTTTATTCCAGTAAATTTTTTATGAATTAGAGTTTTTAAGATTGTTTTGTTCTATTGCTTTATCTCTCCAGGAACTCCTTTTTCACATAAATTACAACTTCTTTACCTATATTCTCTGTTATTTTTTCTCAAATTCTTTTATCTCTTTTTGATTTACATTTTTCTCCTTTCTCTTTTTGTTTCAATCACTACACTGTCCATGGTGTCTGCTTGTTGTTATGTTTTAGTCTTTATTTCTGAAATGATTTTTAAAATTTCTTTTTTCCTATTCTTTCCTGCGTTTCATCTGTTCTTTATTGAACTCCTGTCGCTTACCCAGATTCTTACCTTTTCTGTCTCTAATTTACGCTGCTCTTTCAAAGTCTCTAAAGGTTGCTTTTATAGGTTAATTTGTAATGTCAGGTTATCCGTTTCATCTGTTCTGTGGCTGTATTTTTGTGTGCTTGCATGTTATTCAATTACTTTTCATATTTTTCTTACAGTATGTTAATAAGGGGTCCAATCTATCCGTCTTTGCTGTCTTTGTTTACAGCCTTTGTGGGTAAGAGCGCAACTCTGTGTCACCCGCTTGGGAGTTCCCTCCTCCAGTAGTCCCCTTGAAGCATTAAAATGCTCTGTGTAGGGACTTCCCTGGTGGTCCAGTGGCTGAGACTCTGCAGTCCCAATGCAGGGGGCCTGAGTTCGATCCCTGGTCAGGGAACTAGATCCCACACGCCACAATCATGAGTTCACATGCAGCCCATGCAGGAACCACTGGTGGCGGTGTTTGACCCCACACTCTCACATCTGAGCTTCATAGGGTTCCACGTAACCTAGTTCTGCTGGTGATGTGGGCAGTGAGTCCTCAAGTGTGTGTCCAAAAGGCCAGACTCAAGTTCCGAGCGTTCAAGGCTCTGCCACAAACTCTGTGGGACCCTGAGCAAGCAGTCCTGCTCTCTGACCTTCCGTTTCCTTTTCAAGGAAATGAGGGGCTTAGACCGGAGCAGGGATCATCAAGATTTTCTCTGAAAGACCAGGTAGTATTTTAGGCTTTGGAGGCCTTACAGCCTCTGTCATGGCGATATAGCCCTGTCCTTGTCACTTAATATTTGCAGACAATAGGCCACAAATGTGTATGGGTGTGTGCACCAATAAAAATTTATTCACAGAAATAGGGGCCAAGCCAGTGGGCCATAGCTTGCCAACTCTTGGACTAGTGCCTGGGCTCTGAAGGTCCATTTTGTTGATCCAGGATGCCTTAAGGAAAGTTGTTCCGGAGGCTTCTGCCTTCCCAGGGGTCCTTTCAGCCCTCCATGGAGTGTAGGCCAGCCTCCCAGAGCTCCTCCCTGCCCCACGTGGTCAAGTCCACTTGGGATTGCGTGGGTCCCTACCCCCCCACTTCTCATACCCCTCCTCCTTTCTTCCTGGGGTCAGGAATCATCTTCTGGGGAATCGAGGGCCCAGTATGATAAAGTGGGGCTGAGAACATATAAACGCAGGGCACCTTTGGGACAGTCCAGCTGGAGTAAAGGGCTTAATGGGTTTGACATCAAGTTCCACATGTAATGACTGTCCTGCTCAACAGAACATGGGAGGGTGGGAGGGCCAGAGACCAGCAAGGAGACAGGCCGCAGACACTTCCCTTCTGTCTTCACACAATGGTATCCAATAACAACCGGACAGGATATCTCTAAATGTTTAGGTTTGTCTTTTTTTTCCCCCCAGCTTTTTGGGCAAATTGGTATGGTAGTTGTTGCCTTTAGAAGGACATGCACGCCTTCAAATGCACAACTCTAAGAAACCAGTCAAAGGCTGGCTGACCCAGGGAAACATCAAGAGCCTTCACTGGGCAAAGCCATTGTTTTGAGGACTGGCTGGCTTCACTCTCAGATGCGAGACTGGACAGGGTATTGAGTTGGTCGACAGCAAATCTTCCACTGCACAAGCCAGCTGATAAATGCCAGCAAGCCAACTCTAAGAATAATATATATCTCTGCCTAGAGAGGAAGTCAGGGTGGATGTAGCTAAGGGAGAAGGAGCGTGGGGGAGAAATGGGGAAGGATAGGGACACAGAAGGCAAAGGAACCTGCTGTGCTGGGTTTAAAAGACAAGGAATCAGAAAATGTGATTATTCTTTCTAGAACAGTGCAGGGAAGAATGGGGGAGTGTGGTGAACCGGAGAACCAGAATCCAGAGACAGGGCCTGGTAATAGACCCATCTAACAGGGCTCAGTTTAATGGGAGTGGGTGCCCACGGTGGACTCCACAGCCCTTGGAGGTCCAGGGTGTGCTCTGCATGCATGGGTGTACACATATTGCACACCCAATTGAGGACAGAAGGAGGCGGCATTACAAGGACTAAACTATAGGGACCTGAACACCTGCCTCCAAACGGCCACGTTCATTAATTTCTTTTATTAATTAAAGGAGAAAACTCCCTCGCATTTGGAGTATCTCAGTAAATATCAGGGCTTCCCAGGTGGCTCAGTGGGTAAAGAATCCACCTGTGATGCACGAGATGTGGGTTGGATCCCTGGGTCGGGAAGATCTCCAAGAGGAGGGAATGGCAACCCACTCCAGTATTCTTGCCCGGAGAATTCCATGGACAGAAGAGCCTGGCGGGCTACAGTGCACAGGGTTGCAGAGTCGAACACAACTGAAGCGACTGAGCATGCACACACTCGATAAGTTTCAAGTAGGGAGTTGTATGGTGTGGAATGAACCAGTGACATGGCCTGGGTTGGGGAGAATGATGATGAGTGTGTCAGACTGTCTGTGGGTGGGGGGTCCTGGGCCTCAGTATCCCCATTGGTAAATGGAATGGTGGCCTGGGAGACTTTTTATAGCCCTTTGAACACTTACATTCTGCAGTTTTACAAGTCGCCACTTGCTGTTTACCAGCTGGCAGTGTGAGAGGCTGGACTAGATGACCACATGTGTGCCACACACCTCCCGTTTGTTTTCACAG
Seq C2 exon
TGCTGTTGGGGATTTCCAAGTGGACGACAAGACCAAAGCTTTACTCAAGTACACGGGGGAAGTGACTTGGATCCCCCCAGCCATCTTTAAGAGCTCATGCAAAATCGACGTGACCTACTTCCCGTTTGATTACCAGAACTGCACCATGAAGTTCGGTTCCTGGTCCTACGACAAGGCAAAAATCGACCTGGTCCTGATCGGCTCCTCCATGAACCTCAAGGACTACTGGGAGAGCGGCGAGTGGGCCATCATCAAAGCCCCTGGCTACAAGCACGACATCAAGTACAACTGCTGCGAGGAGATCTACCCGGACATCACCTACTCGCTCTACATCCGGCGCCTGCCCCTGTTCTACACCATCAACCTCATCATCCCCTGCCTGCTCATCTCCTTCCTGACTGTGCTCGTCTTCTACCTGCCTTCCGACTGCGGTGAGAAGGTGACCCTCTGCATCTCGGTGCTCCTCTCCTTGACCGTGTTTCTCCTGGTGATCACCGAGACCATCCCGTCCACCTCACTGGTGATTCCCCTGATCGGCGAGTACCTGCTCTTCACCATGATCTTTGTAACCTTGTCCATCGTCATCACCGTCTTCGTGCTCAACGTGCACTACAGGACCCCGACCACCCACACGATGCCCGCATGGGTGAAGACCATATTCTTGAACTTGCTTCCCAGGGTCATGTTCATGACCAGGCCAGCAAGCAACGAGGGCAACACTCAGAGGCCAAGACCCTTCTATAGCGCTGAGCTCTCAAACCTGAATTGCTTCAGCCGCATAGAGTCCAAGGTCTGCAAGGAAGGCTACCCCTGCCAGGACGGGCTGTGCGGCTACTGCCACCATCGCAGGGCAAAAATCTCCAATTTCAGTGCCAACCTCACGAGAAGCTCCAGTTCTGAGTCTGTTGACGCTGTGCTGTCCCTCTCTGCTCTGTCACCGGAAATCAAAGAAGCTATCCAAAGTGTCAAGTATATTGCTGAAAATATGAAAGCACAAAATGAAGCCAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003130:ENSBTAT00000004070:3
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=0.005
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(17.4=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(55.6=34.0),PF0293211=Neur_chan_memb=PU(86.7=63.6)
Main Inclusion Isoform:
NA
Other Inclusion 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]