BtaINT0038331 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018253 | CHRNA1
Description
Bos taurus cholinergic receptor, nicotinic, alpha 1 (muscle) (CHRNA1), mRNA. [Source:RefSeq mRNA;Acc:NM_176664]
Coordinates
chr2:22120291-22125457:+
Coord C1 exon
chr2:22120291-22120360
Coord A exon
chr2:22120361-22125311
Coord C2 exon
chr2:22125312-22125457
Length
4951 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
CGTGTCCTTTGCCATCCCAGCTG
3' ss Score
6.88
Exon sequences
Seq C1 exon
CGCGGGCCGCCACTCCACCACCAGCCCATGGAGCCCCGGCCACTCCTCCTGCTCCTCGGACTCTGCTCAG
Seq A exon
GTAAGCACCGGGGCTGGGGGCTCTCCTGTGAGGCTGAGGCTCTAGAAGCCCCCAAACTAGAGTCTTGCTTCTTTGATGGGAATACAGAATGGCAGGGCTTCACCAGTCCCAGGCTCTTCTGTCAGCTCCTCACTGATGTTGGCTTGATTGTGTTTGCGGATAAAGATTTTTTGCTTGGGTTACCCAGTTAAAACAGGAGCTGCCTGCTCAGAAACTACAAAGTAAACCCGCCATTCTCTCCCTCCATCAGTGTCTGTATCTGAGTCACCTGGATGATGGGATTCAGCACCTCTTCTAACATCCCGAAGTTAGTATCATATTTGAACAACTATAAGGACTTAGCAGGGTGACTTATGATCACAAGTAGTACAGTTAACTAGTCCTTTTATGGCTTTAGGAGAATTCTGAAAATGAAGAGGATTGACTGACAGCTCCATGTGCTGGAGGGAGAAACCTATTCATAACCACAACCAAACTCTCCATGAGAGAAGAACTATTTTATAATCTTTTAAACTCCTGAAGTTAAAAAAAATTCATATGAATGCATGCCCTTTATTTTTTTAAGGACATTACTCTATGTGAGTTTGGGTTTGAATTGAACCCATAAAAATCTTGCACAGCCCTTGACCTGCATTCAACTCTGGACTGTGTCACAACGCAGCCACTGAAATGCTATCCTGAATCCCAAACTTCCGGTTGAGGGAAATAGATGTTGGCTGATTGTTTCATATAAAAGTTTACTGGTGATATCACCCCAACTGAGAAACAAAACGGCTAACATGCTGTGATTTCCCTTCTCCAATATTGCTCTGACAAACACAGGTCTTCTGGGCAAAAGAGGTGAAGTTTTATTAGTAGTATTTTTCAATAGCAGAATTGACGGAAATAGCCTAAACTCTGGTAAATTATATCCTGTGGGATTTGGACTCAATCCAACCAAAGCTGGCCTGGTGTGTGTGTGTGTGTGTGTGTGTGTTTGCAAACACCACACTCAATGGAAATTCTTAAGTGATATATTTACACTTAAAAATCTTTAAGAGATCTCTTAGGACACCAAAAACCTCCAGAAATTCATGTTGAACTATTTTTTTTAAAGTATGTGATATGTATGTAGATCAAACCTAGAGTTTGATGTCAGTTCACATGGATGATTCATGGAAATTTAGGGCAAGATGAGGCAATCCAACATCTCTTTTTTTATTATAGAGAAACTGAAGCAAAGAGACATAAACTGACCATCTCAAACTGACTTTGGGACCATCCCAAAGCCCCCTGATGTATAAACTTTGGAATGTGATCAGACTTCATTTTTTATGTGCACAGTCAGAAAATATACCCTGAAATTGGAAAGGCAGCCAGAGACACAGCACCAGTCAAAATAAGAATTACCCAGGGTCACTGTTTTTGTTTAGCCGCTCAGTCATGTCCAACTCTTTGTGACCCTATGGACTGTAGCCCACCAGGCTCCTCTGTCCATGGGATTTCCCAGGTAAGAATACTGGAGTGGGTTGCCATTTCCTTCTCCATGGGATCTTCCCAACTGAAGGATCAAACCTGTGTCTCTTGCTTTGCAGGTGGATTCTTTACCACTGAGCCACCTGGGAAGAACAGGACAGAATTCCTTTTGCCCAACACAGCAAGCTGTCGCCCAAATAAAAATACAGAGTGGACCAGTACAATACAAAAGAACACTTTGAAATTGTGGCTGGTCCCCCTGCTTTGATTCAATCCCTTGGGGGCAAAATTCTCATTCATATCAGTGACACTTTTTCCGGTATTAGCTGAACACATAATGATCTCTGTTCTATTTATACAGCACTTTCATTACAACCTTTCCTCTCTCTCAGCTCAGGAATCTCAAGCTCTTCATTGCCACCTTCCTATGGCATATTGCTTTCCAACTTGTTCACAGTTATTTATGTAAATGACAAATGTCGATGTCCATAAGAGTAGGAAGACGGGATCTGTGTCAGATTCATGTCTGAAAACCTCAAAGCTCTTCAGACAATGCTTTGCATGCAGCAAATGTTGGACAAATACATGAATGAATTAGTGTTGCCCCCATCTGAATAAGAATGACCAACATGATTTTGCTGAAAAAGGAAACTTCAACATTATTTATGTGTTTATCTGTGTGTTTGTCAATTTATACCTGCCTTCCAAAGAAAGTATTTACTGTGATTTATTGAATCTGTGAAGAAATTGTCCAATTCTCCAGACCACACTGGAATTGGGAACAAAACCTAGAATTCTGAGTTCAAGTCCTTTAAGTTTTATGTGATAAAACTTTGAGTGATACTTTGCCCTGCTTTGAGGAGGGAAAAAGAACAGAATACCAGTGAATGTGGTCTAAGAAATGGAGACCTTCTCAGGAATTCCTTAGAAACTCATGGCGGAAGGCACAGGGACCCTTGTCCTTGGCAAGGGCACAGAGGCGGGAGTGGTATCCCTGGAACACCATCCGTGCCAGGCTCCCCAGTCCTCCCTGCTCCCTAGTTGACCTTAGGGTCCGCCTGCGTATTTTCCTGCCACATCATGCTGATCCTCTGCTCTCTCTGCTGCTTTCTAGTATGTTCTTCCTGTCAAACTAGAATCAACTGTCACTTAAAAATAAGCAGCCCAAGATAACATCAAAGCAATAACCTGAAACCCAGTGGCCGAGGCTCAGAGTGATCCATGCCAGCACCCCTTTGCCCCCACTGCGGGCTGGGTGAGGCCGGGGGGTAGACAAAGCGTAGAAGACAGAGGATTTCTGTGTCCCAAGGGGCCACCGCAAAAACTCCATCAGACAATATGCAGCTCTAAGGGGTCTCCAATGCCAGTGGTCTGGGGCGATGCCATGTGAAAGCTCTGCATGAACCCTTTGGGAAACCATTTTGAGAAACTAGAAATGAAAAGCTAGGCTAGCTGGAAGTTCCACACACAGAGCCCAGGAAGGTCATAATGAAGACACTTTAGCAACACTGAAAGCTTCAAAACGTTGAATGGACACAACATGCTTGCCTTTAGGGGAGTGGTGAGGTATACAGGTCCTTGTGTCTGACTGTCTCCACTTAGAATCCCACTTGTAACTAGCTGGGAGCCATGACATGTGTCTCTGCTGTTCCGACCTCAGTTTTCCCATCTGTAAAATAGGAGTAAAGACTGACCTCATAGAATTTTATAAGGATTCAATAATGTATCACAAATATAGGACCTTTAATAAAGCTCGACAGGCTAATTAAAACATACTTTGGGGAGGATGAAAATGTTTCAGCTCATTATATAGCCTTAGTTATTTCAAGTTGATCTAAAGCTCTGGATGAGAAATAGTGGTTGAGAGCATAGACTCTGGGTGTAAATCCTGGCTCTACCACTGATGAAATCTGGGTCTCAATTTCCCCATCTGTAAATTGAGGATAATGACAGTATATACTATCATTGTTATGAGGATTGAAAATTTTAGTACATATAAAGCAAGTAGAGGAGTATTTGACACAAAACAAGTTGGATACGTGATTATTTTTGTTGATCAATAGAAATAGAAAAGGGGACTACTTTTTACTTAATAATTGTTTTGGTGACAAACCCTTCCAAACTTAGGATCCAAGCAGAAAAATAATAAAAATAATAATAACCTGTCTTAAAGGTGATTGGTTAATACGAACACAACTGCGGGGGGAAAATGGGAAAGCATCTCACTCATTTCATTTTAAAAGTTGTCTTGGCTGGGGGAAAAGGTGTGGTTTCAGCAATAACCTGCGGAAAGGGGAGATCTGGTTACATGAATCCCGGCAGATGGATTGTGTGTCTACTTCCTCTCCCAGTCCTGAACAGGCAATCCACAAACCACCAGGGCTTGAGTTACAGGGATCCTTCATAAGGCGCTTGGAATTTGGAACACATTTTCTCAGAGGAATAGCAGCACATGTAGTTGTACAATTTCCAGGACAGCCCACAGCACGATCATAATATTAAAAGTGAGTTCAGGAGCATGGTGCAGAGTGACGGGCTCTAACCTGAGCTCTGCCCTAGCCGCGTGACCACAGACAAGTCAGTCCACCACTCGGAACCTCAGGTGAGAATGTCTCTCTGCCTGCTCGCCAGCGAAGACCATGTCATGCTGGACACCTAAAGGCTGTGGGCTCTGAGAATACTGCATGATATTGCCCTTCATCCTGAAGGAAAATGTGGTAAACATTCCTTGGAATTAAATATGCTCCAAATAGGAGACCCAAATCCAGGTCAACAGAATATGTGATTTTCTCTCTTAGCAACTTAATTGGGACATAGATGATTTTTTTATTATGATAAAAATACATAAATATATATGTAAAGCTTACCATGGTAAAATAGACATTACCTAAAATTACCATTTTAAAGCACACAATCCAGTGGCATTAGGTATATTCACAATGTTAGGCAACCATCACCACTATCTAATTCCATAACTCGTTCATCACCAGAAGGACATCCTGGGCCCATTAGCAGTTACTCCCCTTTCCCTGTCCCCAGAGTCCCTGGTAATTGCTAATCGACTCTGTTCTACGGATTTACCTATTCTGGATATTTCATATAAATAGAATCACACAATACATGTCCTGTTGTGTCTGACTTCTTTTAGCATAATGTTTTCAAGGATCACTCATGTTACAGCATGTATCAGAACTTCATTCCTTTTCATGGCTGAATGACGTTCTAACGTATGTATATACCACAAATTGTTTATTCATTTATCTGTTGATGGACATTTGTGTTATTTTCATAGCTGTTAAAATATTGCTGCTATGAACATTCACGTACACATTTTTTGTTTGCTTTTTTGTCTTTTAATTGAAATATAGTTGATTTATTATATCGTGTTAGTTTCAGGTATACAGCACCGTGATTCAGATAGATATATATGTTCACGTTAGTGTGTGTAGAGCGTGGGGGCGGACTCTGACAGTGAGCGTGTCCTTTGCCATCCCAG
Seq C2 exon
CTGGCCTCGTCCTGGGCTCCGAACATGAGACTCGTCTGGTGGCAAAGCTCTTTGAAGACTACAACAGCGTGGTACGGCCCGTGGAAGACCACCGCCAGGCCGTGGAGGTCACGGTGGGCCTGCAGCTGATACAGCTCATCAACGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018253:ENSBTAT00000024298:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0293118=Neur_chan_LBD=PU(18.8=79.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
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]