BtaINT0038356 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013657 | CHRNA5
Description
Bos taurus cholinergic receptor, nicotinic, alpha 5 (CHRNA5), mRNA. [Source:RefSeq mRNA;Acc:NM_174514]
Coordinates
chr21:31489738-31492593:+
Coord C1 exon
chr21:31489738-31489847
Coord A exon
chr21:31489848-31491761
Coord C2 exon
chr21:31491762-31492593
Length
1914 bp
Sequences
Splice sites
5' ss Seq
TAAGTAAGT
5' ss Score
8.07
3' ss Seq
TGTGTGTGTGTGTATTTCAGTGC
3' ss Score
10.75
Exon sequences
Seq C1 exon
GAGTGGATAGATGTGAAGTTGAGATGGAACCCTGATGACTACGGTGGAATAAAACTTATACGTGTCCCTTCAGACTCTCTCTGGACTCCAGATATCGTTTTGTTTGATAA
Seq A exon
GTAAGTTATAGTCAAAATACCATTTTATGTTTTCTTAATAAAGAAATCATATCACCATTAGGCACCAGTATTTTTTTTTTATTCCCTTTGAACATTGTTTGCCTACGTAAAGTCCCATGACTTAATCTTGTGTTCTTTTGTTTCATGAGCCTACAAATATGTTCTGTGGATTCTCTCCATTTTTCTTGTGAATTATTTTCTGATCATAAAAGTGTCCTTGGATTTTAAAAATTTGTAATCCATTTGGAAAGTCCAGGAAGGTATGAAGAAGTTGGGGGAAACATAATCAGTCCCGTGAGCCCACCACATGGAGCCAGCCACAGCTGCTGGCTTACCTGCACAGTGAGCTTACTCTGCCTGGCAGTGCGCTCAGTGCCGTGCATGCTTTAGCCATCTGAGTCTCAAGATAACCTCACGAACTAGGGATGACTACATTTATGTGCCAGATGAGAAAATGGAGGCCAAGGGTAGTTATGTTTTGTCTAAGATCACAGCTCACATGTGGTGGTGGGGGTGGAGGTGTTCATAGTAAAGCAGCCTGACATTCCTGTTTACCTCCTATCTTCAAGCCTACATATTTGCTGACTGCCTTCCAGATTTTTTGGTATTATTTTTTTTAAATAGTTAAGTTCATACTTTATGTTTAAATGCGCATCCTTTTAATTTGCTTAGATGTTTAGATGTTTGCTTGATGTTTCAATAATTTGGAAAATTATGTTGTCATAATTTTCCCACAGTGAGGAATGTTGGGTTGATTATTAGCTCGTATTAATGAGTATTCTACCTAAATGTGTTTCAATTATGGTTTTTGACTTAGGGGAGAGGGTATTTCTGGATGCCAGTTTCATTTTTTTCTAGGACCAACCACTCCAGGACACTGGGGAATCTGTGCTCATCCTAATGTACTTTATCTTATTTGCAAAAAGGCATTGGCTTGAGGACAGAGCAAAGGCTGAGCAAAAATGTTTCTCACTTTTCAAACCTTTACCTCCATGCTTTTCAACATGGAAGGAGTGAACGGAGCTGCAAGGTAGCATGATGCAGCTTCCTGAAGCATCATTTTACTCGAAGTCACTGCAGTTTTATATTTAACATGGATATATTGCAGAGGAGCGTGCAAAAGCTACATGAATTTTAACATAGAGAACAATAAAGATAGCTCATGTTGGTGGTGGTGTTTCCCGCTAGACTTCTCCAGTGTGTGAGTTCACGTGGTAACAGACTTCGAGAGGGACAGCTGTTTTCCAGGGCTCTGCCCAGCTTGGGACTGTTGTTCTTTCCCCATGACTGTAGGAAGTGTCCAGTATCTGTCATGGAGGGGGACAATCACTGGAGGGAGTGGGTCTAGGAATATGGATTCAGGTTCTGGCTCTATGCATGTCCACTGTTATAAACAGCCTAGTTATATTTTGTGTGTGCATGCATGCTAAGTCGCTTCAGTCGTGTCTGACTCTTTGCGACCCCATGGACTGTAGCCCCCCAGGCTCCCCTGTCCGTGAGATTTTCCAGGCAAGAATGCTGGAGTGGGTCACCATTTCCTTCCCCAGGGGAATCTTCCTGACCCAGAGCTCAAACCCGTGTCTCTTGCATCTCCTGCATTGGTTTTTTACCACTAGCGCCAATTACCTTTTGTGTGTAATCAAAGTGAAATCATTTCAACTACATGAATCTCTAGATTCTGTAAATACAGATCTGTTGGTCCTGGAGTAGACATGGAAACAGTGGTTCGACTTCAGTAGAGTTAGATATTTAAGGACTCTAGATTCCCCTACATGTTGTAGGTATATCTCAAGTGTAATAATTTTAAGAATATTTCATGCTATAATGTAAGCTTTCTTATAGACATTAGGCTTGTAAAACATACGCCCGGGTTGTTCACTCTCTGCCTTGTTACTGTGTGTGTGTGTATTTCAG
Seq C2 exon
TGCAGATGGACGTTTTGAAGGGGCCAGTACCAAAACCGTCGTCAGGTACGACGGCACGGTGACCTGGACTCCACCGGCAAACTACAAAAGTTCATGTACCATCGACGTCACATTTTTCCCATTTGATCTCCAAAACTGTTCCATGAAATTTGGTTCTTGGACTTACGACGGATCACAGGTTGATATAATTTTGGAGGACCAAGATGTAGACAAGAGAGATTTTTTTGATAATGGAGAATGGGAAATTGTCAGCGCAACAGGGAGCAAAGGAAACAGAACCGACAGCTGTTGCTGGTATCCTTACATCACTTACTCGTTTGTAATTAAGCGTCTGCCTCTCTTTTATACCTTGTTCCTCATTATACCCTGTATTGGGCTCTCATTTTTAACTGTACTTGTCTTCTATCTTCCTTCAAATGAAGGTGAAAAGATCTGTCTCTGCACTTCAGTACTTGTGTCTCTGACTGTCTTCCTTCTCGTTATTGAAGAGATCATACCCTCATCTTCCAAAGTCATACCTCTGATTGGAGAGTACCTGGTGTTCACGATGATTTTTGTGACACTGTCTATCATGGTCACTGTCTTTGCTATCAACATTCATCACCGTTCTTCCTCAACGCACGACGCTATGGCTCCGTGGGTCCGCAAGATATTTCTTCACAAGCTACCGAAACTGCTTTGCATGCGAAGTCATGTAGACAGGTACTTCAGTCAGAAGGAGGAAGCTCGGAGCAGCCGTGGACCCAGATCTTCTAGAAACGCCCTGGAAGCTGCACTGGATTCCGTTCGCTATATCACAAGACACGTCATGAAGGAGACCGATGTCCGTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013657:ENSBTAT00000018151:4
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=0.011
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(17.6=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(54.9=40.3),PF0293211=Neur_chan_memb=WD(100=47.8),PF0293211=Neur_chan_memb=PU(57.7=16.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCCTGATGACTACGGTGGAA
R:
TCCCTGTTGCGCTGACAATTT
Band lengths:
345-2259
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]