BtaINT0038355 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013657 | CHRNA5
Description
Bos taurus cholinergic receptor, nicotinic, alpha 5 (CHRNA5), mRNA. [Source:RefSeq mRNA;Acc:NM_174514]
Coordinates
chr21:31488056-31489847:+
Coord C1 exon
chr21:31488056-31488100
Coord A exon
chr21:31488101-31489737
Coord C2 exon
chr21:31489738-31489847
Length
1637 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
CAGGTTTCTTTGTTTTAAAGGAG
3' ss Score
6.33
Exon sequences
Seq C1 exon
GATGAGAAAAATCAGTTAATGACAACCAATGTCTGGTTGAAACAG
Seq A exon
GTATGTATTGAATTTGAAGGGCCATGTAACTGTTAACTGGTGCCATTGTTATTACAGAGTTTGTAGCACAGAAGGGACATGAATATTTGGTCTCGGTGGACAAGCAGGAGGCAGAAAAGTGAGGTAGATGGAGTCTTGTATTCATGCAGTTAATACTGAGTGCCTGGCATTTGGCAGGCACTGTTCTGGGCACTGGGGAAGCAGCAGTGAACAAAACAGACAGAAGTCTAGCCCTCAAGGAACGTCATTCCAATGGGGGGCAGTGGGATAAATAGGAAGTTGTATAGTACTTTTCAAGCTGATAAGCTTGGAGAAAAACACTGAAAAGGCAGACAGGAAGTGTGGGGACTGGACTTTTAAATTGGATGGCAGGAGAAGTGCCACTGAGAAGGTAAGATTTGAACAAAGACTTGAAGAAGCAAGCCACGCAAGTATCTGGGGGAGGAGTGTCCAGGCAGAGGGACACAAACGTGCAAAGGCCCTGAGGTTGGAAGGTGCCTGGTGTGTTGAGGGAGTAGCAAAGAAGCCAGCTGCTAGGGGTGAGTGGCCATGGGGATGGGAGTGGGAGATGAGGTCAGTGAAGCTACCAGAGGCCGATGGGTACTCCTAACATAGGTTATGAGTAGTGGCTTCTAGGCCACTGTAGGATCTTGGTTTTTACTCTGAGTGAGATGGGAGCAGGCAAGAATGTAATGATTTATTTTTATTTTCATAGTCCCTTTTATATAAAGGAGTTTTTCTTTCTGTTTCTGGACCGTCATATGTGCCCAAGTGCTGTTGAGTGCTTCCCTTTGTTTGTTCTTTATTACTCCTGACTTTATTTATCTTTGATTGCACTGGGTCTTCATTACTGCGCACAGGCTTTCTCTAGTTGCAGAGAGCGGGGGCTACTCTTTGTTGTGGTGCACAGACCCATTGTCATGGCATCTCTTGTTGTGGAGCATGGGCTCTGGGGCACGGGGGCTTCAGTGGTTATGGTGCAGGGGTTTAGTTGCCCTGCAGAATATGGAATCTTCCCAGGCCAGAGATGGAACCCATGTCCCCTGCATTGGTAGGTGGACTCTTAACCACTGGATTACCAGGGAAGTCCTGTCCCTGATTTTTAATACTTACTACCAGTTCTCTAGCCCCAAACTCTTTAAAGGCGTATGTGCTTTCCTTGGGGTGCAAGTCTTTACCTGATCACAGAATTATTACGATGTGGAGGTGGGATGGTGTGTTTAACTATGTGGAATGTGTCATAAATCTGTCTGCTCTTTGCATGGCCTAGTCCAGCTAAGTCAATGACAAAACGGCTAGAAAAGAGAATGTTTTCCTTGAACCTGGACCTTTGCCTGGCCTGGACCAGGCTGTAGCTCCTGGGTATGGTTAGCTGGTAGAAGAGGTGTCGAGCAGAGCAATGAACGCACCCAGCTCTGGTCCTCACCTGTCTCATGAGGGCCATAGTTACAGCCACCTCAAGAGGGGACAGGGCTGTCCCCCAGTGCCCATAAGAAGGATGTGGAGGTGAGTTTTCTCTGCTGGGAGTAGAGGTGACTTCGTGTCTAAAATATCTGAGTTTGGCAAAAAGAGTAGAGTTTTCACTGTTTTTGGCTATTGCTTTTATTGAAATTGATTCAGGTTTCTTTGTTTTAAAG
Seq C2 exon
GAGTGGATAGATGTGAAGTTGAGATGGAACCCTGATGACTACGGTGGAATAAAACTTATACGTGTCCCTTCAGACTCTCTCTGGACTCCAGATATCGTTTTGTTTGATAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013657:ENSBTAT00000018151:3
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=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(6.9=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(17.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm10)
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]