BtaINT0038369 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015252 | CHRNA9
Description
Bos taurus cholinergic receptor, nicotinic, alpha 9 (CHRNA9), mRNA. [Source:RefSeq mRNA;Acc:NM_001192546]
Coordinates
chr6:60971425-60972633:+
Coord C1 exon
chr6:60971425-60971570
Coord A exon
chr6:60971571-60972478
Coord C2 exon
chr6:60972479-60972633
Length
908 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
TATCTGGGTTAATTGTGCAGGAT
3' ss Score
5.5
Exon sequences
Seq C1 exon
CTGTAGAACCAGCAGATGGAAAATATGCTCAGAAGTTGTTCAATGACCTTTTTGAAGACTACTCTAATGCTCTTCGTCCAGTAGAGGATACAGATAAAGTCCTGAACGTCACACTCCAGATTACACTTTCTCAGATTAAGGATATG
Seq A exon
GTGAGTAACATAGTGTTGACTCTTCTGAATGGTTCGAATGAAACTAACAGTGCTTTCTAAAGGGAATGTCTTACCTGAATTTGACAGAAAATGAGAACAGACAGCTCTGTGTGCAAGCTGGAGGGAGAAGGGAATTCCAGAGGAGGAACACTTTCTACAAAATTAATTGCACTAAATTACCTGAGTCTTTCCATGAACATTAACAGTCTTAGAACATCTCAAGAAAGTTGGTTACGCATTACATGTTCCATTTCTATGAAATGTGTAAAGTCAGCAAGACCATAAAGACAGAAAGAGGAGTTAGGTTGCCAGGAGCTGTGAGAATGATGAGGAAATAGTGATTTACTGCTTGATTGTCATATGATTTCTCTTTGGGAATGACAAAATGTTCTGGAAGCAGAGAATGGGGATGGTTGCATGACATTGTGAATAAACTGGAAACCGCTGAATTGCACACTTTAAATAGTTAAAGTGGTGAGTTTCATGCAATATGAATTTTATCCTAATTTTTAAAAGATGTTTTAAGATGACATACATTGATGCTCATATGTGTTTAGTTACACAAAGTTATGAAACTTCAAAATCTTTTCTTCTGTACATTGTTGATGTTTGCTGACTTTTTCATAAAAAAATAATTCATCAGTTGATCAATTTTCAGAGAAATTTGAGCAGTTGACCCATGCATGATGATTTAAATATTTGTCCACTTGATGTTCCAAACACTAATCAAGCAGGGAAAATATAACCTTGGCAGACAATCAAGGGGATTGATTTGAAAAAACTCTCGCTTACTTATTGGAAATAGATTAGTGCTCTTGGAATTCCTGTTTTGAAGACAGCTGTTTTACAGACAAAATGTGTTTGGTTGAGGTGTCTACTGGACAGTTATATCTGGGTTAATTGTGCAG
Seq C2 exon
GATGAGAGAAACCAAATTCTGACTGCCTATTTGTGGATCCGCCAAATCTGGCATGATGCGTATCTCACATGGGATCGAGACCAATATGATGGACTGGACTCCATCAGGATCCCCAGCGACCTGGTGTGGAGACCGGATATTGTCCTATATAACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015252:ENSBTAT00000039651:2
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=PU(18.8=79.6)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(24.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGATGGAAAATATGCTCAGAAGTTGT
R:
GGACAATATCCGGTCTCCACAC
Band lengths:
278-1186
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]