BtaINT0038344 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003130 | CHRNA3
Description
Bos taurus cholinergic receptor, nicotinic, alpha 3 (neuronal) (CHRNA3), mRNA. [Source:RefSeq mRNA;Acc:NM_174719]
Coordinates
chr21:31512616-31512927:-
Coord C1 exon
chr21:31512774-31512927
Coord A exon
chr21:31512661-31512773
Coord C2 exon
chr21:31512616-31512660
Length
113 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
ACTTGAATCTCTCTTTCTAGGAT
3' ss Score
10.91
Exon sequences
Seq C1 exon
GCTACTTCCCTCAGTGGCCAGCACGTCCGACGCAGAGCATCGCCTGTTTGAGCGCCTGTTTGAAGATTACAACGAGATCATCCGGCCAGTGGCCAATGTGTCTGACCCGGTCATCATCCAGTTTGAGGTGTCCATGTCTCAGCTGGTGAAGGTG
Seq A exon
GTGAGTGTCAGAGCCACAAGCCGTGGCCGTGGGGGATGGAGCTTCTGGAAGAGCCTTTCCCAGAACCAGCCTTGTTTTTGTAATTCACCATCTACTTGAATCTCTCTTTCTAG
Seq C2 exon
GATGAAGTAAACCAGATCATGGAGACTAACCTGTGGCTCAAGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003130:ENSBTAT00000004070:1
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:
PF0293118=Neur_chan_LBD=PU(18.8=76.5)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(6.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTACTTCCCTCAGTGGCCAG
R:
TGAGCCACAGGTTAGTCTCCA
Band lengths:
194-307
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]