BtaINT0038398 @ bosTau6
Intron Retention
Gene
ENSBTAG00000011390 | CHRND
Description
Bos taurus cholinergic receptor, nicotinic, delta (CHRND), mRNA. [Source:RefSeq mRNA;Acc:NM_174271]
Coordinates
chr2:120975092-120975497:+
Coord C1 exon
chr2:120975092-120975143
Coord A exon
chr2:120975144-120975354
Coord C2 exon
chr2:120975355-120975497
Length
211 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGA
5' ss Score
8.24
3' ss Seq
CTGTCCCCCACCCTCCCCAGGCA
3' ss Score
9.77
Exon sequences
Seq C1 exon
ATGGAAGGGTCTGTGTTAACACTAGTGCTGCTGGCCGCCCTGGTCGTGTGTG
Seq A exon
GTAAGAATGGCCATCACCCTCCCCAAAGTGTCCCCATTGCATGATCTCCTCCCTCCTCGCCCGGGACACCCTCTCCCAGCATCAGGCTCACCTCCCCACTCCCACGGCCACTTTTTTTCCCTGGAGGGGCCGCCCCCCGGGGTCCCACTGCATGCCCAGCAGGACCTCAGGGCAGCGTCCTCCCTGGGCCCCTGTCCCCCACCCTCCCCAG
Seq C2 exon
GCAGCTGGGGCTTGAACGAGGAGGAGCGGCTGATCCGGCACCTGTTTGAGGAGAAGGCCTACAACAAGGAACTGCGGCCCGCAGCGCACAAAGAGAGCGTGGAGATCTCCCTGGCTCTCACCCTCTCCAACCTCATCTCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011390:ENSBTAT00000015135:1
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(18.1=83.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGGTCTGTGTTAACACTAGTGC
R:
GGGAGATGAGGTTGGAGAGGG
Band lengths:
188-399
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]