DreINT0046725 @ danRer10
Intron Retention
Gene
ENSDARG00000070724 | chrna4b
Description
cholinergic receptor, nicotinic, alpha 4b [Source:ZFIN;Acc:ZDB-GENE-090505-3]
Coordinates
chr11:12936080-12936399:-
Coord C1 exon
chr11:12936248-12936399
Coord A exon
chr11:12936125-12936247
Coord C2 exon
chr11:12936080-12936124
Length
123 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
ACTTTGCTTCATAAAACCAGGAT
3' ss Score
4.91
Exon sequences
Seq C1 exon
TGTTTTCCATGAGCCCAGCTCATGCCCATGCGGAAGAAAGACTCCTCCAGTCTTTGTTCATCAACTACAACAAGCTTTCACGTCCAGTAGCAAACATCTCTGATGTGGTTCTGGTCCATTTCGGCTTGTCCATTGCTCAGCTCATTGATGTG
Seq A exon
GTGAGTCTCAGATATCCTACTTTTTTCTTTTCCTCTAAATCGTACAGTCTCACCATAAAGTCACTTTCCCTTTTTTTATTACTCTCTTCTGTATGGAAATCTCACTTTGCTTCATAAAACCAG
Seq C2 exon
GATGAGAAGAATCAGATGATGACCACAAATGTCTGGGTGAAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000070724:ENSDART00000018614:2
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=76.5)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(6.8=100)
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:
TGTTTTCCATGAGCCCAGCT
R:
GCTTCACCCAGACATTTGTGG
Band lengths:
195-318
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]