DreINT0046808 @ danRer10
Intron Retention
Gene
ENSDARG00000034307 | chrne
Description
cholinergic receptor, nicotinic, epsilon [Source:ZFIN;Acc:ZDB-GENE-040808-32]
Coordinates
chr5:37845662-37846062:-
Coord C1 exon
chr5:37845907-37846062
Coord A exon
chr5:37845763-37845906
Coord C2 exon
chr5:37845662-37845762
Length
144 bp
Sequences
Splice sites
5' ss Seq
CAGGTTGGC
5' ss Score
5.52
3' ss Seq
GTTTTATTCTTTATCTGCAGGTC
3' ss Score
11.52
Exon sequences
Seq C1 exon
CATTGATGGCAAGTTTGATGTGGCATACTACGCTAATGTGCTGATTTCATCTGATGGCTCCATGTACTGGCTTCCCCCTGCTATCTATCGCAGCACCTGTGCTATTGAAATCACCTACTTCCCTTTTGACTGGCAGAACTGCACACTGGTCTTCAG
Seq A exon
GTTGGCACAGATTGATCCATGGAAATAGATGACAAGATTTTGGATCAAATTATTTCGTTGTATTTTTAATTATTTTCATAAACATATACATTTTATATTGTATATCACATTTATGTAACATTTTGTTTTATTCTTTATCTGCAG
Seq C2 exon
GTCTCAGACATACAGTGCAAATGAGATTGATATTGTACTGGCAGAAGATGAGAACGGAAAGCCTATTGAGTGGGTGGACATTGATCCTGAGGCTTTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000034307:ENSDART00000136428:5
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(24.0=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(15.7=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:
GATGGCAAGTTTGATGTGGCA
R:
GCCTCAGGATCAATGTCCACC
Band lengths:
245-389
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]