DreINT0046818 @ danRer10
Intron Retention
Gene
ENSDARG00000086647 | chrng
Description
cholinergic receptor, nicotinic, gamma [Source:ZFIN;Acc:ZDB-GENE-030131-3805]
Coordinates
chr2:45232042-45232707:+
Coord C1 exon
chr2:45232042-45232163
Coord A exon
chr2:45232164-45232551
Coord C2 exon
chr2:45232552-45232707
Length
388 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGG
5' ss Score
5.85
3' ss Seq
TTGTGTGTATGTGTGTAAAGTGT
3' ss Score
3.31
Exon sequences
Seq C1 exon
CAATGGCGGGATTATCGACTGCGCTGGGCAAACAGGACAGGCTTTGAGGTCTATGAGAACATCACCCGCATGCGTCTTCCATCCAAAACCATCTGGCTGCCTGATATTGGCCTGGAGAACAA
Seq A exon
GTGAGGGATAGAAATAGTATAGAAGATCAATCTGACTTTAAAAAGACTTTTATTCTGTAAATCAGTGGTGACATTTCTTCCATTTGTTTAAAACAGGGTTCACCAAACTTGTTCCTGGAGGGCTGGTGTCCTGCAGATTTTAGCCCCAACCTTAATCAAACACACCTGAACAAGCTAATCAAGGTCTTACCAGGTATACTTGAAACACCCAGGCAGGTGTGTTGAGGCACGTTTGAGCTAAACCCTGCAGGGACAGCGGCCCTCCAGGCAAGAGATTGGTGACCCCTGGTTTAAAATGTTGTCACTTATAGCATAAATTGCTATGTGGTCAGACATGTTCATAAATACAACTTTTGTAATGTCTGTTTTTGTGTGTATGTGTGTAAAG
Seq C2 exon
TGTGGATGGGCGTTTTGAAGTGGCGCTCTATGCTAACACACTGATAGATCCTGATGGCAGTGTGTACTGGTTGCCTCCTGCCATCTACCGAAGCTCCTGTGCCATCAAAGTCAACTATTTTCCCTTTGATTGGCAGAATTGCAGCATGGTGTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000086647:ENSDART00000123966:4
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(18.2=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(23.6=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:
CAATGGCGGGATTATCGACTG
R:
CTGAACACCATGCTGCAATTCTG
Band lengths:
278-666
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]