DreINT0046732 @ danRer10
Intron Retention
Gene
ENSDARG00000003420 | chrna5
Description
cholinergic receptor, nicotinic, alpha 5 [Source:ZFIN;Acc:ZDB-GENE-050417-440]
Coordinates
chr18:40503604-40503874:-
Coord C1 exon
chr18:40503830-40503874
Coord A exon
chr18:40503714-40503829
Coord C2 exon
chr18:40503604-40503713
Length
116 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
TCAATCTCTTTCACATTCAGGAA
3' ss Score
10.2
Exon sequences
Seq C1 exon
GATGAGAAGAACCAGCTGATGACGACCAATGTGTGGATGAAGCAG
Seq A exon
GTAAAGCAGTACTTAATAATCCAGTAATATTTTTCTTATGTGGTTCTGGTAGTATTTTGTTAAAGAGTTTCTTAAGTTTTGTTTGTGTGAGACAAATCAATCTCTTTCACATTCAG
Seq C2 exon
GAATGGACAGACTTGAAGCTCAGATGGGATCCGGATCATTACCTGGGCATCACCTCTATCAGGGTGCCTTCAGACTCCATCTGGATTCCTGACATTGTGCTCTATGACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000003420:ENSDART00000021372:4
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(6.9=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(17.6=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:
ATGAGAAGAACCAGCTGATGACG
R:
TTGTCATAGAGCACAATGTCAGGA
Band lengths:
154-270
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]