DreINT0046809 @ danRer10
Intron Retention
Gene
ENSDARG00000034307 | chrne
Description
cholinergic receptor, nicotinic, epsilon [Source:ZFIN;Acc:ZDB-GENE-040808-32]
Coordinates
chr5:37845056-37845762:-
Coord C1 exon
chr5:37845662-37845762
Coord A exon
chr5:37845257-37845661
Coord C2 exon
chr5:37845056-37845256
Length
405 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCCA
5' ss Score
3.75
3' ss Seq
TTAATCACATGGTCTCACAGAAA
3' ss Score
7.3
Exon sequences
Seq C1 exon
GTCTCAGACATACAGTGCAAATGAGATTGATATTGTACTGGCAGAAGATGAGAACGGAAAGCCTATTGAGTGGGTGGACATTGATCCTGAGGCTTTCACAG
Seq A exon
GTGCCATGCGTACACATTTTATTATTTATTACACACAGACATAGAAGAAAGAAGGAATTATTACTTTAATCGGCCAGAAAATATTTAACTGACAAAAAGTGATGGGTAAAACCAGGGCTGTATCAATATATTAGTATGGGTTAATACAGTAATCAAAGGAGTAATGATACAATCAGTTTTGACAAAGTTACTTCAAAAATGTAATTATTTACATCATTAAAATAATATTACTATATGTCTAAAACGTTATTTAATTTACTTGACTACTACTGAAAATCTATATACATCTCAACAAATAGACAATAAAAGTTAAGTCAAATGTGGGCTTTTAGCTTTATTAAACATCGTAATACTAAACCATTTAAAATGAAACTCCGTATCTTTTTTAATCACATGGTCTCACAG
Seq C2 exon
AAAACGGTGAGTGGGCAATCAAGCACCGGCCCGCCCGAAAGCTGACAAACCAACGCTACTCTCCAGATGACCTGGAGTACCAGGAGGTATATTACAACATCATAATCCAAAGGAAACCGCTTTTCTACGTCATCAACATCATCCTGCCCTGCTCTCTCATCTCCTCTCTGGTCGTTCTTGCCTATTTTCTACCTGCAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000034307:ENSDART00000136428:6
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(15.7=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(18.0=57.4),PF0293211=Neur_chan_memb=PU(26.9=30.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCTCAGACATACAGTGCAAATGA
R:
CTTTTGCAGGTAGAAAATAGGCA
Band lengths:
302-707
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]