DreINT0046810 @ danRer10
Intron Retention
Gene
ENSDARG00000034307 | chrne
Description
cholinergic receptor, nicotinic, epsilon [Source:ZFIN;Acc:ZDB-GENE-040808-32]
Coordinates
chr5:37843402-37845256:-
Coord C1 exon
chr5:37845056-37845256
Coord A exon
chr5:37843517-37845055
Coord C2 exon
chr5:37843402-37843516
Length
1539 bp
Sequences
Splice sites
5' ss Seq
AAGGTGTGT
5' ss Score
6.64
3' ss Seq
TTACTGTCTCTTCTTCTTAGCTG
3' ss Score
8.76
Exon sequences
Seq C1 exon
AAAACGGTGAGTGGGCAATCAAGCACCGGCCCGCCCGAAAGCTGACAAACCAACGCTACTCTCCAGATGACCTGGAGTACCAGGAGGTATATTACAACATCATAATCCAAAGGAAACCGCTTTTCTACGTCATCAACATCATCCTGCCCTGCTCTCTCATCTCCTCTCTGGTCGTTCTTGCCTATTTTCTACCTGCAAAAG
Seq A exon
GTGTGTGTGTGTGCATGTGCAGACATTCTGAGATTATGCTTCGTAAGCCTCAAAATAAATAGTTGTTAATTCTGACATCACATGTCAAAGTTTCTGGAAGGAAAATCTCTATCAACTGACAAAAGTGAATGACGAATGATACTTTGACATGTTCAGTGTGCCGCAATTCTATTTGAGTTTTAATCTCAGAGGGTCAGACCATCCATGTCCTCACTAAAATTTTCACACAATTTTTTTCCTCTCCGTTTTGGGCTTCCACCCACACTGTAACTGTCTTTTTAGTCAACAAAATGTATTTTTATAAAAACCTCTAAAGTGTTGTTATTAAGTTACAGTGTGGACTTAGCAAAACATTAACACACTTTTAGTCATGTGACCAATTCAGCCAAAATAGTGGAGGATTTTGAACAGCCGTTTCTTTGTATATTTTCTGTTTGGAAAACCTTGTTGAAGATTCATTGCGTTCTATTATAATGATCTAGGTGCAAAGTCTAAAGAGCAGGACACAAATAGATAGGGTGTCTGAATCCACTTTTGCTATTTTAAGGATGGGAAAACATGGTTTGTGGTCTAACAGGTCTAACATGGTCTAACAGGGTTGTGCTTATTCTCTTAATGAGTTATGCAAAAGAATAATTTTTCTAACGTTTTAATCCTTTAATTTTTTTAATATGTAAAGATATGTGTGTATTGCTGTACATCCTGTGTGTATTAAGAGTTTGAACATTCATAGACACAAAACTAATGCATTCTGCGCTGGACTTTAGGCCAGCTTTTACCTGGTCAACGGTGCAGTCTATTTCAGTTCTTCAAAATAGCAACGTGCCAACAACACGCAACACATCACACCAGCACGCCTATGAGTCCACAAAGAAGTGCGAACAGATTTTCTATTTAAACAACGTGGTGCAAAGCGTAAAACTTAGGGTTTTGTTAGTCTGAAAATAGCAAAAAATCGCACAAAACACGTCTTGGACCTTATTGCACCGGGTGTAGGAAAGGGTCCATAGTTTGTACATGCTTCTTTAAAGGACATGGAATTTTTATTCAAATCTTTTGTTTTGACACATCTTCTAATCAATGTTCTCGATCACGTTTGTAACCTTATACTTCTGTGTTGATTGCCACAATGTTTCAAAGAGCCAGAATGTAAATAAACATCTTAATGCATCCACAGTACAGGGACAAAAGAATTTTCAGTTGTTTCTTTTGGGACATTTTTCCTGAACTTGTGTAGACAGCAAGATGCATGCAGCAAGAGACCAAAGTGTACAACATGATTTAGTAAAAGATGCTTTTTAAAGTGTGATGTGACTAAACAGCAGTCCCAAACATCTATTGAGTTTTCCCAGTTCAAGTAAGTAGAAGCTTGGACTGAGAAACTTTACTCCACATGTCACAATTACACAAGTAGATAAAATTTCTAGTCTCTTTTTCTTAAGGTAGCACTTCCTCTATCTGTGATTTCTGCTTTTGCTCTTCAACATCTCTTTCTATGATACTGTTGTCTCACACTTTCTTACTGTCTCTTCTTCTTAG
Seq C2 exon
CTGGCGGGCAGAAGTTGACTGTGTCCATTTCTGTTCTTTTGGCTCAGACTGTGTTTCTCATCCTGATTTCTCAGAAAATACCAGAAACGTCACTGTCTGTGCCTCTTATTGGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000034307:ENSDART00000136428:7
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=PD(18.0=57.4),PF0293211=Neur_chan_memb=PU(26.9=30.9)
A:
NA
C2:
PF0293211=Neur_chan_memb=FE(48.7=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:
AACGGTGAGTGGGCAATCAAG
R:
CCAATAAGAGGCACAGACAGT
Band lengths:
311-1850
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]