DreINT0046804 @ danRer10
Intron Retention
Gene
ENSDARG00000034307 | chrne
Description
cholinergic receptor, nicotinic, epsilon [Source:ZFIN;Acc:ZDB-GENE-040808-32]
Coordinates
chr5:37839946-37841269:-
Coord C1 exon
chr5:37841136-37841269
Coord A exon
chr5:37841049-37841135
Coord C2 exon
chr5:37839946-37841048
Length
87 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGT
5' ss Score
11.78
3' ss Seq
TTGCTCCTTTTTTATCACAGGAG
3' ss Score
8.22
Exon sequences
Seq C1 exon
TGGATGAAATTGATGTGAGCAGTACCGCAAACCTCTACAAGAGTCTGGCAAAGACGGCCCCAGAAATAAAAGAGTGTGTGGATGCCTGTAACTTCATTGCTGAATCCACCAAGCAGCAGAATGACACTGGATCG
Seq A exon
GTAAGTGTGTGTGTCTCTGTATTAATGTCAACATTCATGAACAATAGAGTATACTTGCTCCATCTTGTTGCTCCTTTTTTATCACAG
Seq C2 exon
GAGATGGAGAGTTGGGTGCTGATTGGTAAGATGATTGACAAGGTTTGTTTTTGGGCGGCCATCTCTCTATTCTCAATTGGCACCATTGCTATCTTCCTCATGGGTCACTACAACCAAGCACCTGAGTACCCATTTGCTTGGGAGAACAAAAAGTATGTGCCTGAGTAGTGCTCTGAAAACTGGACAGATTTTTAAGTAAGTCAGTCAGTAAGTTTTATAGCTCGGGTTAGAGTACAGCAAGCTGCACATGATGTGAACAATATCATCTGACTTGATATATGATTTTGTCTTATATTTAATATTAGGGTCTATGGGTGTTGCATGTCTAAACTTTTTTGTACTAATTATTATTTACACTACTGGGGTTTTTACAGAAATGTAATTTTTTTTTCAAACATTACAAAAACATTATTTTCAAACATTCATTCGTTCATTTTCTTTTCGGCTTAGTCTCTTTAATAATCTGGGGTCGCCACAGCAAAATTAACCGCCAACTTATCCAGTGGTACAGATGTGAAATAGTTGTCCGTTTCAAATGGTACTAATTTATTTACGCAGCGGATGCCCTTCCAGCTGCATCCATCTCTGGGAAACATCCGTACACACTCATTCACACACATACACTATTTTCAAACATGAGAAAATATACTGAGGAATTCACCTTATTTCATACAAAATAGTGACCTTTCAGTTTGCTGTGGCTGCATTTTATAATCCCACAACAAGTTTTACCATCTCTTTTTACAGTGTGCTATTAAACCAGTGTGTTATGTCAGCCACTTTTGATTTATAAAATACAGTAGTATTTAGCATTAGTATTAAAGAGATGCATACTGATTTTTGTTTGTTCTATGTATTTATTTATTGTACTTCAAATTTACAAATGCAGTGTTCATCCAATTTATTATTAACTAATAATTTTATGGCCTATTTGCAGTAAATAAATAGATTTTCTTAATTCACACTGTCTTAAGATATGCACTGCAAATGCACCAGAAATTGTAAGAACATGTTTAAAGCGTGCATTAGGCAATGTGCTGTTCTGCCTTTTCTATATGTACCAGAAACAAAGGATAAAATAAATCAAGTATTTAAAGTAAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000034307:ENSDART00000136428:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.022 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=FE(18.1=100)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(12.8=55.4)
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:
TCCACCAAGCAGCAGAATGAC
R:
GCAAATGGGTACTCAGGTGCT
Band lengths:
167-254
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]