DreINT0046793 @ danRer10
Intron Retention
Gene
ENSDARG00000019342 | chrnd
Description
cholinergic receptor, nicotinic, delta (muscle) [Source:ZFIN;Acc:ZDB-GENE-030131-6665]
Coordinates
chr24:25538120-25540560:-
Coord C1 exon
chr24:25540442-25540560
Coord A exon
chr24:25538482-25540441
Coord C2 exon
chr24:25538120-25538481
Length
1960 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGG
5' ss Score
10.28
3' ss Seq
CCATATGCACTCTTTCTCAGGAA
3' ss Score
7.84
Exon sequences
Seq C1 exon
CGTACACATCCAGTAATGACTCTGAGGTGTCGGAACAGCTGTACAATGAGATGAAGCCAGCTGTAGAAGGAGCCAATTACATTGTTAAGCACATGCACGACAAAAATGACTATAATGAG
Seq A exon
GTAAGGAGACAATTATATTTGGTAAAACACCTCACTGGAGGTTATTCACTCTTTTAGCCTTATAAAGACCTGAAGTAATTAATTAAGTGATTTTTTTTTTTAAACCAAGAGGATATAATATGAATATCAATCAACATATTGATTAGATGATTGATATATTTTATATTTAATTAATATATTTTAATAATTACTTATTGTATAATTGTATTGTATGTTATAAATACATAGCAAATTGTTCTCTCTATGTAAAGAGTAGAATATTAGTTTCTTCTCTAAACGTAATTTAAAGAAAACATTTCATATATGTGTTAAAGTATTGAAATGTTAAATTGAATTATTAATATATAATATCCTATTTATTATAGACGTATGTTTTTTATATAAACTCACCGGCCATTTTATTAGGTACACCTTACTAGGACCCCCTTTTGCCTTCAGTACTGCCCTAATCTTTAATGGCATAGATTCAACAAGATACTGGAAATACTCCTCATAGATTTTGATCAATATTGACATGATAGCCTCACACAGTTGCTGCAGATCCATGATGCGAATGTTCCATTCCACCACATCCCAAAGTGCTCTATTGATTGAAATCTGGTGACTGTGGAGGCCATCTGTGTGCAGTGAACTCATTATCATGTTCAAGAAACCAGACTGAGATGATTCGTGCTTTATGACATGGTGCGTTATCCTGCTGGATGTAGCCATCAGAAGATGGGTACATAGACTGTGGTGTAGACACGATGCTTAGTTGGTACAAATGGGCCCAAAGTGTACCAAGAAAACATCCCCCTCAACCGTTGATACAAGGCAAGATGGATCCACGTTTTTATGTTGTTGATACCAAATTCTGACCCTACCATTCGAATGTCTCAGCAGAAATCGAGACTCATCAGACCAGGCAATGTTTTTCCAATCTTCTATTGTCCAATTTTGGTGAGCCTGCAAGAATTGTGGCCTCAGTTTCCTGTTCCTAGCTGATAGGAGTGACACCCGGTGTGGGCTTCTGCTGCTGTAGCCCATCCGCCTAACGGCTTGATGAGTTGTACATTCAGAGATGCTATTCTGCATACCTATTGAGTGTAACGAGAGGTCATTTGAGTTACTGTTGCCTTTCTATCAGCTCGAACCAGTCTGGCCATTTTCCTCTGACCTCTGGCATCAGCAAGGCATTTGTGCACTCAGAACTGCAGCTCACTGGATATTTTCTCTTTTTCGGACCATTCTGTGTAAACCCTAGAGATGGTTGTGCATGAAAATCCCAGTAGATCAGCAGTTTCTGAAATACTCAGACCAGCCAGTCTGGCACCAACAACCATGCCACATACAAAGTCCCTTAAATCACATTTCCTCCACATTTTGATGCTCAGTTTGAACTGCAGCAGATCGTCTTGACCATGACTACATGCCTAAATGCGTTGAGTTGCTGCCACCTGATTGGAAATTTGCGTTAAGGAGCAGTTGGACAGGTTTACCTAAAACAGTGGCTGGTGAGTGTATGTGCATACAAAGTTAAAGACAAAATGTGTATTCCTCCTTTAAGTTTTTTATTCTTTTTCAAATATTTTCCAAGTGATATTTAAGGAATTAAGCATTTACTGCATTTACTATATATTTTTTTTCTTCTGGAGAAAGTCTTATTGCTTTTAGTGTGCCAGAAATAAACTTTTTTTTTTATCATTTAAACAATATATTAGCCCCTTTCTTTCTTATTTTTTTCGAATGACTACAGAAAAACAGAAGAAAAAAGTTCATAGAAATTAGTTGTGTAAATCCCCACGTTAAACAGGATTAGAGAAATATAAATAAAATAAATTAGTAGAAATTATTATTGCATAATTAAAAGGGATAATAATTTTGACTTCAACTGTATATGTACATTAATGCATTGTATCATTTGCAATATAAATATAAAAGTATTAAGCTAAAATTATAATCCATATGCACTCTTTCTCAG
Seq C2 exon
GAAAAGGACAACTGGAGCGGGATTGCCAGGACTGTGGACAGGCTCTGCTTCTACGTGGTCACTCCAGTTATGATGATAGGAACCATTTGCATCTTCCTGATGGCCAATTACAATCAGCCACCAGCGTTGCCTTTCCAGGGAGACCCCTTCTCCTATACTGAAGAAAACAGGCGCTATTTGTGACCTTTCATAATAACACAGAAATAGCATAAAGCATATTCTGACAGCAATATAAAGCATGAATATGAATTATCCTTGATTTTCGCTGTTTATGCAGGCTTGATTACTAATATTATGTAGTTATGTATGTTTAATAAGTGTGCTGTGAGAAGAGGCAATAAAGTAATATTGCCTTCCTTTTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000019342:ENSDART00000015391:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.425 A=NA C2=0.100
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=FE(16.3=100)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(13.0=50.8)
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:
GAAGCCAGCTGTAGAAGGAGC
R:
TCAAGCCTGCATAAACAGCGA
Band lengths:
350-2310
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]