DreINT0046791 @ danRer10
Intron Retention
Gene
ENSDARG00000019342 | chrnd
Description
cholinergic receptor, nicotinic, delta (muscle) [Source:ZFIN;Acc:ZDB-GENE-030131-6665]
Coordinates
chr24:25545102-25546069:-
Coord C1 exon
chr24:25545735-25546069
Coord A exon
chr24:25545248-25545734
Coord C2 exon
chr24:25545102-25545247
Length
487 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGA
5' ss Score
9.45
3' ss Seq
ACTTGCAGTGTGTTTTGCAGAAT
3' ss Score
7.35
Exon sequences
Seq C1 exon
ACAGCTGATAAGGAGTGGTTTGGTTGACTTCTTGGTTTAGATAAGAATGAATGTTGGGAAGAAAATTTGTATGTTTCTTAATTAATTTGTTCACATATTCTGTTCTCCTCAGTTTTGTTGAGCACCCCCTACAGTCCCTGTGGTGCAGCCAGTGGATACTGGAGATTATGTATGTGTGGTTTTTTTCTTCTCTGGATTGATTCCACACCTGTCTATGTCAGTCAAGGGAAAGGCTGGACTGGCACAGCACTAACAGAGATAGGAAGTCATACAACAGCAGGCCATGATGAAAACTGTTCTATTGACGGCGTCCTTGCTTTGCTTCATTTTTCAAG
Seq A exon
GTAGGACAAGTTAAATTAATATTTCAAATGTTGGGTTTTCTGTCCTGCTGTTTGTCAGCTATTGTTCTGTCACGCTTTTATAGTATAACAGGTGTATAGTGAGTTATAGGACTTTTTCTATAAATCAATTTAAATTTAGTTTAAAATATAATTAAAATCTATTTAAAATTAGAGCTTTTTTACACTTTGGTTTACATGTGACTCATTTATATATTTGAAATGTGTTTGGAAGCAAATATTAATAAAATAAATCAGTTTTACATAATATGTTATGTAAAATACTCAATCTGAAGATTATCACTATAATTTTTTTATGATGTCTGTGAAATACAAATTAGTTTTCCAGGAGTATGACATTAAGGTATTTGTACTGTAGATCAGTGTTGGTCAACAATATCTAACTGTTAAAGACTTATTTGTGTGTCAAAATTAGAGCTATACCTATAGTAGATCTTGAAATAGGTCTGACTTGCAGTGTGTTTTGCAG
Seq C2 exon
AATGTTGTGGCCGAAATGAAGAGGAGCGCCTCATCAATTATCTTTTTAAGGAGCGTGGCTACAACAAAGAGCTTCGGCCGGTCCAAAATAAAGATGAAACTGTAGATATTTACCTGGCTCTGACACTTTCTAATCTCATTTCCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000019342:ENSDART00000015391:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0293118=Neur_chan_LBD=PU(18.6=83.7)
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:
TCAGTTTTGTTGAGCACCCCC
R:
AGAAAGTGTCAGAGCCAGGTA
Band lengths:
358-845
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]