DreINT0046801 @ danRer10
Intron Retention
Gene
ENSDARG00000019342 | chrnd
Description
cholinergic receptor, nicotinic, delta (muscle) [Source:ZFIN;Acc:ZDB-GENE-030131-6665]
Coordinates
chr24:25540645-25542381:-
Coord C1 exon
chr24:25542267-25542381
Coord A exon
chr24:25540856-25542266
Coord C2 exon
chr24:25540645-25540855
Length
1411 bp
Sequences
Splice sites
5' ss Seq
GAGGTTAGA
5' ss Score
4.15
3' ss Seq
ATTTATTTTGTCTGCTGCAGTTC
3' ss Score
8.59
Exon sequences
Seq C1 exon
GTATCTGATGTTTATCATGGTGTTGGTCACTGTGGTGGTGTTGAATTGTGTCATTGTGTTGAACCTGCATTTTCGGACGCCCAGCACACACGTCATGACGGAATGGACCAAAGAG
Seq A exon
GTTAGACTCTCACTTGTTTGTAGAATAAAAATTAATAAATTGCGCAAGTCATCACAGTGGAAAACATTGCATTTTAATGATGGTGTCAAACGGTAAAAATATAAGAAACAAAACACAAAAAAAGTGAAATTATGCATGAAAATAAGCTGATTCGAATTTTATAACTTGATTGAATAGGTGTTATCAGTAATTATCAGCTCATAGATATGGGCCAGTAGGGGCCTTCTGCACCTACTGGTAGGCTCAGAAGGCTATCATCAATCAACATACTATACATCACATATGGCTGATGGGTACTGCTGCCAAATTTTATATATATACAATATATATATTAATAAATTTCCCATTAATTGTATTTTATTAATGTCTATCAATACCCAACGCTAAACCCAACCATCACAGTAATGTAAAACAGATCTGGTTCTATTGTAGTATAGCTGATTAACCATGTAGATGGATGAAAACAGCCTTCTGAGACTACCAGTAGGTGCAGAAGGCCCCTACAGGCCCATATCTATCAGCTGATAATGGCCATTCAATCAGTTATAACATTCAAAGCGGATGTTGCTGGTTACCCTTTGCTAGTAAGTAAATAAGTCATGCTTAGCAAAGGCAAAGGTGCATAGTGTTTCATTACAAAGTCACAACTACAGTTTGTTCAGCAAAAAAACAACCACTTATGAGTTTTTGTCTTGTTTCTAGTCCAAACATGTAAGATGCATTTTAAAAAATAAAATTAAAAAATAATCTTTTGTGTTTGGTTATAAGTTGTCAGAATTAAGTGAGTTTGTCCTTAAAGTTTGTTGAGTTTGTCTATCTGTGTTCTGAATAATTTTGAGATATTGAGCTTCAAAGTTTTTGCATTCCATAGCAAACAGTATGTGTGTAACATTTGTTTTTTAAATAAAAAGTCTTAAAATGTACACAGCTTATAAAAAACATCCCATAATGTAAATAAGTTGTCATGTAATAAGAATATGTCAATAACTCAATTTTGACAAAAAATGTCAGATAGAACTTTATAATTCCAAGATCACGATTTGTAGATCCATGTAAATCTTACCCTTTTGACAGTTCAGTTTGACAATCTGTTTGTACAATTGTACAGATGTGCAAATTAAATATCAACATTTGAGCCAATATCACCATTATCAGAGAAAGCGTTCCAATGAAAATACAATTTCAGTACAATTTCTTATTTAATTCAATGTGTTACTTGCTGTTGTGTTTATAATTATTTATGATTATAATTAATATAATCAAACTTATCAATAGTGGTATTTATGTGATTTTTATGTGAAACTTGACACTGACTCTGCTTCTTTTACTTGTTAATATATTGTGCAAAAGAGCCTTACTATACTATACAATACTATACATAAGATGGTTTTATTTATTTTGTCTGCTGCAG
Seq C2 exon
TTCTTTTTGGAGCGTCTTCCTCGTCTCCTGCACATGTCCCTTCCAGTCGAAGACCAACCGGTCCCAGAATCAGCACTGCCCCGGCGCTCCAGCTCATTAGGATACATCGCCCAGGCTGAGGAGTATTACAGTGTTAAATCCCGCAGCGAGCTGATGTTCGAGAAGCAGTCGGAAAGGCATGGTTTGGCCGCTCGTCCCACTCCCAAAGCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000019342:ENSDART00000015391:9
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=0.141
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=FE(15.9=100)
A:
NA
C2:
PF0293211=Neur_chan_memb=FE(29.3=100)
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:
GTATCTGATGTTTATCATGGTGTTGG
R:
TGGCTTTGGGAGTGGGACG
Band lengths:
326-1737
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]