RnoINT0036345 @ rn6
Intron Retention
Gene
ENSRNOG00000019527 | Chrnd
Description
cholinergic receptor nicotinic delta subunit [Source:RGD Symbol;Acc:2352]
Coordinates
chr9:94293695-94294968:+
Coord C1 exon
chr9:94293695-94293813
Coord A exon
chr9:94293814-94294643
Coord C2 exon
chr9:94294644-94294968
Length
830 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
TGTCTTGACCCTACTTATAGGAG
3' ss Score
7.4
Exon sequences
Seq C1 exon
GCAAGCCACCAGCAAGCTCTGAGCAGGTCCAACAGGAGCTTTTCAATGAGATGAAGCCAGCCGTGGATGGGGCGAACTTCATCGTCAACCACATGAGGGACCAGAACAGTTACAATGAG
Seq A exon
GTGAGTGACCATGGGATCAGATGTGCGAGTACACTGGGGATCAAGTGAATTCTGTCTTCCCCTCATATACACATGTCAACTTAGATGAAGAGATGCATGGTGGGTAGGACCCTTGGTGTACATTCTCCCAGGAAGGCAGAATTCCTTTGTGAAATCCCACAGCATCACACTGGGCCAAACAGACTGTGGTACACACAGACAGACAGCCCTACTTGACCAGGACAATTTTAAGTACATCTTCTACTCAGATACTCCAGAGACAATCTATTTATTATAGTTATTTACTTTTATATTCATAATCTTTATATACCATATGCAGTGTATTTATATATTGTATATTTATTATACAATTATATTGTGTAAATATATTTTATAAAAATAGGAATTAATAAACAACATATAACAAATATTTTACATATTATATGGTATGTTACATATGAATATATTTTATTATATATTTATTTATGGTATTTGTTTTATTATTATGTTACCTTTGTGGTGCTCAGGGCCTTATATACGCTAGAAAAGAAAGCACTGTACCCCCAGCCCAGCACCATGCCTTTGAAAGACTGGGTGGTCTATTCTTAGGCAACTTCTTAACGGTTCTCCATTGTATCCTCCTGTTCCCATGTGGCTAGAAGCAGCCCTGAGTCCCTAGTAGGAGTAATGGCATCCTGTCCTGACCTACCCTGCTGACGTAAGCCTGAGGTGACCCCACAGACACATAGAAGCCAAGCCTATGAGCTTCCATTTCTGGGTCCTAGCTTAGGGGTGTGAGTCTGCAGTCTGAAGCCCTTCCTTACTCCATGGTGTCTTGACCCTACTTATAG
Seq C2 exon
GAGAAGGACAACTGGAACCAGGTGGCCCGCACAGTGGACCGTCTCTGCTTGTTTGTGGTGACGCCCGTCATGGTGGTGGGCACAGCCTGGATCTTCCTGCAGGGTGTCTACAACCAGCCCCCACCCCAGCCTTTCCCTGGGGACCCCTTCTCCTATGATGAACAGGACAGGCGCTTCATTTAGAGCAGGCATGAGTAAAACAGTCAGGCAGACGGCGGTCTGAGAATTGTCCTTGAGCTTGTGCCTATCTGGGGCTGTGTGGCTGGGCTGAGGTCATGGGAGGAAGAGCTCCCTCCCAGGAGCAATTCCTTTCTAAATAAAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019527:ENSRNOT00000026504:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.550 A=NA C2=0.233
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=FE(16.5=100)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(13.1=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:
GTGGATGGGGCGAACTTCATC
R:
AGCTCTTCCTCCCATGACCTC
Band lengths:
347-1177
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]