MmuINT0036285 @ mm10
Intron Retention
Gene
ENSMUSG00000026251 | Chrnd
Description
cholinergic receptor, nicotinic, delta polypeptide [Source:MGI Symbol;Acc:MGI:87893]
Coordinates
chr1:87192214-87192641:+
Coord C1 exon
chr1:87192214-87192323
Coord A exon
chr1:87192324-87192485
Coord C2 exon
chr1:87192486-87192641
Length
162 bp
Sequences
Splice sites
5' ss Seq
CAAGTTGAG
5' ss Score
-10.48
3' ss Seq
TTATGGTCTCCATCCCACAGCAA
3' ss Score
8.25
Exon sequences
Seq C1 exon
GCCTGGGTAGACAGCCGTCTACAGTGGGATGCCAACGACTTCGGGAACATCACTGTCCTGCGCCTGCCCCCTGACATGGTGTGGCTACCAGAGATTGTACTGGAGAACAA
Seq A exon
GTTGAGAGGAACCCTCCCAGCCCCCCTCTGCCTCATTCCCTTCCTTATGCTCCCCAGCCTGCGCCTCCAGCCCTGCCTGCCCACCACCCTCTCCTGCCTCCTGCGGTCCTGCCGGTTCCTGGCCAGCCAGGACACACAGTGATTATGGTCTCCATCCCACAG
Seq C2 exon
CAATGATGGCTCGTTCCAGATTTCTTATGCCTGCAATGTGCTTGTCTATGACTCGGGCTATGTGACCTGGCTGCCGCCCGCCATCTTCCGCTCCTCCTGCCCCATCTCAGTCACCTACTTCCCTTTCGACTGGCAGAACTGCTCCCTCAAATTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026251:ENSMUST00000073252:4
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=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(16.2=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(23.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACAGCCGTCTACAGTGGGAT
R:
AGCAGTTCTGCCAGTCGAAAG
Band lengths:
244-406
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types