MmuINT0036297 @ mm10
Intron Retention
Gene
ENSMUSG00000014609 | Chrne
Description
cholinergic receptor, nicotinic, epsilon polypeptide [Source:MGI Symbol;Acc:MGI:87894]
Coordinates
chr11:70617605-70618310:-
Coord C1 exon
chr11:70618155-70618310
Coord A exon
chr11:70617706-70618154
Coord C2 exon
chr11:70617605-70617705
Length
449 bp
Sequences
Splice sites
5' ss Seq
TCGGTAGGA
5' ss Score
7.45
3' ss Seq
AGACTGGCCCTGTTTCACAGCTC
3' ss Score
5.68
Exon sequences
Seq C1 exon
TATTGATGGGCAGTTTGGAGTGGCCTACGACAGCAATGTTCTAGTCTATGAGGGAGGCTATGTGAGCTGGTTGCCCCCAGCCATCTACCGCAGCACCTGCGCAGTGGAGGTCACCTATTTCCCCTTTGACTGGCAGAACTGCTCTCTCATTTTTCG
Seq A exon
GTAGGAAGAATCACTTCAATCATGATATTGAGAAGGGCCTAGAGCAGGGGACAGGGCCTGCTAAGGAGGGATAGGTGGGGTCTTCTTTGGAAGGTCTTTGGGAAGGAGTTGGAGTGAGGCACTGGAGTGAAGGGGTGGGAAGCTGGTGTAGGTTTGCAGTAGGCGTGGGCACAGGTTTCTTGCTGCCATCTTGTAGTTTGAGCGCATAGTCGCAGCTATTCCCCAGGAGGAGTCTGAGGCATAAAAATTACTTGAGTCCAGGAATCCCTTGGATAGCACGGTAAGCCCATCAGCAACCCAAAACAGAACAGAAAAGGAAGCAGGATTGGGAACGCGCTGGGGAATGTGGGCAAAAGAAGAGAGCCATATTACCCTGCCAGATTGAAGCTTCCAGGGTGGAACTAAGATGGCTGCCAGCTTCTGGGGTAAAGACTGGCCCTGTTTCACAG
Seq C2 exon
CTCCCAGACCTACAATGCTGAGGAGGTGGAGTTCATCTTTGCCGTGGATGACGACGGCAATACCATCAACAAGATTGACATTGACACGGCAGCTTTTACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000014609:ENSMUST00000102556:5
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(24.0=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(15.7=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:
TTGATGGGCAGTTTGGAGTGG
R:
GGTAAAAGCTGCCGTGTCAATG
Band lengths:
254-703
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