MmuINT0036204 @ mm10
Intron Retention
Gene
ENSMUSG00000027107 | Chrna1
Description
cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle) [Source:MGI Symbol;Acc:MGI:87885]
Coordinates
chr2:73574321-73574631:-
Coord C1 exon
chr2:73574486-73574631
Coord A exon
chr2:73574366-73574485
Coord C2 exon
chr2:73574321-73574365
Length
120 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGA
5' ss Score
8.24
3' ss Seq
GGGATCTTCTCTCTTCTTAGGAT
3' ss Score
9.5
Exon sequences
Seq C1 exon
CTGGCCTTGTTCTGGGCTCCGAACATGAGACGCGTCTGGTGGCAAAGCTCTTTGAAGACTACAGCAGTGTAGTCCGGCCAGTGGAGGACCACCGTGAGATTGTACAAGTCACCGTGGGTCTACAGCTGATCCAGCTTATCAATGTG
Seq A exon
GTAAGACCAGGGCTGGGGGCTCCCTGTGGCACCCACCCTGTGGGACCCCATCTCACACTGGATCATCTCCCCTTGGCTTCCCTACTCATGCCCTAAAGACGGGATCTTCTCTCTTCTTAG
Seq C2 exon
GATGAAGTAAATCAGATTGTGACAACCAATGTACGTCTGAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027107:ENSMUST00000028515:2
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=PU(18.8=79.6)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(6.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTGTTCTGGGCTCCGAACAT
R:
CTGTTTCAGACGTACATTGGTTGT
Band lengths:
186-306
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