MmuINT0036260 @ mm9
Intron Retention
Gene
ENSMUSG00000041189 | Chrnb1
Description
cholinergic receptor, nicotinic, beta polypeptide 1 (muscle) [Source:MGI Symbol;Acc:MGI:87890]
Coordinates
chr11:69606201-69607114:-
Coord C1 exon
chr11:69606967-69607114
Coord A exon
chr11:69606411-69606966
Coord C2 exon
chr11:69606201-69606410
Length
556 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGT
5' ss Score
9.27
3' ss Seq
ATTCTGTCTCCCTCCTCCAGAGA
3' ss Score
10.43
Exon sequences
Seq C1 exon
GTCACCTACTTCCCCTTTGACTGGCAGAACTGCACCATGGTGTTTAGTTCCTACAGCTATGACAGCTCTGAGGTCAGCCTGAAGACGGGCCTGGATCCTGAAGGAGAGGAGAGGCAGGAAGTCTACATTCATGAAGGGACCTTCATTG
Seq A exon
GTGAGTGGACGTGGTTCTCACATCCAAGGCTGAGAGGCAGGTTCTCTTATGGATGCTCAGTGAACCTGGTGGGGTCAGCAACTTGGGGATGATGATCAATACTGCAAATATGGCAAAGGAAGCCAAGCGTGGTAAGTCAGACCTTTAATGCTAGCACTTGGAGGGGCAGGGTGAGGCAGGGGTATTGCTGTATATTCAGGGCCAGTCTGGACTACATTCAGATGCCCTGATTCTTAAAACAGACAAGCAAAAAATAGATGCAGCATACACAGGGATGATGAGATAGCTCAGTGGTAGAAGCTCTTGAAATGTAAACTTGACAGCCTGAATTCAGTCCCGGGAATCTACAGTGGAAGGAGAGAACTCCCAAAAGTTGTCCTTGAACCTTTGAATTCACATGGTGGCATGTACACACACGTGTACACACACACACACACACACACACACACACACACACACACACACTAAACAAATATGGAAGTTGAGGCTTGTTTATTAGAGGTAAGCTGCCATATCAGGCGCAGCTGGGTTTACTTATTCTGTCTCCCTCCTCCAG
Seq C2 exon
AGAATGGCCAATGGGAGATTATCCACAAACCTTCTAGGTTAATCCAACTTCCAGGGGATCAGAGAGGTGGGAAGGAAGGGCATCATGAGGAAGTTATCTTCTATCTCATTATTCGGCGGAAGCCTCTCTTCTACCTGGTCAACGTCATTGCCCCATGCATCCTCATCACGCTCCTGGCCATCTTTGTCTTCTACCTCCCACCAGATGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041189-Chrnb1:NM_009601:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.060 A=NA C2=0.014
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(22.4=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(18.7=57.7),PF0293211=Neur_chan_memb=PU(9.3=31.0)
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:
CCCCTTTGACTGGCAGAACTG
R:
CTGCATCTGGTGGGAGGTAGA
Band lengths:
347-903
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: