MmuINT0036267 @ mm9
Intron Retention
Gene
ENSMUSG00000027950 | Chrnb2
Description
cholinergic receptor, nicotinic, beta polypeptide 2 (neuronal) [Source:MGI Symbol;Acc:MGI:87891]
Coordinates
chr3:89564594-89566430:-
Coord C1 exon
chr3:89566321-89566430
Coord A exon
chr3:89565564-89566320
Coord C2 exon
chr3:89564594-89565563
Length
757 bp
Sequences
Splice sites
5' ss Seq
CAAGTAGGT
5' ss Score
7.33
3' ss Seq
ACTGCCCCATTCCTTGACAGTGC
3' ss Score
8.24
Exon sequences
Seq C1 exon
GAGTGGGAAGATTATCGCCTCACATGGAAGCCTGAGGATTTCGACAATATGAAGAAAGTCCGACTCCCTTCTAAGCACATCTGGCTCCCAGATGTGGTTCTATACAACAA
Seq A exon
GTAGGTGACCCTGGAGTGATGAAGGTTAGGGAAGACCAGAGGAGTGCTTGGGAAGGGATGAGATCATGGTGGGTGGGAATACAAGATAAGCATGCTGTTGTGAGAGGGAGAGGGCTTTCCCTTAGCAGATGGCAGGCAGGCGTTATCCACAAAGACAGACCCAACTAGTGGGATGCAGTGTAGACAGTCATGGTGACTTGGACCTTGAACTGATCCTCCCAGCTACTTAGATTGCTGGGGTAAGAATATTAAAGACTGACAGTTCTCAGTGCCTAGCTTGATCAAAGAGTGAGAACTTCTGGAAGCCTGGGTGGCGACATAGAACTTATATGGTCCTAGTTTCACCTAGATTCTGTTCTGCTCCCCTCAATGAATCTTCTCCCCTGTAAGGCACAAAACTGTCAACTGATGGCTTTTGTCCACACCCTTTCATTCCTTGAGGCTCCTTGCCCTGGCCTCTCCAGCTCCCTCACCTGTTTACCCTCATGTGGACTATCAGCTTATATGATGTGGAACAAGTAGCAGATGTGTCCCCCCTGCCCCCAATCATTCTCTTCAACCACTGAATGGATTCACAAGCCTCCTGAACAGGAGGAGACCCATTCTTACCACCAACCTGTGAATATTCCCACCCCTATCTCCATTTCTGGGCAATCTCCATGTATTAGATGATCACTTCCAGCCAGGTCCTTCTTGCTGGGTTGATGAGTGGGATGCAGACTCTCAAGCCAGGCCTGACTGCCCCATTCCTTGACAG
Seq C2 exon
TGCTGACGGCATGTACGAAGTCTCCTTCTATTCCAATGCTGTGGTCTCCTATGATGGCAGCATCTTTTGGCTACCGCCTGCCATCTACAAGAGCGCATGCAAGATTGAGGTGAAGCACTTCCCATTTGACCAGCAGAACTGCACCATGAAGTTCCGCTCCTGGACCTACGACCGCACTGAGATTGACCTGGTGCTCAAAAGCGATGTGGCCAGCCTGGACGACTTCACACCTAGTGGGGAGTGGGACATCATCGCACTGCCAGGCCGACGCAACGAGAACCCAGACGACTCCACCTACGTGGACATCACCTACGACTTCATCATTCGTCGCAAACCGCTCTTCTACACCATCAACCTCATCATCCCCTGCGTACTCATCACCTCGCTGGCCATCCTGGTCTTCTACCTGCCCTCAGACTGTGGTGAAAAGATGACACTTTGTATTTCTGTGCTGCTGGCGCTCACGGTGTTCCTGCTGCTCATCTCCAAGATTGTGCCTCCCACCTCCCTCGACGTACCGCTGGTGGGAAAGTACCTCATGTTCACCATGGTGCTAGTCACCTTCTCCATCGTCACTAGCGTGTGTGTGCTCAATGTGCACCACCGTTCGCCTACCACGCACACCATGGCGCCCTGGGTCAAGGTGGTCTTCCTGGAGAAGCTGCCCACCCTCCTCTTCCTGCAGCAGCCACGCCACCGCTGTGCACGTCAACGCCTGCGCTTGCGAAGGCGCCAGCGGGAACGTGAGGGGGCAGGCACACTATTCTTCCGCGAAGGTCCTGCAGCTGACCCATGTACCTGCTTTGTCAATCCTGCATCAATGCAGGGCTTGGCTGGGGCTTTCCAGGCTGAGCCCGCTGCAGCCGGTCTGGGGCGCTCGATGGGCCCATGCAGCTGTGGCCTCCGGGAAGCTGTGGACGGTGTACGCTTCATTGCGGACCATATGCGAAGTGAAGATGATGACCAGAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027950-Chrnb2:NM_009602:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.008
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(17.5=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(54.4=34.6),PF103294=DUF2417=WD(100=40.4),PF0293211=Neur_chan_memb=PU(95.8=63.0)
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:
TCTAAGCACATCTGGCTCCCA
R:
AGTCGTAGGTGATGTCCACGT
Band lengths:
358-1115
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: