MmuINT0036278 @ mm9
Intron Retention
Gene
ENSMUSG00000035200 | Chrnb4
Description
cholinergic receptor, nicotinic, beta polypeptide 4 [Source:MGI Symbol;Acc:MGI:87892]
Coordinates
chr9:54882449-54884308:-
Coord C1 exon
chr9:54884199-54884308
Coord A exon
chr9:54883440-54884198
Coord C2 exon
chr9:54882449-54883439
Length
759 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
TATGTCCTGCCCTACCCCAGTGC
3' ss Score
7.18
Exon sequences
Seq C1 exon
GAATGGACTGACTACCGCCTGGCCTGGAACAGCTCCTGCTATGAAGGGGTGAACATTCTGAGGATTCCTGCAAAGCGAGTCTGGTTGCCTGACATCGTGTTGTACAACAA
Seq A exon
GTAAGTGATGGGGTGGCCAAAGTCTAGAGTTAGGCCAGGACAGCAGGCCAGCCTCCAAGACTGTCTACTCCTGAATCCAACCGCAGCCTTCCTTTTCTACACTTCCCTCAGGCTTCTAGGCCTTGGAGCTAGAGAAAGAGAGGTGATGGAGACAGAGTCTTCTGAGTGGGAGGGCGGGAAGGGAGGTCCAGAGGCCCTGTGCTGCTCAACACAGCGGGCACTGGGCTAGCCTTTGGGCCCTCAGGCCAGTGCCTTTGCTTACAATCCTTGTCTCACCATTCTGTTTCTTTGTGACTTGGTGGCTTTGTCAGTGGTAGGGGCTGCAACCTTGACCTGTCATGTGTGCAGTTCATGGTAGCAGCTGAGTCAGGAGGATCAGGAACCCAGGAGTTTGAGATCAGTCTCGCCAAAGAGAACAAGATGAAGGGAGACAGGATCAAACAAGACAAGGGTCCATATTTCTTCTCTCCTACTTAATCATTGAAGGAGCTTGGTGGAGTCCTCCACACTCCCCAGGTCTTGCTGTCCAACCTGGAAAAGGAAGAACACAGTGAATGCACTGCTTCTTAAGGCTCCTGTGGGGCTTTAACTGAGTTAATTCCGTGAGAGGCCTTCAGTGTCTCATGGTTTGCCAAGAAAAGCAGGCTTGTTTCAGTGAGGAAGACAAATGACTCCCAAGGGCTCTTGGGGGTTCTGAGAACAGGCCAGGCCTCCTCTGTAGATCTGTGATGCTCTCCTCTATGTCCTGCCCTACCCCAG
Seq C2 exon
TGCCGATGGGACCTATGAGGTGTCTGTCTACACCAACGTGATCGTGCGTTCCAACGGCAGCATCCAGTGGCTGCCCCCTGCCATCTACAAGAGTGCCTGCAAGATAGAGGTGAAGCACTTTCCCTTCGACCAGCAGAACTGCACCCTCAAATTTCGCTCCTGGACCTATGACCACACAGAGATTGACATGGTTCTTAAATCACCCACAGCCATCATGGATGACTTTACCCCCAGCGGTGAATGGGACATTGTGGCCCTCCCGGGTCGAAGGACAGTGAACCCACAGGACCCCAGCTATGTGGACGTGACCTATGACTTCATCATCAAGCGCAAGCCACTCTTCTACACCATCAATCTGATCATCCCTTGTGTGCTCATCACGTCGCTGGCTATCCTGGTCTTCTACCTGCCCTCCGACTGTGGGGAGAAGATGACGCTCTGCATCTCAGTGCTGCTGGCACTCACATTCTTCCTGCTGCTCATCTCCAAGATCGTGCCTCCCACCTCCCTTGACATTCCCCTCATTGGCAAGTACCTCTTGTTCACCATGGTGCTGGTCACCTTTTCCATCGTCACCACTGTGTGTGTCCTCAATGTGCACCACCGTTCACCCAGCACTCACACCATGGCATCCTGGGTCAAGGAGTGCTTCCTGCACAAGCTGCCCACCTTCCTCTTCATGAAGCGCCCTGGTCTGGAAGTCAGCCCCGCCAGGGTCCCTCATTCCAGCCAGCTGCACTTGACCACAGCTGAAGCTACGTCCACCTCTGCCTTAGGCCCCAGCAGCCCATCCAACCTCTATGGGAATTCCATGTACTTTGTGAACCCTGTCCCTGCCACTCCTAAGTCTGCAGTCAGCTCCCACACGGCAGGCCTCCCCAGGGATGCCCGGCTGAGGTCCTCTGGGAGGTTCCGGCAAGATCTACAGGAAGCATTAGAGGGCGTCAGCTTCATCGCACAGCATTTGGAGAGTGATGATCGAGATCAGAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035200-Chrnb4:NM_148944:4
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.012
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(17.5=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(54.4=33.8),PF103294=DUF2417=WD(100=38.1),PF0293211=Neur_chan_memb=PU(86.5=63.7)
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:
TCTGAGGATTCCTGCAAAGCG
R:
TCCTGTGGGTTCACTGTCCTT
Band lengths:
342-1101
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: