MmuINT0036226 @ mm10
Intron Retention
Gene
ENSMUSG00000027577 | Chrna4
Description
cholinergic receptor, nicotinic, alpha polypeptide 4 [Source:MGI Symbol;Acc:MGI:87888]
Coordinates
chr2:181037419-181039305:-
Coord C1 exon
chr2:181038992-181039305
Coord A exon
chr2:181037571-181038991
Coord C2 exon
chr2:181037419-181037570
Length
1421 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
ACTTTCTGCCTCCCCCACAGCTA
3' ss Score
10.14
Exon sequences
Seq C1 exon
CCTCCTCCCCTCTCGCCGGCGGCTGGAGGCTGCAGGTCCGGGCGGGGCCGCGCCGCGGAGCCCACAACCTCGAGCTCCCGCCCCGCCGCCGCACCCCGCGGGACGAGCTGCGGAGCCCGGTTTGGGGACGAGCGGCCGCGACACGGGGCATGAAGTTGGGTGCGCGCGGGTCTCGGAGCGGAGGCGCGGTACTGCCGGGAGCCGCCCTCGTCTAGAGCCCGTTCTGTGAGCCATGGAGATCGGGGGCTCCGGGGCGCCGCCGCCGCTGCTGCTCCTGCCGCTCCTGCTGCTCTTAGGGACCGGCCTCTTGCCTG
Seq A exon
GTAAGTTTCGAAACGCGAAACGGGCCTTTTTCTCCCGGGTCCTGGCACCTAGGACTCCGGGGCTAGGGGAGAGGAGGCCCGGGGCTGCGGTTCCAAGCCGCGGGTGCGAGCAACGGGATAGCCACAGAGACTCCTCCACCCACTACAGCTTCGATGTCCTGCAGTGCTAGCTGAGCCAGAGAGGAAGGAATCAGCCTCCAAGTGCTGGGAGAGGGGGTTTGAGTAAAGGCGGGGGGGGGGGTGGTCTGACTGCATTTCGGAGCTGGAATCAGAACCTCCAAGTAGGATAGAGGTGGAGTCCACCTAGGAGGGAGGTTCCATCCAGCCAAATCTCGCCTTCAGACCGCCCCCATGTCTGTCCCTGTTTTCAGGGATCTACCCCTACCACCCCCCGGAGTTCCACCCTACCCTTTCTGCTCCCCCAGGCTTCCTCCACCTCTCTTCCTCTGAGCGGACACCTTTCACTCTAACCCGTGATGGGGCTTCCTGCAGTTATTTAATCCTGGCCTTCCCACTGAGCAGAGGGGTTATGCCTTACTGGTCGGTTCAAGACACCAGGAAGAATGAGGTTGAGGTGGGGAGGCTGGGGGGGGGGGGACTCTAGGAGTCCTCTCCTAAGGAGTTCCCATGTCTCTCAGGTGAGCAAGAGCCAGTAGACAGCAGAGGCTCCCCTCTTTCTTCCCAACCCCCTCTTTTGATGCAGCAACCCAGCAAATGGAGGTAGGGAGGCCCCCTAGCCACGTAGGGGGCCAATGGAGAGGACACAGATGGGCTGCTGGCTGGTGGAATGAGGGGGCACCCTCTTCATGAAGCAGTGTGGCGCTTATCCATGGAATCTTATATCCGTCTATGAACACAAGGTCCTGGCAGCCCCGAGGCTCTGCGTTCATTGTCAGGCTGTACCCTAGAAGCCCAGGCAGCAGGACCACTCCTGTGGACAGAGGCTCAAGCTCCTGCAGCCATGAGATGTGGTGCACAGTCCTCTTTCATTCACCACCACCACCCATCCTAGCTGCCCCATACACCTTCTGCCACCCAGCCCCACCCCCCAACCCCTGCTGTCCCTTTACATCCTTTGTCTCTGCCGGTCACTGGAGATAGGGCACTTCCATCCAAAGTGATTGTCTGCAGGGGAGCTCTACCCCATTAATTCAGTGTTCACTATGTCAGTTGTCTTGTTTTCCTGGTGGAGTGCAGGAGGGCCTGATCCATTCATTCTTGGGGCCCTGGAAAGGCTTCCTTGAGGGGAGGAGTGGAGGTGCGGGGGGGGGGGGGGGACGACGACGACAAGGCAGCATGCCCAGGGGCCTGAGGTGGAAGAGAAATCAGAAGGAAGGGCTGTGATGGCATGGGGTCTGGTGTGGGGCTAGAGCAGCAGCTTCTGTGGTCACCTGTCCTTAAACTTTCTGCCTCCCCCACAG
Seq C2 exon
CTAGCAGCCACATAGAGACCCGGGCCCATGCGGAGGAGCGGCTCCTGAAGAGACTCTTCTCTGGCTACAACAAGTGGTCTCGGCCAGTAGCCAATATCTCAGATGTGGTCCTTGTCCGCTTTGGCTTGTCGATTGCTCAGCTCATTGATGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027577:ENSMUST00000067120:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.036 A=NA C2=0.025
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0293118=Neur_chan_LBD=PU(18.8=76.5)
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:
GAGCCCACAACCTCGAGCTC
R:
GGCCGAGACCACTTGTTGTAG
Band lengths:
342-1763
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