MmuINT0036206 @ mm9
Intron Retention
Gene
ENSMUSG00000027107 | Chrna1
Description
cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle) [Source:MGI Symbol;Acc:MGI:87885]
Coordinates
chr2:73409470-73411426:-
Coord C1 exon
chr2:73411317-73411426
Coord A exon
chr2:73409666-73411316
Coord C2 exon
chr2:73409470-73409665
Length
1651 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGC
5' ss Score
7.47
3' ss Seq
CTCTCTTACCCTGACCACAGCGC
3' ss Score
7.79
Exon sequences
Seq C1 exon
CAATGGGTCGATTACAACTTGAAATGGAATCCAGATGACTATGGAGGAGTGAAAAAAATTCACATCCCCTCGGAAAAGATCTGGCGGCCGGACGTCGTTCTCTATAACAA
Seq A exon
GTAAGCAACGCCACAGGACCAGGCAGGGTGGGCCAGCGTCCCCTCGGAAGGACTGCCACATGCGTTTCCCCATCGTTTGCATTAAATAACCCTTAAAACCAGAACCACGCTGACAGGCAAGGAGTGCCATATGGCATCCCATGTTATGAATAGAAACAATTATGGAAGCCAAATTGAATCAGGGCTGTGGGTGGGACATTAATCCCAGAGAGCTACAATGGTGCTTGTGGCAACCACAGGAGACACCGAGACTTCCTGTCTGAATTCCTTGGGATCGAATACCTTCCCCCCAACCCCCCCGCCCCAGGGGTCTCAACTCTCGGGAGTGTTATTCATCACATCCTGAACGCCATCCCACCATCAGTGCCCGGATGCCTCCCTTGCCATCCACTGGGCCCTGCAACAGACTGTGTGTTGTGAAATTATAATGTGATTCACGACACTTGGCTTAATTACACGCTCATTATCATATGCCCTTCATTTGTCAGGGAATATTCATTTCAAAGAGCATCCTTCCAAGGCAGGAACAGGAGCATGCGCAGTCAGCTAGCTAGAGGATTTGCAGTCTGATCCCGTGCTTTACAGCAGATGTTCCTGGGGCTGGTAGGAGCTGTGGATGAAAATGGTGCCCTCTGGCGGCCATCCCAGCATCTAGCACACAGCTAGAGCTGGGATTGCAGGGTGAGCCAAACTCCCCACTGTTTGGTGGTGCCTTTCTGGGGAGAGATGTTGATAGATGCAGTGTCTTGTCTTCAGTAGAACTCCACAACTCTCATTCTCTCCGAAGACTACCAGAAGCACCTCCGTGGCTAGAGAAAAGGGCTGGGGATGCAGCTCAGTGGTAGAGGATTTGTCTAACTTGTGAAGCCCTTATATTGAATCCCGAGAATTAGAGGAAATGAAAGGTTTTTGTTTTTGTTTTTTTAATCTGTTTCCAGTTTCTGAAAAGGGACCCAGCTATGTGACCATGTTAGATCTTCCAACTCACGTGGCCTTCCTAGATGCCTGGCGCCAAAGACCACACTTAGGCAGCGAGGGGCTCCCCCCCCTTCTCTCCCAGCTAGTGTTCGCTCCACTGCTGGTCAGGGGCATCTGAGTTTGTGACTTGTCCCACCGAGTTCTAAACAGCTCTCAGAAGAACACCAGTTCTGCCCCTCCCCCATACAACATTCAGCTGCTAGGAGTGTTTTATTTTAGATTTCTAGTCTTTCCAGCCAACTCTGAAAGCACACAGATGGAGTCTGCCATTACAGGTGTCTCTGGGGACAGGACAGGAAAGGCTGAGGTGCAGCGGGCCTGTGTCACTTGTGACTCTGTAAAGTCTGTAGATTACCTACCTCATTCATCTTCCCAGAATCTGACTTGGGCCTTGCTTAGCGCTCAGAAATCTGTATTTGGCTTTCTCTCATTGATTCATTGATAGACTGGGCTTTGCTACGTAGCCCAGACTGACTGAGGAATCTGAGTCCGCCTGCCTCAGCTTCTAGAGTTCTGGAATCACAGTACACGCCATCACACTTGGCCAGTGCTTAGGAATGTGTGGTTTTTGACCATCACCCAAGTGAGTGTTGGTGTAGGACAAATTTGGGAAGCACCACCATCGACTGGAATGCAGTATTGGAGACATTGTCCTCTCTTACCCTGACCACAG
Seq C2 exon
CGCAGACGGCGACTTTGCCATTGTCAAATTCACCAAGGTGCTCCTGGACTACACCGGCCACATCACCTGGACACCGCCAGCCATCTTTAAAAGCTACTGTGAGATCATTGTCACTCACTTTCCCTTCGATGAGCAGAACTGCAGCATGAAGCTGGGCACCTGGACCTATGACGGCTCTGTGGTGGCCATTAACCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027107-Chrna1:NM_007389:4
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=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(17.3=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(31.2=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:
TGGGTCGATTACAACTTGAAATGGA
R:
GGGTTAATGGCCACCACAGAG
Band lengths:
302-1953
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: