MmuINT0036304 @ mm10
Intron Retention
Gene
ENSMUSG00000026253 | Chrng
Description
cholinergic receptor, nicotinic, gamma polypeptide [Source:MGI Symbol;Acc:MGI:87895]
Coordinates
chr1:87210903-87212694:+
Coord C1 exon
chr1:87210903-87211036
Coord A exon
chr1:87211037-87211314
Coord C2 exon
chr1:87211315-87212694
Length
278 bp
Sequences
Splice sites
5' ss Seq
AGTGTGAGT
5' ss Score
6.96
3' ss Seq
CAATGTGTTGTTGCCCTCAGGGG
3' ss Score
9.41
Exon sequences
Seq C1 exon
AGAATGGTCCAGAAGTGAGGCAGAGCCAGGAGTTCTGTGGCAGCCTGAAGCAAGCCTCCCCAGCCATCCAGGCCTGTGTGGATGCCTGTAACCTCATGGCTCGTGCCCGACGCCAGCAGAGTCACTTTGACAGT
Seq A exon
GTGAGTGGGACAGGGTGGGCAACTACCCAAGTGTAATGTGGGGACAAGGTGGATGGGGTGTTCTGCTTAGGTTCAGTGACAGACAAAGCAGAGGTAGGAAGTGGGAAGAAGGACCAACAGGTCAGAGACCATAAAAGAAGACAGGTTGGTACCCAGACAGAGGTAAGAAGGCTGAATAGAGAATGGAGGCCAGCTGGGGACCTAACAGTGAAAGAGTGAGCCAGGCTGGCTGCTGCCCCTGCTCACACCCCTGCCACACAATGTGTTGTTGCCCTCAG
Seq C2 exon
GGGAACGAGGAGTGGTTGCTGGTGGGCCGAGTGCTGGACCGAGTCTGCTTCCTAGCCATGCTCTCCCTCTTCATCTGTGGCACTGCTGGCATCTTCCTCATGGCCCACTACAACCAAGTGCCTGACCTGCCGTTCCCCGGAGACCCCCGCCCCTACCTGCCTTTGCCAGACTGAGCCAACCAATCCCTCCTGGGCCCTGGAGTCAGCTATGAGGGCCATGCTGTTTGTAGAGCTGTATCCCGTGTTGATGCTGAGTGTGCTCTTGGGGAAATACCCAAGGCTTCCTGGGAGAAGATAGAGAAATAAAGAGACAGAGGGGGATTTCTGCAGTGGTTGGTGATGGGTATGGTCACATGACTTTGAGCAGTTCTGATAGGTCACTTTGAAGCCCTAAGAGCTCTGCCTTTCCTGATGTCATTGACTGGGCAAGGTTTTACCCTTTGAGGCCTGAGAAAATTTCCTCCTGCCATTTTGTAAGATTTATTTCTATTATTTCTAACTATATGTATGTATGTACGTACATATGTGTGTATGTATATATTGGGAGTGGGTTATGTGCACATGAGTGAGCATGCCTGTTGGAAGTTGGCAGAGGATGTCAGAACCCTAGAGTTGGAGTTATAGGTGGTCATGAGCAACCAGACAGTGGGTTGCTCATGTCCTCTATAAAAGCAGCAAGTGTTCTTAACCACTGAGCTGTTTTCCCAGCTCCAACATCTTCCCTATGTGAACTTTCTCTAGAAGGTTCGTAAGGGATGTGGGGAACTCTCTTAACTGCAGAGAACATGAACTGGACGTGGTGGGGCCTTTAGTCCTAGCACTAGGGAGGCAGAGACAAATCCATCTGTTTGAGGTCAGTGTACATGGTGAGATCCTGTCTCAAAAAAGGATGGGGGTGAGGGTGGAGATAGTTCAGTGGTTAGGAACACTGGCTACTTTCCCGGGGATCTGGGTTGGTTTCCAGCACCCATGTAGCATCTGTTACTCCAGTTGCAGGCGATCCAACACCCTCCTCTGGCTTTGCAAAACGCCCATGCATATAGTGCAGACATATGCACAGACAGAACACCCATATACACAAGATAGAAAAAAAAAAGCCTTTTTTTTATGGAGATAGGGGTGTGGGATCTAAGTACAGAGTCTTGGCTTTTATGAGGTCTAGAATTTTTAAAAGTGTAACCCATTTTAACTAGCAAGGTTCTTCTAGATGCCACAGCACAAATGTGTACCTTCAGCAGTACGTCCCATTCGTCTAATGTAATACTTCCTCCCACCCCCACTGATCACAAAGGATTTCTTGAGTTTTACTATCTCCCCCCCCCCCATTGTTAGAAATTCTTCACAGTATGGATAGTCAAGAGGCACTGTTCAAAATAAAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026253:ENSMUST00000027470:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.022 A=NA C2=0.070
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=FE(17.8=100)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(12.6=53.4)
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:
CCTGTGTGGATGCCTGTAACC
R:
AGCTCTACAAACAGCATGGCC
Band lengths:
296-574
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