MmuINT0036308 @ mm9
Intron Retention
Gene
ENSMUSG00000026253 | Chrng
Description
cholinergic receptor, nicotinic, gamma polypeptide [Source:MGI Symbol;Acc:MGI:87895]
Coordinates
chr1:89103962-89104880:+
Coord C1 exon
chr1:89103962-89104117
Coord A exon
chr1:89104118-89104782
Coord C2 exon
chr1:89104783-89104880
Length
665 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGA
5' ss Score
3.73
3' ss Seq
TTCCCACTCCTGACCCACAGATC
3' ss Score
9.76
Exon sequences
Seq C1 exon
TGTGGACGGTGTCTTCGAGGTGGCTCTCTACTGCAATGTCCTCGTGTCCCCCGACGGTTGTATCTACTGGCTGCCGCCTGCCATCTTCCGCTCCTCCTGCTCCATCTCTGTCACCTACTTCCCCTTCGATTGGCAGAACTGTTCCCTCGTCTTCCA
Seq A exon
GTGAGACTGATGATGATGTTGGGGGTTGTGGGCGGGGCTTCAGGGAGCTAGCTGCTCTAGGGTGGGTCTGGGTAGTGGTGGGAGACCAGCACCAGAGGCTCCACAAGGCTGAGCCTCCTGCTAAGTCCCCTCACCTATCCTCCATTGCTTCAGCTTCCTGCCTGGGTCCCAAGGGGAGACCCTATTGTCTTGAGTATGTGGCTAAGAACATCTGGGTATGCCTACATACACATAGAACCATAGACAGGCAGGCTGTCCTGGAAAAGAGAAGCCTGGCCAAAGCCAGGATGTGATCTGAGCCAAACCTATGCCCTCTGGGCTCACTTTCCTCATCCATAAGCAGTGAAGGGAGGTCTTGGGAGAAACTGGCAGGACCCCAAGTGTCATCTTCTGATAGGCTTGTATTTCTACCCTATGGTCATTGGTGGCAGTAGGAGAGACAGGGTGGCTCTGAGTTCTTTGGCCAGACGGGAGCACGGAACCCCCAAAGAGCCTGTGCTCCCCTGGCCCTGCATGCTAGCACCAGGGCTTGCTGGAGAACTCAAGAGTGTGACACTGCATATGTCAAAGCCTAATGTCCACAGCTGCCATCAGGCGACGGTGTCTGTGGCCTCATGGACAAGTCCCTCTGCTTCACTTACCCTCTTCCCACTCCTGACCCACAG
Seq C2 exon
ATCCCAGACTTACAGCACCAGTGAGATCAACTTGCAGCTGAGCCAGGAGGATGGGCAAGCCATTGAGTGGATCTTCATTGACCCGGAGGCTTTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026253-Chrng:NM_009604:5
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(24.1=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(3.2=8.8),PF0293118=Neur_chan_LBD=PU(45.2=97.1)
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:
TGTGGACGGTGTCTTCGAGG
R:
CTGTGAAAGCCTCCGGGTCAA
Band lengths:
254-919
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: