MmuINT0036302 @ mm9
Intron Retention
Gene
ENSMUSG00000026253 | Chrng
Description
cholinergic receptor, nicotinic, gamma polypeptide [Source:MGI Symbol;Acc:MGI:87895]
Coordinates
chr1:89102386-89102789:+
Coord C1 exon
chr1:89102386-89102454
Coord A exon
chr1:89102455-89102649
Coord C2 exon
chr1:89102650-89102789
Length
195 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAAA
5' ss Score
-1.58
3' ss Seq
ACCCCCTCCTTCTGTTGCAGGGG
3' ss Score
11.77
Exon sequences
Seq C1 exon
AGAACTGAGGCACCATGCAAGGGGGCCAGAGACCTCAGCTCCTCTTGCTGCTGTTGGCTGTCTGCCTGG
Seq A exon
GTGAAATACTAGGGATTTGAGACCTGGGGTGGAGGGTGTGGAAGGAACAGATCAGGAGTACAAGATTACAGTGGATGGAGGGTCTGGGGGTTACCTGTACTCTCCCTAGCCCCAGCACCCTCCCCGCCCCCAGTCTCCACCTTATCCCTCTGTGCCTCCTCCTCCTCTGGAGCGAACCCCCTCCTTCTGTTGCAG
Seq C2 exon
GGGCCCAGAGCCGCAACCAAGAGGAGCGTCTGCTTGCGGACCTGATGCGAAACTACGACCCCCACCTGCGGCCGGCTGAGCGCGACTCAGATGTGGTCAATGTCAGCCTGAAGCTTACCTTGACCAACCTCATCTCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026253-Chrng:NM_009604:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0293118=Neur_chan_LBD=PU(18.1=83.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAACTGAGGCACCATGC
R:
GGGAGATGAGGTTGGTCAAGG
Band lengths:
207-402
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: