MmuINT0036280 @ mm9
Intron Retention
Gene
ENSMUSG00000026251 | Chrnd
Description
cholinergic receptor, nicotinic, delta polypeptide [Source:MGI Symbol;Acc:MGI:87893]
Coordinates
chr1:89087227-89087704:+
Coord C1 exon
chr1:89087227-89087317
Coord A exon
chr1:89087318-89087549
Coord C2 exon
chr1:89087550-89087704
Length
232 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGG
5' ss Score
8.37
3' ss Seq
CACCCTACCCCTCTCCCCAGCCC
3' ss Score
8.35
Exon sequences
Seq C1 exon
CTGAAGGGAAGACAAACCCTAGTCAGTCAGAGGTGGGGGATGGCAGGGCCTGTGCTCACACTGGGGCTGCTGGCTGCCCTTGTTGTGTGTG
Seq A exon
GTAAGGATGACATAACCCCCTTCCTGGGGGCCTTCTATGCCCACCTGGGCCACCGCCTCCCTAACATTATACCTAATTCCCACTCCCACTCTGCCCTTTCTAACCCTAGGCATCCCACCCTCAGGGAGCAGCTGGCTTTCCTCTGCTCTGCCCAGCCCAGGGCTGCCCCAGCAGGAGCACAGGGAAGGCTCCTTCCTAGGTCCAAACACCAGCACCCTACCCCTCTCCCCAG
Seq C2 exon
CCCTCCCAGGCAGTTGGGGCCTGAATGAGGAACAAAGGCTGATCCAGCACCTATTCAATGAGAAGGGCTACGACAAAGACCTGCGGCCGGTGGCTCGAAAGGAGGACAAAGTGGATGTCGCCCTAAGTCTCACCCTCTCCAACCTCATCTCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026251-Chrnd:NM_021600:1
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=0.108
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0293118=Neur_chan_LBD=PU(18.5=78.8)
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:
GGGAAGACAAACCCTAGTCAGT
R:
GGGAGATGAGGTTGGAGAGGG
Band lengths:
239-471
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: