MmuINT0036283 @ mm9
Intron Retention
Gene
ENSMUSG00000026251 | Chrnd
Description
cholinergic receptor, nicotinic, delta polypeptide [Source:MGI Symbol;Acc:MGI:87893]
Coordinates
chr1:89087550-89088139:+
Coord C1 exon
chr1:89087550-89087704
Coord A exon
chr1:89087705-89088094
Coord C2 exon
chr1:89088095-89088139
Length
390 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
ACCCTGTTGTTTGATTACAGAAA
3' ss Score
7.47
Exon sequences
Seq C1 exon
CCCTCCCAGGCAGTTGGGGCCTGAATGAGGAACAAAGGCTGATCCAGCACCTATTCAATGAGAAGGGCTACGACAAAGACCTGCGGCCGGTGGCTCGAAAGGAGGACAAAGTGGATGTCGCCCTAAGTCTCACCCTCTCCAACCTCATCTCCCTG
Seq A exon
GTGAGTAGACCTTCGTGGGATAGCCTGAGCTGGGGAGAGGATGGCAAGAAGGGACAATTGCTCAAAGGCTCCTGACCAGCTAGCTCCTCTTCTGGGAGACATGCATGACTATTCTTTGTGCCAGATGGTGCCACGGGCCTTTAGCCACCCAAAGCCATCAGCTCTGCCTGCCACTGTCAAGCTATCCCTGTGCTCCCCCGGGACTCACATCAGCAGCCTCTGCCCTTCGCTTCCGTAGTCTGCTGATCCACCTCGATCTGTTGCTCTAGAAGACCCTGGCCCTTCCAGCTGCCGTGGTCCCTGGGAACCAGGCAGATTAGATTCTGCTGACTGAGTTTGGGTGAAAGGTAGATGGGAACCTTTGGCTACAACCCTGTTGTTTGATTACAG
Seq C2 exon
AAAGAAGTGGAGGAGACCCTCACCACCAACGTGTGGATAGATCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026251-Chrnd:NM_021600:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.108 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PU(18.5=78.8)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(6.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAGTTGGGGCCTGAATGAG
R:
TGATCTATCCACACGTTGGTG
Band lengths:
190-580
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: