MmuINT0036250 @ mm10
Intron Retention
Gene
ENSMUSG00000029205 | Chrna9
Description
cholinergic receptor, nicotinic, alpha polypeptide 9 [Source:MGI Symbol;Acc:MGI:1202403]
Coordinates
chr5:65967124-65967927:+
Coord C1 exon
chr5:65967124-65967511
Coord A exon
chr5:65967512-65967781
Coord C2 exon
chr5:65967782-65967927
Length
270 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
AGGTGCTTCTCTTTGAACAGCCG
3' ss Score
5.94
Exon sequences
Seq C1 exon
TCCGCCTCCAAATGCTGCTAGAAAGGCAGGGGTGGTCCCTGGGTGTCAGCTGCGTCTCCAGTCATTCGGCTTCCCTTGGATTCGGCACCCTCTGCCTTCAAGCCAAATCAACTGCATGCGCTATGATACCTCCCCAAGTGCAGTCCTGCTTACCGGCCTCCCCGGAGCTCTTGGCATTAAGGTCACTGGAGCCACAGTCTCAGCTTACCAGAGGGGAGGGCGGGCAGTCTCCATCTGTTTTGTGACTGTGGCAGTGAGGGTGCTTTGTAGACAGAAGTGGGAGTCCTCGCTGTCTGGCTGGGACGTTCTACATGTTGGGAAAGGATGAACCGGCCCCATCCCTGCATCTCCTTTTGCTGGATGTATTTTGCTGCTTCTGGAATCAAAG
Seq A exon
GTGAGAGGCTAGCGCAGTGCTCCATATGGGCTCCTCTGGAGCCTTTTGGTGAGAGATGGGGTAGGGCTAGAAAGACAAGAGCACATGGGCGTGCTCAGCCTCTTTCTGACTCTTGATCATCAGGGTGGGTAAGACCAGCCAAAAAAGAAAGAAAGAAAGAGCTCATCCACTCATTCCAAAGCTACCCTAGCTGTGTGGCTCCATCCCTCATTTTGACCCCAGAGCTGGTCTTATTTTGAAACGCTGATCCAGGTGCTTCTCTTTGAACAG
Seq C2 exon
CCGTAGAGACAGCAAATGGAAAGTATGCCCAGAAATTGTTTAGCGATCTTTTTGAAGACTACTCCAATGCTCTGCGTCCAGTAGAAGATACGGACGCGGTGCTGAACGTCACTCTGCAGGTCACGCTCTCCCAGATAAAGGACATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029205:ENSMUST00000031108:1
Average complexity
IR
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=0.030
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0293118=Neur_chan_LBD=PU(18.8=79.6)
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:
GGCATTAAGGTCACTGGAGCC
R:
CTACTGGACGCAGAGCATTGG
Band lengths:
300-570
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