MmuINT0036252 @ mm10
Intron Retention
Gene
ENSMUSG00000029205 | Chrna9
Description
cholinergic receptor, nicotinic, alpha polypeptide 9 [Source:MGI Symbol;Acc:MGI:1202403]
Coordinates
chr5:65969115-65971348:+
Coord C1 exon
chr5:65969115-65969269
Coord A exon
chr5:65969270-65970815
Coord C2 exon
chr5:65970816-65971348
Length
1546 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGC
5' ss Score
7.47
3' ss Seq
TCATCCTCATTTGCTCCTAGGGC
3' ss Score
8.3
Exon sequences
Seq C1 exon
GACGAGAGAAATCAGATTCTGACAGCCTACCTGTGGATCCGCCAAACTTGGCACGATGCGTACCTCACGTGGGATCGAGACCAGTATGACGGGCTGGACTCCATCAGGATTCCCAGCGATCTGGTGTGGAGGCCGGACATTGTCCTCTACAACAA
Seq A exon
GTAAGCGCTGCCCACACTAGAGGGGTCTGGGAAACAAACCTGCTGATTTAATACAAACTTGAACATCATTTAAAACACATGTGGAGTGTGAGCCTGTGTCCTTATTCAAATCGCAGATGGTCAGAGTATCAGATCATAAAAGCCTAGTGTTTGCCGTCCTCTGTGTCCCTGCAGTGGTAGAAGCATCATTTTGACCGTTGTCCTCTCCGTGCCCAAATCCCGTCTTTTACAACTCCCGATACAGGCTGAGCTGGCCACCCTGTGCCAGCGTGAGCTACATCTTCACTCACTGTATCTATAATAACCTTTCTCCTCCTGCCTCTCTCTTCCTCTTCCTCTTCCGTGGTGGTTTTATTTGTTGCTGTTGCTTTGTTTTGATCTTTCTGTTAAGATCAAGCTCCCGTGAATCTGACAATCTTCCTGCTTTGGCCCCCCAAGATCTCTACCACTCGAACTTAGCCCTGTTCCTCAGTAAACTGGAAGGCTAGGACTTCTATGTGAGAATTTCCTGGAGATACGATTTAATCTGCTCACAATCCAGACATTATGTAACAGAAATGCTACAATGGCTAGATAGGAAGAGCCGCCTGGAATCTGTCCTGTGGGTTTCAGACCGTAGAGTGGAGGGGAAATTTATCTTGCGGCTGTTTGGGCTCTGCTCAGAGCAAAGCACATGGGTTCATATTTCTGAGACTGTAAAGCATACGTGAACCACCTAGAGATCTTGAAAAAACTCAGATTTGGATTCAGTAGTCATAGGGTGGTCCTGCAGTTCTGAGTTCCCACGAGCTCCAGAGAGCAGTGGTTGTCCCTGGCTACTGGCTATCCTCCAGACAGAGCCAGACCTAACTCAAGCTCAATGTCGCCACCTTCTTCCCATCACCATGGGAGCTCCTCTATCTTTATAAAGATTTATTTATTGTTTATTTTATGTATATGAGTACACTGTAGCTGCACAGATGGTTGTGAGCCTTTATGTGGTTGTTGGGGATTGAATTTAGGACCTCTGCTCGCTCCTGTCAGCCCTGCTTGTTCTGGTCAACCTCACTCACTCAGGCCCTGCCCGCTCTGGCACAAAGATTTATTATTATATATGTTTATTATTATATATGTCTCAAGATTTATTTATTATTATTATTATAAATAAGTACACTGTAGCTGTCCTCAGACACACCAGAAGAGGGTGTCAGATCTCATTACGAGTGGTTGTGAGCCACCATGTGGTTGCTGGGACTTGAACTTAGGACCTTTGGAAGAACAGTCAGTGATCTTACTGGTTGAGCCATCTTGCCAGCCCTCCTCTGTCTTTATTCTGGAACCTAAGCTCTTGTGGATTGAGAGGGGTTCTTCTACTGTTCATATAAAAATGGGACCTCCTGGTAGAGAAGATGGGTACATTGGAAGTGATTCCAAACTCACAGAGAATGGGGACCCACTGCCAAATATACTGAAGCGACAGACACAGGGCATTGTCAGTAAGCAGTCCAGGACTTAAGTCAGTCAGGTTCCTCAGCAAGCGCCTGTCATCATCCTCATTTGCTCCTAG
Seq C2 exon
GGCCGATGACGAGTCTTCAGAGCCGGTGAACACCAACGTGGTCCTGCGGTACGATGGGCTCATCACCTGGGACTCACCAGCCATCACCAAAAGCTCCTGTGTGGTGGATGTCACCTATTTCCCCTTCGACAGCCAGCAGTGCAACCTGACCTTTGGTTCCTGGACCTACAATGGGAACCAGGTGGACATATTCAATGCCCTGGACAGTGGTGACCTCTCTGACTTCATTGAAGACGTGGAATGGGAGGTTCAGGGCATGCCTGCCGTGAAGAACGTCATCTCCTACGGCTGCTGCTCGGAGCCTTACCCAGACGTCACCTTCACTCTCCTTCTGAAGAGGAGGTCTTCCTTTTACATTGTCAACCTCCTCATCCCTTGCGTCCTCATATCGTTCCTCGCTCCGCTGAGTTTCTACCTCCCAGCAGCCTCCGGGGAGAAGGTCTCTCTGGGAGTGACCATCCTATTGGCCATGACTGTATTTCAGCTAATGGTGGCAGAGATCATGCCAGCCTCAGAAAACGTCCCTCTGATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029205:ENSMUST00000031108:3
Average complexity
IR
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(24.6=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(55.6=64.2),PF0293211=Neur_chan_memb=PU(24.1=31.3)
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:
TACCTCACGTGGGATCGAGAC
R:
CATGCCCTGAACCTCCCATTC
Band lengths:
354-1900
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