MmuINT0036214 @ mm10
Intron Retention
Gene
ENSMUSG00000066279 | Chrna10
Description
cholinergic receptor, nicotinic, alpha polypeptide 10 [Source:MGI Symbol;Acc:MGI:3609260]
Coordinates
chr7:102111266-102113619:-
Coord C1 exon
chr7:102113087-102113619
Coord A exon
chr7:102112488-102113086
Coord C2 exon
chr7:102111266-102112487
Length
599 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
AAATGCTTTCTGTCCCACAGGAA
3' ss Score
10.32
Exon sequences
Seq C1 exon
GGCGGACACGCAGCCACCTGCCTCGGCCAGCACCAACGTGGTTGTGCGGCACGACGGCGCTGTGCGCTGGGACGCACCGGCCATCACACGCAGCTCGTGCCGTGTGGATGTCTCTGCCTTCCCATTTGACGCTCAGCGCTGTGGCCTGACCTTCGGCTCATGGACGCACGGCGGGCACCAGCTGGATGTGCGACCTCGGGGCACTTCCGCCAGTCTGGCCGACTTCGTGGAGAACGTTGAATGGCGTGTGCTGGGCATGCCAGCGCGCAGGCGCGTGCTCACCTACGGCTGCTGCTCCGAGCCCTACCCAGACGTGACCTTCACTCTGCTGCTGCGCCGCCGTGCAGCTGCCTATGTGTGCAACCTACTGCTGCCCTGTGTGTTCATCTCCCTGCTGGCACCTCTGGCCTTCCACCTGCCCGCTGACTCCGGGGAGAAGGTGTCTCTGGGCGTCACCGTGCTCCTGGCGCTCACCGTCTTCCAGCTGATCCTGGCCGAGAGCATGCCACCTGCAGAGAGCGTTCCACTCATCG
Seq A exon
GTGAGTCTGAGGGCTTGGGAGAGTGGACACTAGGTCAGAAGAGTGACTGCTGCAGAGGGTGAGAGAGCATAGACCTGACTGGGGGAACACCCTTGACTGCTGGGGTCTTGATGGAGGAATATCTGGTGCCCAGTGTCATAATAAACAAATTGTAGTGATAGCTGTGTGCCAGGCATTCGCCTGTGCACGTGACATTTGTTCATTCACAGGAGCAATACCATGAACCAACGAATAGGTTATTCCAGGTGTACAGACAGGATAGTTCAGGTTGCAACCACAATCCGATACCCAGTAGGGAAAAAAAATAGGTAGCAGATATCTTCTGATGGTTTTTCGAGACAGGGTTTCTCTGTGTAGCCCTGGCTATCCTGGAACTCACTCTGTAGACCAGGCTAGCCTCAAACTCAGAAATGTGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGTGTGCACCACCACTGCCTGGCCTTAGCCCTTACTTTATCCTTCCCCACATCGGGTCTGAGGGCCTGATGCTGTCCCCCTTTCCATTTATAATGAGGCAGCTGGGAAGCTTCATTTCCTGTTTGGGGCTCAAAATGCTTTCTGTCCCACAG
Seq C2 exon
GAAAGTACTATATGGCCACTATGACCATGGTCACATTCTCCACAGCGCTTACCATCCTCATTATGAATCTGCATTACTGTGGCCCTAATGCACATCCAGTACCTGCCTGGGCTCGGGTCCTCCTGCTGGGACACCTAGCCAAAGGCCTGTGTGTGCGGGAACGAGGGGAGCCCTGTGGACAGTCCAAGCCATTAGAGTCAGCCCCCAGCCTCCAGCCTCCTGCAGGTCCCCCAGCGGGCCCTTGTCATGAGCCACGGTGTCTATGCCACCAAGAAGCCCTTCTGCATCACGTAGCTTCCATTGCCGGCACCTTCCGCAGCCACCGGGCTGCCCAGCGCCGCCATGAAGATTGGAAGCGCCTGGCCAGAGTAATGGACCGCTTTTTCCTAGGCATCTTCTTCTGCATGGCTCTGGTCATGAGCCTCCTGGTACTGGTGCAAGCCCTGTAAGGGCCAGGAACTGGATTTCAGGGAGCTGTGATCACCTCAACACCACCAGGTGGGGATGGCAAAGCCCAGGTGGTTGTTGGTACTCAGAAACACTAGCCAGTTTCTCCCCAAAGTGCTGCTAAGAGTCAGAGACACCTCTTCAGGACCAGCACTTCTGACCTCAAACCCACAAACAGCCTTTGTGATCTGCATGCCCTAATGGAAGGGGATCTAAAGCTTGCCTCTCCCCTAATTCCAACATGAGTGAGGTCAAAGTACAGACTTGGAGGCTAAGACTCAGTGCCAGCTGAGCAAGGTGATATAATTCCAGCACAAGGAGGCTGAGACAGGAAGATTACCCTAAGGTCTGTAGCCTGAGCTACAGAAATTTTTGTCTAAAAATAAATAACCACCCCAGTGTCTACACTTGGAATCATAGCTATTAGCCGGTGGAATCCAGGTTATTTTCCTTTGTCGAGTTAGAGTCTCGCTATGTAGTCCTTGCTGGCCTGGAACTTGCTATGTAGCCCAGGTTGGCTTTGAACTCACACAGATCCACATGCCTCTGCCTCTCCAAACACAGGTGCCACTATGCCTGGCTTGGGTGTAGGTTACTAATTAAAGGGACAAAGCTACACATTTGCTTGTCACCCTTAGCAGTTGCTATTACAGATTCTCATCTTGCTTCTCACTGCTAGGCTCTCCCGGGAGGGAACTCACTGTCTAGTTTCCAAAACAGAAGGCTGTGCAGACATTTGACTCGGAGCTTCGATCCATAATAAATGAGTGCTCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000066279:ENSMUST00000084830:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.017 A=NA C2=0.107
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PD(55.6=64.2),PF0293211=Neur_chan_memb=PU(40.9=31.3)
A:
NA
C2:
PF0293211=Neur_chan_memb=PD(58.4=53.3),PF0293211=Neur_chan_memb=WD(100=58.0)
Main Inclusion Isoform:
NA
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:
CTCACCGTCTTCCAGCTGATC
R:
GGGCTTCTTGGTGGCATAGAC
Band lengths:
343-942
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