MmuINT0036211 @ mm10
Intron Retention
Gene
ENSMUSG00000066279 | Chrna10
Description
cholinergic receptor, nicotinic, alpha polypeptide 10 [Source:MGI Symbol;Acc:MGI:3609260]
Coordinates
chr7:102114969-102116713:-
Coord C1 exon
chr7:102116257-102116713
Coord A exon
chr7:102115115-102116256
Coord C2 exon
chr7:102114969-102115114
Length
1142 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATG
5' ss Score
9.43
3' ss Seq
AATTCTCATTCACCCTCTAGAGT
3' ss Score
7.14
Exon sequences
Seq C1 exon
TTCTGCTGAGAGCAGCAGGCTTGCTCAGAGCCCAGGTACAGGGAATGGATTGAAGGGGGGTTTGAGGTGCTGTAAGAGGAGAAGAAAGGGGGAGAGAGGAAAGAAAACAGAAACCAAGACCATTACAGAGGAAGAAAGCAAATTGAGACAGAGAGGTAAAAGACGGCACTAGTCATATGGAAAGGGACGGAAGATGGAGCCAGAGAGGCTGTGAAGAGCAAAGGAGAAACTGCAGGTACAAGGACCAGGTATAGTACTGCAGGCAGGTGCAAACAGGAGACCAGAAGGAAAGCCGCAATCTCTGGTTTCCAGGTACTGTCCACCTCATCCGTGCCAGCAGGGCCTGTTGCTTTACATCTCCTCAAGACCTGCCCACCCTCTGGCTGTGGTAGCGACATGGGGACCAGGAGCCACCACCTGGGTCCTGGGTTTCTGCTCCTGCTCTTTCTCCCTGCAG
Seq A exon
GTAATGAACCAGGTCTATCTGACACCGCCATTATTCCTGTCCACCACAAGCCTCCAGTCCCTACCCTTCTCTTCAGTGCCTGCTGAGAGCAAGCTATCTGGGGAATGTGGAGGAGAGGGTGCTGAAGATGGGAGTGGGGGAGAAGTAACTGTAAAAAGTCAGGTGTGCAAACCCCTTTAGCTCCTTGGGTACTTTCTCTTGCTCCTCCATTGGGGACCCTGTGTTCCATCCAATAGCTGACTGTGAGCATCCACTTCTGTTTGCCAAGCACCGGCATAGCCTCACAAGAGACAGCTATATCAGGGGCCGTTCAGCAAAATCTTGCTGGCGTATGCAATGGCATCAGCTTTTGGAGGCTGATTATGGGATGGATCCCCGGGAATGGCAGTCTCTAGATGGTCCATCCTTTCGTCTCAGCTCCAAACTTTGTCTCCATAACTCCTTCCATGGGTGTTTTGTTCCCAATTCTAAGAAGGGGCAAAGTGTCCACTCTTTTTTGGTCTTCGTTCTTCTTGAATTTCATGTGTTTTGCAAATTGTATCTTGTATCTTGGGTATTCTAAGCTTCTGGGCTAATACCAACAATATGAACTAACCAGTACCCCCGGAGCTCGTATCTCTAGCTGCATATGTAGCAGAAGATGGCCTAGTCGGCCATCATTGGGAAGAGAGGCCCCTTGGTCTTGCAAACTTTATATGCCTCAGTACAGGGGAACGCCAGGGCCAAGAAGTGGGAGGGGTGGGGGGGGGAGGGTATGGGGGACTTTTGGGATAGCATTTGAAATGTAAATGAAGAAAATCCCTAATTTAAAAAAAAGGTCAGGTGTGGCCTCAAACACCTATAACCACAGTGCTGTAGGAACCTGAGCCAGGAGGATTGCTGGGATTGCTGGCCAACCAGACTAGCTGAAAAAAACGGCAAGTTGCAAGTTCAGTGCGAGACCCTGTCTCAAGAGAACAGGGTAGAAAGTGATAAAGCCAGAAACCCAGTCCTCTCCTCTGGCTTCTGAAGACATATGAGTAAATGGCACAGAGCATCAAAAATGTGTGAGACCACGGAACAGGTGACAAGGCTCTAGCTGGGGGGTGATAGATGTGAACAGAGACCGCTGGATGACAGTCAAATTCTCATTCACCCTCTAG
Seq C2 exon
AGTGCCTGGGAGCTGAGGGTAGACTGGCTCACAAGCTGTTTCGTGACCTGTTTGCCAACTATACAAGTGCCTTGAGACCAGTGGCAGACACAGACCAGACTCTAAATGTGACCCTGGAGGTGACGTTGTCTCAGATCATTGATATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000066279:ENSMUST00000084830:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.012 A=NA C2=0.000
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
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGCTGTGAAGAGCAAAGGAG
R:
GTGTCTGCCACTGGTCTCAAG
Band lengths:
343-1485
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