MmuINT0036239 @ mm9
Intron Retention
Gene
ENSMUSG00000031491 | Chrna6
Description
cholinergic receptor, nicotinic, alpha polypeptide 6 [Source:MGI Symbol;Acc:MGI:106213]
Coordinates
chr8:28516967-28518896:-
Coord C1 exon
chr8:28518787-28518896
Coord A exon
chr8:28517946-28518786
Coord C2 exon
chr8:28516967-28517945
Length
841 bp
Sequences
Splice sites
5' ss Seq
CAAGTGTGT
5' ss Score
3.84
3' ss Seq
GTGTGTGGTTTCATTTCCAGTGC
3' ss Score
9.73
Exon sequences
Seq C1 exon
ATCTGGAAGGACTACAGATTGCGTTGGGATCCAACGGAGTATGATGGCATCGAGACACTTCGAGTTCCAGCAGACAACATCTGGAAGCCTGACATCGTTCTGTATAACAA
Seq A exon
GTGTGTGCATCTAGAGAGATTCACCGTCGATTTTGTTTTTGTTTTGTTTTTTTTTTGGGGGGGTTGGTTTTTTATTAGCAAGAAAACTACTTTTGGCTTTCTTTTTTATTATATTATTTTTATATTATATTCTTTATTTACATTTCAAATGTTATCCCCTTTCCTAGTTTCCCCTCAGAAAAACCCCCTATCCTCTCCCCTCTCCCCCTGCTCCCCAATCCACCCACTCCTGCTTCCTGGCCCTGGCATTTCCCTATACTGGGGCATAGAACCTTCACAGGACCAAGGGCCTCTCCTCCCGTTGATGACTGACTAGGCCATCCTCTGCTACATATGCAACTAGAGACACGAGTCCCTCCGTGTGTTTTCTTTGATTGGTGGTTTAGTCCCAGGGACCTCTGAGGTTACTGGTTAGTTCCTTCTAGGGGGCTGCAAACCCCTTTAGCTCCTTGGGTACTTTCTCTAGCTCCTTCATTGGGGAATCCTGTGCTCCATCCAATGGATGGCTGTGAACATCCACTTCTGTATTTGTCAGGCACTGGCAGAGCTTCTCAGGAGACAGCTATATCAGGCTCCTGTCAGCAAGCTCTTGTTGGCATCTGCAATAGTGTCTGGGTTTGGTGGTTGTTTATGGGATGGATCCCCAGGTGGGGCAGTTTCTGGATGGTATTCCTTCCGTCTCTACTCTGAACTTTGTCTCTGTAACTCCTTCCATGGGTATTTTGTTCCCCCTTCTAAGAAGGATTGAAGTATCCACACTTGGTCTTCAAAATCTTTGGCCCTGGTGACCCACAGCAAAGCTACACACAGTGCTGCTAATGGTGTGTGGTTTCATTTCCAG
Seq C2 exon
TGCTGTCGGCGACTTCCAGGTCGAAGGCAAGACCAAAGCTCTTCTCAAGTATGACGGTGTGATAACCTGGACCCCACCAGCCATCTTTAAGAGCTCCTGCCCAATGGACATCACCTTCTTCCCGTTTGACCATCAAAACTGCTCCCTGAAGTTTGGTTCCTGGACTTATGACAAGGCAGAAATCGACCTTCTCATCATTGGCTCTAAAGTAGACATGAACGACTTTTGGGAAAACAGTGAATGGGAAATTGTCGACGCCTCTGGCTATAAGCATGACATCAAGTACAACTGCTGTGAAGAGATTTACACGGACATAACCTACTCCTTCTACATCAGGAGGTTGCCCATGTTTTACACCATCAACCTCATCATCCCCTGCCTCTTCATTTCCTTCCTCACGGTGCTGGTTTTTTACCTTCCCTCCGACTGTGGCGAGAAAGTGACTCTTTGCATCTCCGTTCTGCTTTCTCTCACTGTCTTTTTGCTGGTGATTACAGAGACCATCCCATCCACATCTCTCGTGATCCCACTGGTGGGTGAGTATCTACTGTTCACCATGATCTTTGTCACGCTGTCCATTGTGGTGACCGTGTTCGTGCTGAACATACACTACAGGACCCCAGCAACGCATACCATGCCCAAGTGGGTGAAGACCATCTTCCTTCAGGCCTTCCCCTCGATTCTGATGATGAGGAAACCTCTGGACAAGACAAAGGAGGCAGGAGGTGTTAAGGACCCCAAAAGCCATACCAAGAGGCCTGCCAAGGTCAAATTTACTCATCGAGGAGAATCCAAACTTCTAAAGGAATGCCACCACTGCCAAAAATCAAGTGACATAGCACCTGGAAAGAGAAGATCAAGCCAGCAGCCTGCACGGTGGGTGGCAGAGAATTCAGAGCACTCGTCCGATGTTGAAGATGTCATCGAGAGTGTTCAATTCATAGCAGAAAACATGAAGAGCCACAATGAAACAAACGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031491-Chrna6:NM_021369:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.069
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(17.4=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=PD(55.6=35.2),PF0293211=Neur_chan_memb=PU(86.1=62.4)
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:
ACAGATTGCGTTGGGATCCAA
R:
GAGGCGTCGACAATTTCCCAT
Band lengths:
358-1199
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: