MmuINT0036233 @ mm9
Intron Retention
Gene
ENSMUSG00000035594 | Chrna5
Description
cholinergic receptor, nicotinic, alpha polypeptide 5 [Source:MGI Symbol;Acc:MGI:87889]
Coordinates
chr9:54848259-54850316:+
Coord C1 exon
chr9:54848259-54848303
Coord A exon
chr9:54848304-54850206
Coord C2 exon
chr9:54850207-54850316
Length
1903 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGT
5' ss Score
6.99
3' ss Seq
GTGACTTTCTCATTTTAAAGGAA
3' ss Score
8.92
Exon sequences
Seq C1 exon
GATGAGAAAAACCAGCTAATGACCACCAACGTCTGGTTGAAGCAG
Seq A exon
GTGTGTATAGCAATCACACAGGCACGGAGCGAGCAGCTGGCTACACTGTTCATTACAGGCTACAGCAAGGAGGAGCTTGCGTGTGTGCCCTGTGGATTGTCAGGTTGAGAACGCTGAGAATAAATAGATGGAACTATTGTACTCATTGTGCATGTATACTGTGCATATTTGTTTTGAACCAGGGTCTTGTTATACAGCTTCAGTCTTCCGTCTTCATCCTCCCAAGTTCTGGAATTACCACTGTGTCTGCTTTAGTTGACTTTTTTTGTGGGTCTGATATGTGTTAAGCACTGGAGAAACTGCAGTAATGGAGCAGACAGAACTCACTGTTCCCCCAGAAACCTCATCCAAGTGGAAAGAGAGTGAGCCATAGTGCCTTAGAGACCGACAGTCTGAGAGAGGTCACGTGGCAAAGAGGATGGAGAGTGTTGGCTACTATACTTGTTAGCAAAAAGAAACACCCAACCAAGCCATAAAAAAATGACTGAAAAGGCAAAGTTTGTACAAAGTCTCAAGGGAGATGATGCAAGCCTTATGGGCAGCTAGGGGACAAGACTCTTCTGGGTAGAGGGGCCAGCAAGTCAAAGGCCCAGAGGCAGGATTGCATCTAGTAAGGGAACCAGTGTGGCTAGAGGTGTGTGAGCCATGGGGAGGGGTATGGAGATGGGGTCAGAGGAGCAACAAGAAGCCGCTAGAATATTCAAAGCCACTAGAGTATTAGTTTATAGGACACCACAAGGATTTGGAGTTTTACTTTCATTTGTTGTTATTTTAAAAAAGATTTATTTCTATTTATGTCTGAGTTATTTAGTTTGCATATATACACACATACACGAAATGTCCAAGGAGGCCAGAAGAAGGCATTGCATCCCCTGGGCCTGGCATTACAGAGGGTTGTAAGCTGCTGTGTGGGTGCTGGGAACTGGACCTGCTCTTCTCCAGGAGCAGCGAGTGCTCTTCGCCCTGAGCCATCTGCCTAGCCCCAGGATTCTGGCTTTTAATTTGATTGCAATGGGACAGGATAAGGATGCAACTAATTATTTTATTATCATTGTTAACATGCTAACTGTGCATGTTACTGGGATTCACTGTGATATTTTCATGCATGCAGACCTCATGCATTGACCGTGTCCATCCACCCTGTAATCACCCTCCTCCTCCTCCAGCCCCCTCCGCATTCCCCAGTGACCCCCTTTGTAATTAATTATTTTTATGGACAGAGCACCTTTTACATGAAGGGCTTTTAAATTCTGGGCCACCATTCTTGTGTCTCTGGCTGCTGTTGAGTGCCCCCCCCCCCCATTGTTTATTCTTTCTCTGTCTCTGATTATTTATACCCACCACCAGTTCCCTAATCCCAGACTTACAAAAGACAGGTTGATGTTGTTTTTTTGTCTGTTTGCTGCGCAGGGGATTGAACCTAGGGCCTGAAGGATGCCAGGCAGGTCTACTGATGAGCTACATCTCTAGTTCATTTCTTAGCTTGATACAGTCACAGAATTGTTACTGTCTGGGCACTGAGCAGAATACTTAAGTGTATGGGGTGTGTAATAAATCCAACTCTCCTTCCACCAAATCAGGGCACAGTACAGCTGGGAAGGGGAACGTGTTTCCTAAACCTGGACTTTAGGGACTGGTCCATGGCTTCAGGTTTTGAGTACAGTCAGCTGGTGGGAGAAGAGGGGCCAAGTAGAGAAGCTTGAATGTATCGCATGAGCCTCACCTGTGCCCCATCAGGACCACAGCGAGAGGCATTGTGCAGAGAATGGCTTATTATTAGTCGAGGTTTACTGAATTAGAGCAGAAATGATTCATGCCTAAGTTCTGGGTATGACAAAAAGTATAGTTTAAACTTATTTTATTATTGCTTGATTGAAATGGAGGTGACTTTCTCATTTTAAAG
Seq C2 exon
GAATGGATAGATGTAAAGTTAAGATGGAATCCTGATGACTATGGTGGAATAAAAATTATACGTGTTCCTTCAGACTCTCTGTGGATCCCAGACATCGTTTTGTTTGATAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035594-Chrna5:NM_176844:3
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=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=FE(6.9=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(17.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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: