MmuALTD1022500-2/2 @ mm10
Alternative 5'ss
Gene
ENSMUSG00000035594 | Chrna5
Description
cholinergic receptor, nicotinic, alpha polypeptide 5 [Source:MGI Symbol;Acc:MGI:87889]
Coordinates
chr9:54981015-54998163:+
Coord C1 exon
chr9:54981015-54981115
Coord A exon
chr9:54981116-54981247
Coord C2 exon
chr9:54998012-54998163
Length
132 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGG
5' ss Score
4.94
3' ss Seq
CCTAAAAACTTGTTATGCAGGGT
3' ss Score
3.53
Exon sequences
Seq C1 exon
GTCCTTCAGAGTCCTCCAGTTTATCCATCTCATTTACAAGGAAGAGAAAATAGACGCACAAAGGAAGAGTGATTTGAACAAGATGCAGATCTCGAATGCAG
Seq A exon
GTCTTCTGATATGGATCACTTAGTATCTACAGCAGGGGCATGAAAGTCCACAGCAGGGAGGCAGTCTTGTTGGCTCACTCGGGGATCCAGAGTTTACAGTTCCAAAGGAAACAAAACCGCACCAAAACAGAG
Seq C2 exon
GGTTGCCTGAGCTATCCTCTGCTGCAAAACATGAAGACAGTTTGTTTAGGGATTTATTTGAAGACTATGAAAAGTGGGTTCGTCCTGTGGAACACCTGAGTGACAAGATAAAAATCAAGTTTGGCCTTGCAATATCTCAGTTAGTGGACGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035594-0-2,1-2-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0293118=Neur_chan_LBD=PU(19.1=76.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
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:
GTCCTTCAGAGTCCTCCAGTT
R:
ACTGAGATATTGCAAGGCCAAACT
Band lengths:
242-374
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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