MmuEX0041282 @ mm10
Exon Skipping
Gene
ENSMUSG00000075316 | Scn9a
Description
sodium channel, voltage-gated, type IX, alpha [Source:MGI Symbol;Acc:MGI:107636]
Coordinates
chr2:66515315-66527084:-
Coord C1 exon
chr2:66526608-66527084
Coord A exon
chr2:66521766-66521846
Coord C2 exon
chr2:66515315-66515432
Length
81 bp
Sequences
Splice sites
3' ss Seq
TAACCTTCTCACCTCTGCAGGGG
3' ss Score
10.07
5' ss Seq
CAGGTTACC
5' ss Score
-1.62
Exon sequences
Seq C1 exon
GTCCTGAACCTGTTTCTGGCTTTATTACTGAGTTCCTTTAGTTCTGACAATCTTACAGCAATTGAAGAAGACACCGACGCAAACAACCTCCAGATTGCAGTGGCCAGAATTAAAAGAGGGATCAATTATGTGAAACAGACCCTGCGTGAATTCATTCTAAAGTCATTTTCCAAAAAGCCAAAGGGCTCCAAGGACACAAAACGAACAGCGGATCCCAACAACAAAAGAGAAAACTATATCTCAAACCGTACCCTTGCGGAGATAAGCAAAGATCACAATTTCCTCAAAGAAAAGGATAAGATCAGTGGTTTTAGCAGCAGTCTAGACAAAAGCTTTATGGATGAAAACGATTACCAGTCCTTTATTCATAATCCCAGCCTCACAGTGACAGTGCCCATTGCACCTGGGGAGTCTGATTTGGAGAATATGAACACAGAAGAGCTTAGCAGTGACTCAGATAGTGACTACAGCAAAGAG
Seq A exon
GGGTAAAACCACAGTGGAACGCCCCAGGATACAGCTCTGTGCTTTAACTACGCAGAGACACATGTGACCACTTTTACACAG
Seq C2 exon
AGACGGAACCGATCAAGTTCTTCAGAGTGCAGCACAGTTGATAACCCTCTGCCAGGAGAAGAGGAGGCAGAAGCTGAGCCTATCAATGCAGATGAGCCCGAAGCCTGTTTTACAGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075316_CASSETTE1
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.313 A=1.000 C2=0.700
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=5.0),PF065128=Na_trans_assoc=PU(61.4=84.9)
A:
PF065128=Na_trans_assoc=PD(0.1=0.0)
C2:
PF065128=Na_trans_assoc=FE(17.7=100)
Main Inclusion Isoform:
ENSMUST00000100063fB3597
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCACAGTGACAGTGCCCATTG
R:
TTCTGCCTCCTCTTCTCCTGG
Band lengths:
170-251
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