MmuEX6101781 @ mm10
Exon Skipping
Gene
ENSMUSG00000075316 | Scn9a
Description
sodium channel, voltage-gated, type IX, alpha [Source:MGI Symbol;Acc:MGI:107636]
Coordinates
chr2:66480080-66488086:-
Coord C1 exon
chr2:66487982-66488086
Coord A exon
chr2:66487375-66487645
Coord C2 exon
chr2:66480080-66484604
Length
271 bp
Sequences
Splice sites
3' ss Seq
ACTTTTCGTGTCTTTTGCAGAAC
3' ss Score
12.28
5' ss Seq
TAGGTAAGG
5' ss Score
9.31
Exon sequences
Seq C1 exon
CTTGGAGGTCAAGATATCTTTATGACAGAAGAACAGAAGAAATACTATAATGCAATGAAGAAGCTGGGGTCCAAGAAACCACAAAAACCAATTCCGAGGCCAGGG
Seq A exon
AACAAATTCCAAGGATGCATATTTGACTTAGTGACAAACCAAGCTTTTGATATCACCATCATGGTTCTTATCTGCCTCAATATGGTAACCATGATGGTAGAAAAAGAGGGGCAAACTGACTACATGAGTTTTGTGCTATACTGGATCAACGTGGTCTTCATCATCCTGTTCACTGGGGAGTGTGTGCTGAAGCTGATCTCTCTCAGGCATTACTACTTCACTGTGGGATGGAACATTTTTGATTTTGTGGTAGTGATCCTCTCCATTGTAG
Seq C2 exon
GAATGTTTCTCGCTGAGATGATAGAGAAGTATTTCGTGTCTCCTACCCTGTTCCGAGTCATTCGCCTGGCCAGGATTGGACGAATCCTACGCCTGATCAAAGGCGCCAAGGGGATCCGCACGCTGCTCTTTGCTCTGATGATGTCCCTTCCTGCGCTGTTCAACATCGGCCTCCTGCTTTTCCTCGTCATGTTCATCTACGCCATCTTTGGGATGTCCAACTTTGCCTACGTTAAAAAGGAAGCTGGAATTAATGACATGTTCAACTTTGAGACCTTCGGCAACAGCATGATCTGCCTGTTCCAAATCACCACCTCTGCGGGCTGGGATGGACTGCTGGCCCCCATCCTCAACAGTGCACCTCCTGACTGTGACCCAAAAAAGGTTCACCCAGGAAGTTCAGTGGAAGGGGACTGTGGAAATCCATCTGTGGGAATTTTCTACTTTGTCAGCTACATCATCATATCCTTCCTGGTTGTGGTGAACATGTACATTGCTGTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075316-'36-34,'36-33,37-34=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence exclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=0.000 C2=0.215
Domain overlap (PFAM):
C1:
NO
A:
PF0052026=Ion_trans=PU(20.4=47.3)
C2:
PF0052026=Ion_trans=PD(79.1=42.2)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAAGAAGCTGGGGTCCAAGA
R:
CCAGCTTCCTTTTTAACGTAGGC
Band lengths:
297-568
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