MmuEX6090572 @ mm10
Exon Skipping
Gene
ENSMUSG00000001027 | Scn4a
Description
sodium channel, voltage-gated, type IV, alpha [Source:MGI Symbol;Acc:MGI:98250]
Coordinates
chr11:106328020-106335731:-
Coord C1 exon
chr11:106335375-106335731
Coord A exon
chr11:106329997-106330473
Coord C2 exon
chr11:106328020-106328155
Length
477 bp
Sequences
Splice sites
3' ss Seq
ATCTGTCCCTTGCTTCCCAGGTC
3' ss Score
10.04
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
Exon sequences
Seq C1 exon
CTGCGTGTCTTCAAGCTGGCCAAGTCATGGCCAACACTCAACATGCTCATCAAAATCATTGGCAACTCAGTGGGTGCGCTGGGCAACCTGACCCTGGTGTTGGCCATCATCGTCTTCATCTTCGCCGTGGTGGGCATGCAGCTGTTTGGCAAGAGCTATAAGGAATGCGTGTGCAAGATTGCCTCAGACTGCAGCCTGCCCCGCTGGCACATGCACGATTTCTTCCACTCCTTCCTCATCGTCTTCCGCATCCTCTGTGGGGAGTGGATCGAGACCATGTGGGACTGCATGGAAGTGGCCGGCCAGGCCATGTGCCTCACCGTCTTCCTCATGGTCATGGTCATTGGCAACCTGGTG
Seq A exon
GTCCTGAATCTGTTCCTGGCTCTCCTGTTGAGTTCCTTCAGCGCTGACAGTCTGGCAGCGTCAGATGAAGATGGTGAGATGAACAACCTACAGATCGCCATCGGGCGTATCAAGTGGGGCATCGCCTTTGCCAAAACCTTCCTCTTGGGGCTGTTGCATGGCAAGATCCTGAGCCTCAAAGACATAATGCTCAGTCTCGGGGAGCCTGGGGGTGCTGGGGAAAACGGGGAGAGCCCTCCCGAGGATGAGAAGAAGGAACCACCTCCGGAAGATGGGAACAAGGAGCTGAAAGACAATCATATCCTGAACCACGTGGGCCTGACTGATGGACCCCGCTCCAGCATCGAGATGGACCACCTTAACTTCATCAACAACCCCTACCTCACTATCCATGTGCCCATTGCCTCCGAGGAGTCCGACTTGGAAATGCCCACAGAGGAGGAGACTGACACCTTCTCGGAGCCTGAGGACATCAAG
Seq C2 exon
AAGCCACTACAGCCTCTGTACGACGGGAACTCCTCCGTCTGCAGCACAGCTGACTACAAGCCCCCCGAAGAGGACCCTGAGGAGCAGGCTGAGGAGAACCCTGAGGGGGAGCTACCTGAGGAGTGTTTCACAGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001027-'17-18,'17-16,18-18=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=0.447 C2=0.630
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(62.1=100)
A:
PF0052026=Ion_trans=PD(4.2=5.0),PF065128=Na_trans_assoc=PU(59.7=84.9)
C2:
PF065128=Na_trans_assoc=FE(19.9=100)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATGCAGCTGTTTGGCAAGAG
R:
AACACTCCTCAGGTAGCTCCC
Band lengths:
350-827
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