MmuINT0139699 @ mm10
Intron Retention
Gene
ENSMUSG00000001027 | Scn4a
Description
sodium channel, voltage-gated, type IV, alpha [Source:MGI Symbol;Acc:MGI:98250]
Coordinates
chr11:106348900-106349389:-
Coord C1 exon
chr11:106349117-106349389
Coord A exon
chr11:106349019-106349116
Coord C2 exon
chr11:106348900-106349018
Length
98 bp
Sequences
Splice sites
5' ss Seq
AAGGTCCGT
5' ss Score
6.16
3' ss Seq
CGTTTCTCTCCCTGCCTCAGACC
3' ss Score
9.07
Exon sequences
Seq C1 exon
ATGGCCAGCTCATCTCTGCCCACCCTGGTCCCCCCTGGTCCCCACTGCCTGCGCCCCTTCACCCCAGAGTCCCTGGCAGCCATAGAACAGCGGGCAATGGAGGAGGAAGCCCGGCTGCAGCGGAACAAGCAAATGGAGATTGAAGAGCCTGAGCGGAAGCCACGCAGTGACCTGGAAGCTGGCAAGAACCTCCCACTCATCTATGGGGACCCCCCACCTGAAGTCATTGGCGTCCCCCTGGAGGACCTGGACCCTTACTACAGTGACAAGAAG
Seq A exon
GTCCGTGTGTGGGAGGGCTCCCTGTCTGTCCGTCCGTCTGTCCGTCCATCCTTCCATCCATCTGTCTGCCAGGCTCACCGTTTCTCTCCCTGCCTCAG
Seq C2 exon
ACCTTCATTGTGCTCAACAAAGGAAAGGCCATCTTCCGATTCTCTGCCACCCCTGCCCTCTACATGCTGAGCCCCTTCAGCATCGTCCGGCGGGTGGCTATCAAGGTGCTCATCCACGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001027:ENSMUST00000021056:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.396 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion 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:
CTGGAAGCTGGCAAGAACCTC
R:
TGAAGGGGCTCAGCATGTAGA
Band lengths:
181-279
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