MmuINT0139711 @ mm9
Intron Retention
Gene
ENSMUSG00000001027 | Scn4a
Description
sodium channel, voltage-gated, type IV, alpha [Source:MGI Symbol;Acc:MGI:98250]
Coordinates
chr11:106185190-106185575:-
Coord C1 exon
chr11:106185522-106185575
Coord A exon
chr11:106185328-106185521
Coord C2 exon
chr11:106185190-106185327
Length
194 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
GTGTGTACCCCATCCTGCAGAAA
3' ss Score
8.08
Exon sequences
Seq C1 exon
GCCACTTTCAAGGGTTGGATGGACATCATGTATGCAGCTGTGGACTCCCGGGAG
Seq A exon
GTGAGTGGGGTCACTGAGTTGGTAAGTTGGAGGAGCAGCAATAGCGGTCCATTCTGTCCTCCCCACTCTCACCTGACACCTTCACCCCACCACACTATCTCCTTGGAAGACCAGCAGCCTGGGGAGGAGGGGCATCCTCCTCACAGTACTATGGGGATCAAAGAGAAACTCCATGTGTGTACCCCATCCTGCAG
Seq C2 exon
AAAGAGGAGCAGCCAGACTACGAGGTGAACCTCTACATGTACCTTTACTTCGTCATCTTTATCATCTTCGGCTCCTTCTTCACCCTCAATCTCTTCATTGGCGTCATCATTGACAACTTCAACCAACAGAAGAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001027-Scn4a:NM_133199:20
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(7.5=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(15.4=76.1)
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:
GCCACTTTCAAGGGTTGGATG
R:
TCTTCTGTTGGTTGAAGTTGTCA
Band lengths:
187-381
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: