MmuINT0139707 @ mm10
Intron Retention
Gene
ENSMUSG00000001027 | Scn4a
Description
sodium channel, voltage-gated, type IV, alpha [Source:MGI Symbol;Acc:MGI:98250]
Coordinates
chr11:106326131-106326879:-
Coord C1 exon
chr11:106326706-106326879
Coord A exon
chr11:106326254-106326705
Coord C2 exon
chr11:106326131-106326253
Length
452 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGT
5' ss Score
7.77
3' ss Seq
TGAGCATGCACTTCTTCCAGGTC
3' ss Score
7.63
Exon sequences
Seq C1 exon
GCCTTCGAGGACATCTACATTGAACAGCGGCGAGTCATCCAAACCATCCTGGAATATGCTGACAAGGTCTTCACCTACATCTTCATCCTGGAGATGCTGCTAAAGTGGGTGGCCTACGGCTTCAAGGTGTACTTCACCAACGCCTGGTGCTGGCTCGACTTCCTCATTGTGGAT
Seq A exon
GTGAGTCTCCTGGATCTGGCCACACAGCCGGATGTCATGGCCTTTAGATAACCCAGGCTCTGGGAGGTAGGACCTATCTGAATCTACACAGTCAGACCTCCCAGGTTAGCACTGCTCCCTATAGACCAGCCTCTTCCTTCCCAGACATGACAGCCCAGACCTGGAGCCTTATGCTCCCTGCCAGTGTAATTCTTATATGCTCTTTGATAGATACACGGAACCTGAGGAGATGGGTACTGTCCTTCCCAATTATGGTTGTAGGTGACATCATTGAGGTGAACCCTGGTCCTACAGGTGCTAGAGGCCACAAGCCTACTCTTCCCAGAAGACAGGATTATCCATCAGGGATGGGGTCTACAGGAGACACACAGAAACTGGGGTATCTCTCTCATGTGTCCCAGGCTAGAAGAAAGCCAGGGACCCTCCACCTCCTGAGCATGCACTTCTTCCAG
Seq C2 exon
GTCTCCATCATCAGTCTGGTGGCTAACTGGCTGGGCTACTCTGAGCTGGGGCCCATCAAATCCCTGCGCACGCTCCGGGCCCTGCGACCTCTGAGGGCACTGTCCCGATTTGAAGGCATGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001027:ENSMUST00000021056:17
Average complexity
IR
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=PU(17.1=67.2)
A:
NA
C2:
PF0052026=Ion_trans=FE(17.5=100)
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:
GCCTTCGAGGACATCTACATTGA
R:
CCTCATGCCTTCAAATCGGGA
Band lengths:
297-749
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