MmuINT0139803 @ mm9
Intron Retention
Gene
ENSMUSG00000023033 | Scn8a
Description
sodium channel, voltage-gated, type VIII, alpha [Source:MGI Symbol;Acc:MGI:103169]
Coordinates
chr15:100801951-100803391:+
Coord C1 exon
chr15:100801951-100802092
Coord A exon
chr15:100802093-100803184
Coord C2 exon
chr15:100803185-100803391
Length
1092 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
ACGTGGCCTTCCTCTTTCAGACC
3' ss Score
11.57
Exon sequences
Seq C1 exon
GCAATGCCCAGAGGGGTTCCAGTGCATGAAAGCAGGAAGAAATCCCAACTACGGCTACACCAGCTTCGACACCTTCAGCTGGGCCTTCCTGGCACTGTTCCGCCTCATGACTCAGGACTACTGGGAGAACTTATACCAGCTG
Seq A exon
GTGAGTACACTGGGGTATGGCAAGCTGGGGACTTTCTGTGCGACACACCCATACTGCAGACATTAAGTATGATCTGGGAACGGCGTTTCTCGATCCCTCGGGATGGATGAATTCAGCCAGCTCTTAGCCCAGTTTCTTGACTGTTTAGTCAGCTGTGGAAGCTGACACCCCGACCGCCTCAGAGCGCCTGCTTCCTCTCAGGTTGCTCTCCGCAGTGTGCATCTTCTTTTGGACTTCTGCTGTCAGCACGTTTGTTTAAGAAACAGCAAACACTTGTTTGTGCAGGGCCCCTTCCTAGGTGCTTAAATGATGGGGTCTCTCTCCAGAGGACCTTGAAGTATGACTTATCAATATTTTTAGAGCCATACTGCATTTGGTCTTGTTCAGGTGTGTGGTCCCCATTCCAAGATGACTTCATTGTCTTGTAACTCACAAGTCATAATGAGGGAACTGGTGGCGCTGATTTGCTAACCTTAGAAGTCCTGACAAGCCACTGCATTTGTCTCTGGCTGATGATGCTGGTTGGTTAGAGGACAGAAAATAACTCTCCCTCTGCAAAAAGGAGCCTCTTTAAGAGAAGCTTCAGTTTCCAATCCCCAAGTCAGTCCTTACTGTTGAGCATAACAGACACAAAATCCCACTAAGTGCTTGCTGACTGAAAGACTCAAGATGAGCCAGGCCTGTGGTGTAGGTTAAGATCCCCGTGCTCAGGAGACGGGGGTGGGGGAGGGGGTATGGGGGTGTGGGGTGGGGGGGGTGGGGGGTGGGGGTGGAAGGAGGTAGGAAGGTCACTGGGGAGTTTGAAACCAGTCTGATTTACATAGCAAGCTCCATGCCAGCCAGGGCTACATTGCAAGACCTTTTCTAAAACAGACAGGCAGACAGAATATTTTTCTGTGAAAGCAAAATACAAGGAGACATTCTTCTACAATGGAAGTGAGAGATAAGCAATAGGAAGACATTTGACCACTGGGATATGGAGTGGGAGCAAGGTACCATGCAAGGAAACTCTGAGCCCCCCCCCCCCCAAGCCGGCATCAGTCCCTGCTGAGGAACCCGGCTCACACTGAGAACGTGGCCTTCCTCTTTCAG
Seq C2 exon
ACCTTACGAGCGGCTGGGAAAACGTACATGATCTTCTTTGTCTTGGTGATCTTCGTGGGTTCTTTCTATTTGGTGAACTTGATCTTGGCTGTGGTGGCCATGGCTTACGAAGAGCAGAACCAGGCAACACTGGAGGAGGCAGAGCAGAAAGAGGCAGAGTTCAAGGCGATGCTGGAGCAGCTCAAGAAGCAGCAGGAGGAGGCGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023033-Scn8a:NM_011323:8
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=0.068
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(18.7=100),PF057587=Ycf1=FE(17.2=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(12.4=44.9),PF057587=Ycf1=FE(24.9=100),PF0310514=SPX=PU(19.9=55.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGAGGGGTTCCAGTGCAT
R:
CTGCGCCTCCTCCTGCTG
Band lengths:
342-1434
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: