MmuINT0139787 @ mm10
Intron Retention
Gene
ENSMUSG00000023033 | Scn8a
Description
sodium channel, voltage-gated, type VIII, alpha [Source:MGI Symbol;Acc:MGI:103169]
Coordinates
chr15:101015624-101016598:+
Coord C1 exon
chr15:101015624-101016094
Coord A exon
chr15:101016095-101016480
Coord C2 exon
chr15:101016481-101016598
Length
386 bp
Sequences
Splice sites
5' ss Seq
GACGTAAGG
5' ss Score
7.23
3' ss Seq
CTTCCTTCCTCTGTGTCTAGAAA
3' ss Score
9.58
Exon sequences
Seq C1 exon
GTGCTGAACTTATTTCTGGCCTTGCTTCTGAGCTCCTTCAGCGCAGACAATCTGGCGGCCACGGACGACGACGGGGAAATGAACAACCTGCAGATATCGGTGATCCGGATCAAGAAGGGCGTGGCCTGGGCCAAAGTGAAGGTGCATGCCTTCATGCAGGCACACTTCAAGCAACGGGAGGCTGATGAAGTGAAACCTTTAGACGAGCTGTATGAGAAGAAGGCCAACTGCATCGCCAACCACACCGGCGTGGACATTCACAGGAACGGCGACTTCCAGAAAAATGGAAATGGCACCACTAGCGGCATCGGCAGCAGCGTGGAGAAGTACATCATCGACGAGGACCACATGTCCTTCATTAACAACCCAAACCTGACCGTGCGGGTGCCCATTGCTGTGGGCGAGTCTGATTTCGAGAACCTCAACACAGAGGATGTTAGCAGCGAGTCAGACCCCGAAGGCAGCAAAGAC
Seq A exon
GTAAGGTCCCAACCAAGAAAACCACCCACGTTGTGTGTGAGCTCTCCAACAGGGCACTCTCAGCCCCAAAGACTGGCTCGGTTCTAGGCTTAACAGAGAGATCTACAATAGCCACTCTGTGAGCCAGCCCAGTGCCCTGGAGTGGTGCTAGGTCTTCCCTTGGGAACCGAGCTCCCTGGGCTAGTCCAGAGTTAGTTGCATCAATTCTGGAGTACCTGGGCCTGAGGCTGCAGTCAGCCCTTTAGTTTGTCCCGGCTCTGAATCCACGTGACCCTGTGGTTAGTGTCTGTCTGTAGCGTGACCCCCAGCAGAAGTCACGTGCGTGTGATCCGGGCACGTGTCCCTGCACAGCTCCCTGAGCATCCTCTTCCTTCCTCTGTGTCTAG
Seq C2 exon
AAACTGGACGATACCAGCTCCTCAGAAGGGAGTACCATCGACATCAAGCCTGAGGTGGAAGAAGTCCCAGTGGAGCAGCCTGAGGAATACTTGGATCCAGACGCCTGCTTCACGGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023033:ENSMUST00000108909:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.223 A=NA C2=0.575
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=5.1),PF065128=Na_trans_assoc=PU(61.0=84.7)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(17.9=100)
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:
CCTTCATGCAGGCACACTTCA
R:
CTGAGGAGCTGGTATCGTCCA
Band lengths:
348-734
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