MmuINT0139791 @ mm10
Intron Retention
Gene
ENSMUSG00000023033 | Scn8a
Description
sodium channel, voltage-gated, type VIII, alpha [Source:MGI Symbol;Acc:MGI:103169]
Coordinates
chr15:100955410-100957118:+
Coord C1 exon
chr15:100955410-100955528
Coord A exon
chr15:100955529-100957028
Coord C2 exon
chr15:100957029-100957118
Length
1500 bp
Sequences
Splice sites
5' ss Seq
TTCATATCC
5' ss Score
-14.87
3' ss Seq
GCCCCTTAACTCCTCTCTACAGT
3' ss Score
-1.2
Exon sequences
Seq C1 exon
ACTTTTGTAGTATTAAACAGAGGGAAAACTCTCTTCAGATTTAGCGCCACTCCTGCCTTGTACATTCTAAGTCCTTTTAACCTGATAAGAAGAATAGCTATTAAAATTTTGATACATTC
Seq A exon
ATATCCTTTTCTGCACTGGGAATGAGTGTGCACGTCCGGGGCTTTGACAACTGCAGTGTGTGCATCCCCACCAGGAGTGGAGCAGCCTGAGGGTTAGGAATGAAGTTGCACTGGATTGCCAAGCCGAGCTTCAGCAGACACTGAGGGGCAAATTAAGACGTTTTAACCTTATCCTGAGGTCTTGGCTTTTCGGTAATTTCATTCCATGATAGTTCAGCTTGTTAACATATTAATATCTGATCCAAGAATTTTTTTTGAAGACCACATCTTGAATCACAAATAGTTGAATGAATGCTTTATTTTTATTTTCTTTTTTCTTGAGCAAAGAGCTTATGCATTCCTGGTAGCTCTCGGATGAAATCAACTCCTTGGAGCAGAGGTTTAGATACAGACTGTGGATAAATAGGAATTTTTCTGGGATCTGCCTCGCGCCCCCCCCCTTAGGTAGGAAAGTGCCAACCTTTATATCTTATTAATATAGATCAGATGGCACATGGCAAATGATCTGATGGGTTTAACAACCTGGAACACTGGATAAACTTGTGTGATGGGCACTTAAGGAAAGAGGGCTTGGTCCCTGGACAACCTGTGATGCAACTCAGGGCTCCAGCTGAGCCTCTGCCATGTCCAACTCATAGCTGAAATCTATGGTCTGCGAGTACCACAGTCGTGAGACTGTGGTACGATCCGTTAAACTTTGTCCCTTCCAGGACGACATTAACGACATTAACGCCCTGCCACAACTTCAGTGTGAGTGACTCCTGCTGACTTTCATCTCTCTCAATAGACAGGAACAGAAAAGGGCCGAGAAGATCCTGGGCTGTGAGGGACACCCACAGTGATCAGGCTGACTCACCCCATTACCTACGTCTCGGGGCTGCTGGGGCGCAGGCACCCTGGAAGCCAGGCCCTCACAGGCCACACTGGTCTTCAGGCGAGACACATGCACATCGACTGGATTATTTATTATTATTATTATTATTTTATTATTATTATTATTATTATTATTATTATTATTATTATTGCTTGTGGAGATAATCCAGCCCCTCGGCATTTGCAGGAGGAAAACGAGCCACCACGCACCTGTAGATTTTCAAATAACTAATCATACGAGATAATTAACAGTCCGGGATGACTGAAACAAAAAAATGTAGATTTATTTCCTCACCTGGTGGCCTCAGGGCCTTTGGTCGCTTCTGGCTGCTTTTCACAGAGGTTTAAGTATTTAGAGATTGACCCATTCTCATCTTGCAAGGTGTTCAAGTTTATACCCAAAAGTAGTGGGGCAGTGACAGTTCTGTGGGCAGGGGAGTGGCTGTCCAGCCCCACTACCAGTCAGATGGGATGTCCAGGGCTTTCCTTGTGGTGGCGGTGGCCAGTTTCCCTCACCACCTGTCTCCTGCCAGCCTGTGAACTTAGCTCCGGTGAGACCTGGTATGAGCCGGGTTTGTTTCCTAAGCGTCCGGGTCAGACCTCGCTCGCCCCTTAACTCCTCTCTAC
Seq C2 exon
AGTCTTCAGCATGATCATCATGTGCACCATCCTGACCAACTGTGTATTCATGACTTTTAGTAACCCTCCCGAATGGTCCAAGAATGTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023033:ENSMUST00000108909:3
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:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(0.8=6.5)
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:
ATTAAACAGAGGGAAAACTCTCTTCA
R:
TCCACATTCTTGGACCATTCGG
Band lengths:
198-1698
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