MmuINT0139796 @ mm10
Intron Retention
Gene
ENSMUSG00000023033 | Scn8a
Description
sodium channel, voltage-gated, type VIII, alpha [Source:MGI Symbol;Acc:MGI:103169]
Coordinates
chr15:101033478-101035705:+
Coord C1 exon
chr15:101033478-101033582
Coord A exon
chr15:101033583-101035434
Coord C2 exon
chr15:101035435-101035705
Length
1852 bp
Sequences
Splice sites
5' ss Seq
TTGGTAGGT
5' ss Score
7.03
3' ss Seq
CTTCTGTCTTTCCTCTGCAGAAC
3' ss Score
12.8
Exon sequences
Seq C1 exon
TTTGGAGGTCAGGACATCTTCATGACAGAGGAACAGAAGAAGTACTACAACGCCATGAAGAAGCTAGGCTCCAAGAAGCCACAGAAGCCCATCCCCCGACCTTTG
Seq A exon
GTAGGTACACTGGGCAAGCTAACGGATGGCACACTGTACATCTGTTTGGAAAGAACACATGAGGGAGGGCTGCTACAAAGGAAGAGGTGACTGGCTGCCTAGTGCTGCCCGCTGGTCCTCTCCTAGATGCCCAGTACCAAAGCTCAGAAAGAGCTCTGCAGCCAGGATTAGGAATCAGGTGGGTTTGCATCAGTGCCTGGCCTGTGATGGGAGCCCTCCTGCAAGACAGCACACTGCCAGAGGGGAACGAAGGAAAGTGATCCCTCCTCTGCCTGTTCAAGGCAGGATTCAGGAGCCAGGCATGGTGGTACCAAGGCAGGACTGTCATAAGGTTAGAGGCCAGCCTGAGCTACATAGTGACATCACCCTTTAAATAACAAGAGCACTAAGGTTTGGTCAATATTTTCACAGCTGTCCTGCCCTAAAGCATGGTAGCAGTAAGGGTGTGACAGCAGGGTGCTTACATCCCATAATCAGGAAGCAGAGGGGAGGTACTGAGAGCTGGCTCCTCCTCCTTATTCCCTCTGGACGCTCACCCCCATCCCCACCCCTACCCCTACCCCTACCAGTGGGACAGTGCTTAGTAATCTTCTGGTGTTCTTCACTCCAGTCAACCACCACATTGGAAATTTCAGAGAGAGCACGCTGTCCCCTTCCTGTCCAGGCTTTCACCTTGAGCTAGAAATGAAAAGCAAGCAGAAAGCCTGTCTCCCAAGCTCCATGCACACCTGCGTTTGGAAGCCACCCTAAACTGTAAAGTCATGGGCTGCCAATTGGTGGTGACACACATCTTTAATCCCAGCATTCTGGAGGCATAGACAGGTAGATCTTTGAAGTTCAAGACCAGCCTGGTCTACCGAGGGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACACTGTCTTGAAAAACAACAACAAAACCACCATGGAGCCTGCTGAGCTAAGAACATGCACTGCTCCTGTGGAGGATCCAGGTGTGGTTGCCAGCATCGGGGTGGGTCACCAGCTCACAAGCGCCTGTAGCTCCAGTTGCAGGGGATCCAGTGTCACACTGTCCCCTCCGGGCACATACCTTATACATATACTAAATGTAAATAAGTCTTTGGGGATGGGGAAGGTTCAAGACAGGGTTTCTCTATGTAGTCCTGGCTGTCATGGGACTCACTCTGTAGACAAAGGCTGGCCCTGAACTTAAGAGATCCACCTGCCTCCACCTCCCAAGTGGTGGGATTAAATACATGCACCACCACTGCCCGGCCATAAATCTTTAAAACATATGTCATATATAAATACTATAAGTGCTTGCATATATACACACACATATAGGCCAGTAATCCCAGCATGCAGGAGGCTGAGGAAGAGGATGTCTGTGAGTTCCAGGCCAGTGTGGGCCACACAGTTGAGTGGCAGACCAGCCTGACTACAGAGGGAGACCCTGCCTCAAACTATTTGGAGGCTGGGAGAGAGGCAAGGATGGCCATCCCTCTTCTGACTAGAGACCAGTGAGAAGGAAGGAGGCTGGGTGAGGTTGTCAGGAGGTGCATAGTGAACCCAGCGTGAGTACAGAGCCACAGACCAGTTCCCCTAATCTCTAGAGTAAAGTAGCCACTGGGGTCGGGGCAGCATCAGGACGGGGAGAAAGTCCCCAGGCGTGGTGATGTCAGCTCAGGTCAGCAGAACAATACTTGAGGACACTGGACCAGCTATCCCAAAGTGGGCTCTGCAGGTGCTCCAGACAGATGCCGGCAGATACTGTAGCCTAGAAGGCAACAAGGAGAGCACCGGGAACAGGGCAGAGCAGCCCGTGGGTCTACAGGCTTCCGCGAACGGGCTTCTGTCTTTCCTCTGCAG
Seq C2 exon
AACAAAATCCAAGGGATTGTCTTTGATTTCGTCACGCAACAAGCCTTCGACATCGTGATCATGATGCTTATCTGCCTTAACATGGTGACCATGATGGTGGAGACAGACACACAGAGCAAGCAGATGGAGAACATTCTCTACTGGATTAATCTGGTCTTCGTCATCTTCTTCACCTGCGAGTGTGTGCTCAAAATGTTTGCCTTGAGACACTACTATTTCACCATTGGCTGGAACATCTTTGACTTTGTGGTGGTCATTCTCTCCATTGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023033:ENSMUST00000108909:25
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(20.5=47.3)
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:
TGGAGGTCAGGACATCTTCATGA
R:
ACAAAGTCAAAGATGTTCCAGCCA
Band lengths:
351-2203
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