MmuINT0139789 @ mm9
Intron Retention
Gene
ENSMUSG00000023033 | Scn8a
Description
sodium channel, voltage-gated, type VIII, alpha [Source:MGI Symbol;Acc:MGI:103169]
Coordinates
chr15:100847472-100848955:+
Coord C1 exon
chr15:100847472-100847626
Coord A exon
chr15:100847627-100848781
Coord C2 exon
chr15:100848782-100848955
Length
1155 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGA
5' ss Score
7.54
3' ss Seq
AGCCGCTATGTCTCTTTCAGGCC
3' ss Score
9.34
Exon sequences
Seq C1 exon
GTTGTGTCCAGAGGTTCAAGTGCTGCCAGGTCAACATCGAGGAAGGACTAGGCAAGTCGTGGTGGATCCTGCGGAAAACCTGCTTCCTCATTGTGGAGCACAATTGGTTTGAGACCTTCATCATTTTCATGATTCTCCTCAGCAGTGGAGCCCTG
Seq A exon
GTGAGAGTCAGGGAAGAGCGGCTGCGGCTGGCGGGGGAGGGTACAAAGGAACAGCGAGCAGAGGGTGGGCGAGGACAGATAGGCCAAGCTCCCAAGAACAGGAATTTGTTCAAGCGCTTCGAGCTGGCTGGCATATCTGGTGCTGAGTCTAGAATCCACCCTTCTTCACCTCTGGCCTTAAGACGACCCCCTCGACCCTGCAACACTCTTTACATGGGGGGTGAAGACAAACCTGTCACTGCCAGTTTTTGCTCTACCCCAGGCAGCTTCCTGAGGTGAGAGTCCCTCTCCGCTTCCAGACTGCTTGCTCTTCGTTTCTGTTTCCCGAGGTAGATAGGATGGAGCCCTGGAAAACCCACCTCATAGCAAGTGTTCAGAGATCCAGGTCTGCTCTGGCCTCAGTGCTCAGCTGCAGGGAGCCATGCAGAACTGAACACAGATTCCGCTTCTCGTGGGCTCATTCTCTTGGCATTTGTCCCCATATTCCGCCGGATTGTCACAGAGAACCCTTCAGAGTCTGAGAAGGGCAAGTGCTGCTTTTCCAGAGGACCTGAGTTTGGTTCCTAGCACCCATAGCAGGCCATCCACAACTGCCTCTAACTCCAGGCACAGGCGGTTCAGCATAGCATCCCTAGGCACCTGCACTCCTGCACACACACCCTCACACAAACACACACAGAGATACACACAGACATGTGATTGAAAAGAAGTTTTTTTATATATATAAAAATAAGCAGCCAGGCACAAAGAAAACCTCTATTGGAATCATCTTACTTGTATGAAATGCCCCCGAAAGGCAGATTAGTGTACCGAAGACCAACAGGATGAGGGGTCCAGAGGTAACAGCTAGAAAATGTGTGGATAATGAAAACGTTATAAATTCATGTGATGGATATGTATTATCCTAAAAGCCATTGATTTGGAGATTTAAATATGGGATGCAAATTATTTCTCAGTAAAGCACTTCCCTGGACTCAGTGGTTACTCTTCATACTTCCAGCCCTGGGTTCCATCCCCAGCTTCACTAGCTAATAAGCAAGGAGGGGAAGCCAGGGAGCAGAGAGGAGGAACAGGAGCCTGACGGTGGGCAGCTTGTGTGAGGAGCCGGGATGCTAGCACACTCCCATGATTCAGCAGCCGCTATGTCTCTTTCAG
Seq C2 exon
GCCTTCGAGGACATCTACATTGAGCAGAGGAAGACCATCCGTACCATCCTGGAGTATGCGGACAAGGTCTTCACCTACATCTTCATCCTGGAGATGTTGCTCAAATGGACAGCCTATGGCTTCGTCAAGTTCTTCACCAATGCCTGGTGCTGGTTGGACTTCCTCATTGTGGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023033-Scn8a:NM_011323:18
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=0.000
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=PD(20.2=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(17.0=67.2)
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:
TGTGTCCAGAGGTTCAAGTGC
R:
AGCCACAATGAGGAAGTCCAAC
Band lengths:
327-1482
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: