MmuINT0139801 @ mm9
Intron Retention
Gene
ENSMUSG00000023033 | Scn8a
Description
sodium channel, voltage-gated, type VIII, alpha [Source:MGI Symbol;Acc:MGI:103169]
Coordinates
chr15:100799452-100800698:+
Coord C1 exon
chr15:100799452-100799673
Coord A exon
chr15:100799674-100800634
Coord C2 exon
chr15:100800635-100800698
Length
961 bp
Sequences
Splice sites
5' ss Seq
AAAGTAGGT
5' ss Score
6.84
3' ss Seq
GTCTCTTCCCACTTTTCTAGCAA
3' ss Score
9.07
Exon sequences
Seq C1 exon
GCCTGAAGACAATCGTGGGCGCCCTCATCCAGTCTGTGAAGAAGCTGTCAGACGTGATGATCCTGACGGTGTTCTGCCTGAGTGTCTTCGCCCTGATTGGCCTGCAGCTCTTCATGGGGAACCTTCGAAACAAGTGTGTCGTGTGGCCCATAAACTTCAACGAGAGCTATCTGGAGAACGGCACCAGAGGCTTCGACTGGGAGGAGTATATCAACAATAAAA
Seq A exon
GTAGGTGTCCCTCCTCGGCGAGAGGGAAGCGTCACCCCAGGTTCTGGTCAGACCCCACCAAAAGAGCTACCAAAAAGTGGTCCGGCCCAGAGAGGCACAGCGCAGCGCAGCCAGATGGAGCTTGGAAAGCCATTCCCTTGTCTCCGAGGCAGAACTGCACAGGAGCTCTCAAGCCTGCTGTTACCAGTTTTATCTTATTTTATTTCATTTCGAGACACATGTGAAACTACTAGTCACTCGAGAGAAATAAAAATCAATTAAGTCGCCACAAGGAAGTGTTGCGAAGGAGAACTCAGGGACGGCACCTTCCGATTAAAAGTAGGGCACGGTAACTAATGACTAGTGCGGAGTTTGGGAACATACTGATAAAAATATTACAAGGATAAAAGGGCAAACCGTGTAAAGGGATGCCGATCTCTGAAACTTACTTTAGATCGGCGTTTTTCAGCCTAGGGGTCAAGACCCCCGGGGAGGGTCACATTCCCCCCCCGGGGGGTGGGTCACATATCAGACATCCTGCAATCAGATATTTACATCATGAGTCATAACTAGCAAAATCACAGTTATGAAGTAGGAACGAAATAATTTTATGGTTGGTGGTCAGCACAACATGAGGTGTTGCAGGCACTAACGGGCCACCGTGTTAGGAAGGTTGAGAACCACCCACCGCCTAAGACCCTCTGACTCAGCAGCAGAAGCGGGCATGTGGAGCTGAGGCAGGGGAGTCAAGTGCTCGTGGGTGCAGCGTCACCTCAAGGGCTTTAGGGCGGCTCCTAGTTCTAGCCAGAGTACAGGAGATCATTAATGGGAGGAGTTCTCCTTAGCTTCCTGCTGCTGGGAAAGACTTATCTGAGCTAAAATCAATAGTGGCTTCTGCCAGTAACGCTGAGGCGCACGTAACCGAATTCTCCCGTTGACCAGAATCTGCCTATTCATTTCCTGTCTCTTCCCACTTTTCTAG
Seq C2 exon
CAAACTTTTACATGGTCCCTGGCATGCTAGAACCCTTGCTCTGCGGGAACAGCTCTGACGCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023033-Scn8a:NM_011323:6
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:
PF0052026=Ion_trans=FE(29.5=100),PF057587=Ycf1=PU(19.4=70.7)
A:
NA
C2:
PF0052026=Ion_trans=FE(8.4=100),PF057587=Ycf1=FE(7.7=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:
GCCTGAAGACAATCGTGGGC
R:
CCGGCGTCAGAGCTGTTC
Band lengths:
286-1247
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: