MmuINT0139557 @ mm9
Intron Retention
Gene
ENSMUSG00000034533 | Scn10a
Description
sodium channel, voltage-gated, type X, alpha [Source:MGI Symbol;Acc:MGI:108029]
Coordinates
chr9:119600562-119603478:-
Coord C1 exon
chr9:119603174-119603478
Coord A exon
chr9:119600681-119603173
Coord C2 exon
chr9:119600562-119600680
Length
2493 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGA
5' ss Score
9.84
3' ss Seq
TGTGTTCTGCTTTGTTCTAGACA
3' ss Score
10.18
Exon sequences
Seq C1 exon
AAGAGTGTAAATCCTTCCCCAAGAAGAATGAGAAGATGGAGTTCCCCTTTGGGTCCGTGGGAACTACCAACTTCAGACGGTTCACTCCAGAGTCGCTGGCAGAGATCGAGAAGCAGATCGCTGCCCACCGCGCCGCCAAGAAGGGCAGACCTAAGCAAAGAGGACAGAAGGACAAGAGTGAGAAGCCCAGGCCTCAGTTGGACTTGAAGGCCTGTAACCAGCTGCCCAGGTTCTATGGCGAGCTCCCAGCAGAGCTGGTCGGGGAGCCCCTGGAGGACCTGGATCCTTTCTACAGCACACACCGG
Seq A exon
GTAAGAATGTCTGCACTCAGCTCTTGCGGAAGGAGCCTCAGTCCCACCCAACCCAGGAAGTCCTGACCCCGCCCCCAATGTAGTAGCTGTTCACTAAAGAATAGGCCGAGGTAAAAGAGGGGGAGTGCACCTCTCTCTGAATCTTAGGAACTCTGTGATGGGGTAAACTGAACCCAAATCCCCAAAGCAGACAGCTGCTGCAGAACTCGCTTGGAAAGTTGGCTGTTCCCATGGATGAGACCCAGCCTAGAGCCTCTAGAGATGTTATCTCTCTTTGCAGATCAAGAGCAGGGATTTTGCTGGGCAGTGGTGGCACATGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGTGGATTTCTGAGTTCGAGGCCAGCCTAGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTATACAGAGAAACCTTGTCTTGAAAAAAACAAAAACAAAAAACAAAAACAAAAAAACCAAAACAACAACAACAAAAGCAGGGGTTTTGAAGTTGAAAGGGATGCCTTGAGCCAGGGTCCTCTAAAGTATAGTCTCAGAGCCCTGGAGTTTTCCAAACTCTCCCATGGGCTACTGAAATCAAACCATCTTAAAACAGTAGTTCACTATCACCTGTCTCTTACTTACATCATCTTGTAAACGTATAACAAAGGGAGCAACATCATTCACAGCAGCCACGGGAAGATGTGCCTATGTGCTTCTGCGTTTTAAAGTTATATATGTATGTATGTATGTATATATATAGTGTGTGTGTGTGTAATATTCCTAATATAGCATGGGGACACTCTTTCCTTCCATGATGCTGTGATAACATAACATACTTGGACTTAAGCAACTTAAGGCAGAAAGGATTTATTAGCTTATTGTTCCAGGCTACACGCCATCAAGGTAGCAAAGTCATGGGAACGGGAGTGTGAGGGAGCAGGCTACATCATGTCTGTAGTCTGAGGACGACGAATGCAGCATATGTGTGCTCAGTTTTCTTTCTCTCCTCTTACACGGTCAGGATCATCTGCCCTGGGATAGTGCCATCCACAGGGATTGTGGTCCTCCCACCTTAATTACCATGATTGAGACAATTCCCCCATCTTAGTTAGGGCTCTATTGTGGTGAAGAGATACCATGACCATGGCAACTCTTACAAAGGACAACATTCATTTAGAGCTAACTTACAGGTTCTGAGATGCAGCCCATTATCATCATGGCAGTGTCCAGGCAGGCATGGCACTGGAGGAGCTGAGAGTTCTATGTGTTGTTCTGAAGGTAAATAGGAGAAGACTGGCTTCCAGGTAGCTAGGAGGAGGGTCTCAAAGGCCCCCGCCCCCAATGACAAACTTCCTCCAACAAGGCCAAACCTCCTCTACTCCCTGGATCAAGCATATTCAAACTACAACAGATCGGTAAATATATACGTTGCATAGGTATACATATATAAATTTCTATCATATATATATATATATAAACACACATGAGCAAAGCAAAAGAATAAATATAATAAACTAGATTATTTAATGATTCTTTTTAATCAAAAGAGTGAGAGTTAATAGTCTCATGAGGTGACAGTTTCCTCTGCTGTGCAGCCAAACATGGTAAGTACATGTTTGGGAACGAGAAAGAACTGAACAAGCCATTGCAAATATAGTTGTAGAAGAGATAGGACAAGGGATGTCTTCCCCCTTCTCTCTCTTCCCAAGAACCCATCCCTCCTAAATGCACAGAGGAGGGGACTGAGATGGTTTCGAGCCAAGGCCCAGGTAGTAGAAACGGGAACATCTCAGGACCAGGGCCCTCCAGTCAGAAGGGCATTAAATTCCGGGGCTGCAGACATGGCTCAGTCAGTAAAGGACTTGCGGAACAAGCGTGGGAATCTGAGTTTGATCCCTAGAAAAACATGTGGGGACAAACAGTGGAACACACTTGTAATGTCACTCTGGAAGAGGAGGGGCAGGGGAGGGGGAGGGAGAAGGGGAGGAAGAGGAGGAGGAGGTGGCAGCAGAGGCAGGTGGACCCCTGGGGCTCACTGTCTGGCCAGCCTAGCCTTCTCAGTTAGCTCCAGGCCACTGAGAGTTTGTCTAAGGCTCCTGAGGAATGACATTTGAATTTCCCCATCAACGCACACAAGCGCGCGCGTGCACACACACACACACACACACACACACACACACACACACACAAGTGTATGCACACACGCTAGATTGAATGCAACTGAGCTCAACCACCTGTAGTCAGAATCCTGCCCTGGTGTGCTGCACTTGAGTGAGCCTTGAGTGAGCAGCCTGCCCATGAAGCACTCTCAGTGGGCTTGCCCGTGGTTCATAGTCAGCCACGGAGTCCACATTCCTGTGGGGAGGGCTGAGGATGTGGCCTCCGCCCCTCCTCTAGACGCTCAGTGAGCTGTGGTTCTTCCTGCTCAGGCTTCTACCAGGAGGCCACTCGGGATTCTTGTTTCTCACGGAGCCCACTTGTGTTCTGCTTTGTTCTAG
Seq C2 exon
ACATTCATAGTGTTGGATAAAAGCAGGACCATTTCCAGATTCAGTGCCACTTGGGCTCTGTGGCTCTTCAGTCCCTTCAACCTGATCAGAAGAACAGCCATCAAAGTGTCCGTCCACTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034533-Scn10a:NM_009134:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.267 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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: