MmuINT0139690 @ mm10
Intron Retention
Gene
ENSMUSG00000057182 | Scn3a
Description
sodium channel, voltage-gated, type III, alpha [Source:MGI Symbol;Acc:MGI:98249]
Coordinates
chr2:65524604-65525786:-
Coord C1 exon
chr2:65525695-65525786
Coord A exon
chr2:65524877-65525694
Coord C2 exon
chr2:65524604-65524876
Length
818 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
ATATAGTTCTCTCTTCAAAGGTT
3' ss Score
6.71
Exon sequences
Seq C1 exon
ATATGTGACAGAGTTTGTGGACCTGGGCAATGTCTCAGCGCTGAGAACGTTCAGAGTTCTCCGAGCATTGAAAACAATATCAGTCATTCCAG
Seq A exon
GTGAGAGCCAGGTTAAACACCGAGGCTGACTTTAATCAAACCATAATAATATTGGAATTGCAACCCCACCATCAGCCATGTGGCTTTTTGTTCAAGTCTATCATATTCAAAGATACCAGACAGTGTTTCACTGTTGGTTCAGTTCCTTTAAAGCGTTGATCATTTCAACTTTCTTCATTAAAGCCAGCCTCTGAGTTTAACAGAAAGTTGCATGGGATATATCATCGATGAGTGTTTCTGTACTCCCACTCCTGCATTTAAGATGTCTGCATTTAAGATGTCTTCTCTCCTGCATTCTGAAAAAGCTTTGATGTCATGCCCTGACTGACTGCCTTGTATTTTCCCATTTCCTTCAGATCTATTTCAAAAATAGATCACTGTTTGTAAAAGAGGAAAGGCTATGGCTCAGCATGTGCGTGGCCTGGGATCTTCAGGGCCTTAAAATTCTTTTCGCCTTTTAATTCACTGCTACTTGCAGGCTGGCAGAAAGAATGGGCTGAGAGAAACAGCTTCACGAAACACACAAAACTGAAAGAAAAAAAGTAATCTAGTATTTTACATGTTTGGGGTTACCCTTGATAGCACACAAACAGAACTTCCTAAAGCTTTGTGAACATTGGTTCAGAACCTGCAGCAGCATGGTGTTCATATAGAAGTGGTCAGCCTTCCATCTGTTTGCAAGTCATGAGACTGTACATAAAGCTTTTATGTCTATGTAGCCAAGCTACCATTCATGGAGGATGTGGAATGTGTGCACCTATTATGAACTCTTGTCATACATCACACTCCTAAGCAGACATATAGTTCTCTCTTCAAAG
Seq C2 exon
GTTTAAAGACCATCGTGGGGGCCCTGATCCAGTCGGTGAAGAAGCTGTCTGACGTCATGATACTCACTGTGTTCTGTCTGAGCGTCTTTGCTCTCATCGGGCTGCAGCTCTTCATGGGCAACCTGAGGAATAAATGCTTGCAGTGGCCTCCAAGCGATTCTGCTTTTGAGATCAACACTACTTCCTACTTCAATGGCACAATGGACTCAAATGGGACATTTGTTAATGTAACAATGAGCACATTCAACTGGAAGGACTATATCGCAGATGACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057182:ENSMUST00000100069:6
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:
PF0052026=Ion_trans=FE(11.6=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(34.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACAGAGTTTGTGGACCTGGG
R:
GTCCTTCCAGTTGAATGTGCTCA
Band lengths:
343-1161
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