MmuINT0139677 @ mm10
Intron Retention
Gene
ENSMUSG00000057182 | Scn3a
Description
sodium channel, voltage-gated, type III, alpha [Source:MGI Symbol;Acc:MGI:98249]
Coordinates
chr2:65483043-65484466:-
Coord C1 exon
chr2:65484346-65484466
Coord A exon
chr2:65483198-65484345
Coord C2 exon
chr2:65483043-65483197
Length
1148 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAG
5' ss Score
9.06
3' ss Seq
TATTAATATTGCCTTTTTAGGAT
3' ss Score
9.69
Exon sequences
Seq C1 exon
AAATTAAATGCAACCAGCTCTTCTGAAGGAAGCACAGTTGACGTTGCTCCGCCCCGAGAAGGTGAACAAGCTGAAATTGAACCTGAGGAGGACCTTAAGCCAGAAGCTTGCTTTACTGAAG
Seq A exon
GTAAAGAAATTAACTTGCTGAAATGCTTCATCCCTACAGAATCTGAATAAGCCTCATTTAAAAGACACATATAAAAAAAATGGCAAGGGCATGTTTATTTTGTTTGCCCTGTTCCATCCACTCTATATGTCTTAAGTTGCTTCAGATCTTAAAAATTCCAGATTAGACTACAGACGAGCCTGTGTCTGGACCAATGAGAAAGTATGCTAAGCGCATATGTTGTTTTTGTTGTTTCTTCTGTTTTTCTCTGGTTGTCCTTATCCTCCAGACTGTAATAGCATTTGAAATGCACATCATTCTGGACTGTCACACCATTGACATGACAGTCCCTTCAAAATGCACAGGAGTCGGGTAACTGGACTTATACAAGCTACAGTAATTATACTCACTCCTCCTAGTTCCAAATTTGTCTAATTTGTGCTCTGACCAGAGCTGTTTGGAAATGATGTTGTGTTATAGAGTGTTGGCACGCTGCCATGTGGTTCTCCTTGTGGCGAGCTCATCTCGTAATAAAGATTTATTGATTTGTTGCGATGGGGTTTGATGCGACAAGTAGTAGCTGAGAGAGAGCAACAGATTGGACAGAAATTGGAAATCATAAGTTGTCTAGGAGGCAGAGAAGAAGAGAGCAGAATAAGAGGCACGGACTGCAACATGAGTCATAGGTGTGACTAAGAAAAGAAGCAAGGCTAAATATAAATTAGCTTGAGAAGACTGACAGTGGCTGACACCTAGGGAGGCAGTGGGGTTTTCTATGCTTGAAAAGAAGGGAGTGAGTACCCAGGGTCACATGGGAATATGCATAAACAACTTGAATATCTGGCTTTGCTCCCAAACCAGTGTGATGAAATAGGACTCTATTTTCCTCAGTAGCCTCAAGGCAAAGTGATTCTAACCTGTATTGAAAAATATAAACCATTTTTTTTTACTCAAACAAATGTATGGAAATTCCATAAATTCTAAATCTATAAATTTAAGTATGATTCATTATATAGGAGAGTGTTGAAACAAAACTGGTCAGGAAAGCAGCCAGCTACCTATAAAATGAGCTAGAGTTGGGGTAAGGAAGAAGTAAAAATGTTATTTTTTTTCATATTAATGATCAAAGTCTATTTCCCTAATTTATTTTATTAATATTGCCTTTTTAG
Seq C2 exon
GATGCATTAAAAAATTTCCCTTCTGCCAAGTAAGTACGGAAGAAGGTAAAGGAAAAATCTGGTGGAATCTTAGGAAGACCTGCTATAGCATTGTGGAACACAACTGGTTTGAGACGTTCATTGTGTTCATGATTCTCCTCAGTAGTGGTGCTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057182:ENSMUST00000100069:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.696 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(18.2=100)
A:
NA
C2:
PF065128=Na_trans_assoc=PD(20.0=84.6)
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:
AATGCAACCAGCTCTTCTGAAGG
R:
CAAAGCACCACTACTGAGGAGA
Band lengths:
270-1418
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