MmuINT1030760 @ mm10
Intron Retention
Gene
ENSMUSG00000057182 | Scn3a
Description
sodium channel, voltage-gated, type III, alpha [Source:MGI Symbol;Acc:MGI:98249]
Coordinates
chr2:65507147-65508662:-
Coord C1 exon
chr2:65508462-65508662
Coord A exon
chr2:65507280-65508461
Coord C2 exon
chr2:65507147-65507279
Length
1182 bp
Sequences
Splice sites
5' ss Seq
AACGTTAGT
5' ss Score
1.4
3' ss Seq
CATCAGTATTTGGTTTGCAGGGT
3' ss Score
5.3
Exon sequences
Seq C1 exon
TCTCTCTTGAGTATCCGTGGCTCCCTGTTTTCCCCAAGACGCAATAGCAAAACGAGCATTTTCAGCTTCAGAGGTCGGGCGAAGGACGTGGGGTCTGAGAATGACTTTGCGGATGATGAACACAGCACCTTTGAAGATAGCGAGAGCAGGAGAGACTCACTGTTTGTGCCGCACAGACCTGGAGAGCGACGCAACAGTAAC
Seq A exon
GTTAGTCAGGCCAGTATGTCATCCAGGATGGTGCCAGGGCTTCCAGCCAATGGGAAGATGCACAGCACTGTGGATTGCAATGGTGTGGTTTCCTTGGTGGGTGGACCCTCAGCTCTTACGTCACCTACTGGACAGCTTCCGCCAGAGGTGATAATACATAAACCAGCTACTAGTGACACTTTACTAAAATTGAAAAAAAATAAAAAAATTTCAGGCCTGGGCAGATGAACCTGTTCTGTGATCCTAATTCCTCCAAATGAAAGTGCTTAAAAGTAACATGATTAAGTGATCTAGAAAACAAAACAAAAAACAAACACGCAAAAAAGCAAAACAAAACAAAACCCAAACTTGATTTGTATGCAACTATCAGCTTTCTAGGTTAAAAGTACTCAAAATTTAGAATCTGAGATAAAGCACATATCTACAACTTCAGTAGATTTGTTACAAATACAATATAATGAGCACTTTCACAATCAAATCTTCATTATAAATGTTTCCCTTAAATTATATAATCATCCATCAGGTCTTATTCTAAAATGTTGTATTCTTAAAATTAAATATTATAATGACAAATGTATTGACGATGGACAGTTTTAGACATCTGTCTATATTATAGTGCTGTTTGAAAAAAAATTCCAAAATAAAATGTGTTGATGAAATAGCATATGGAAATAAAGAAATCTCAGGAAAGCACACACATTTCATTGTACATCTGTGTTTGTGCATGGAAAAAATGGCCCATATATGTCAGTATGTCAATATAGCCTCAAAGAAAATAACTCAGCCTTGAGACTATATAATACTATCCAGTTTTGTGGAAAGATTGATCTATTTCTCACTGCTATAAGTTGAAGAATAATTTGTATTTGAATGAAAAACTAATTACAGCATGCTTATAAAAAAATTCCCCCCTAAACGTTGCCATGTTGTTTAAAATGCTTGCGTAAAATAGTTGCTTTATAAAATTGCATCTAGCCAGTGAGCGCTTGTCAAAGGATCTGTGGTCTTTAAAAGAAAACATGTTTATAGAATATGATAACCTATGTAATATCTTCATGTATTATCACTTGAGTTTGTTACCTGAAATAACTTGCACGAAGCATGATTGTCCAGAGAGATGCTATATATTCTTGTGTTGTCAATGGAGAAGGGTGGTTTGAGCCATCAGTATTTGGTTTGCAG
Seq C2 exon
GGTACCACCACTGAAACAGAAGTCAGGAAGAGAAGGCTAAGTTCTTACCAGATCTCGATGGAAATGCTGGAGGATTCCTCTGGGAGACAAAGAGCCATGAGCATAGCCAGTATCCTGACCAACACGATGGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057182:ENSMUST00000100069:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.597 A=NA C2=0.178
Domain overlap (PFAM):
C1:
PF119333=DUF3451=FE(46.8=100)
A:
NA
C2:
PF119333=DUF3451=PD(0.7=2.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTCTCTTGAGTATCCGTGGCT
R:
CCTCCATCGTGTTGGTCAGGA
Band lengths:
334-1516
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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