MmuINT0139729 @ mm10
Intron Retention
Gene
ENSMUSG00000032511 | Scn5a
Description
sodium channel, voltage-gated, type V, alpha [Source:MGI Symbol;Acc:MGI:98251]
Coordinates
chr9:119529957-119534034:-
Coord C1 exon
chr9:119533663-119534034
Coord A exon
chr9:119530090-119533662
Coord C2 exon
chr9:119529957-119530089
Length
3573 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGC
5' ss Score
9.44
3' ss Seq
TGTCTCCTGGTTGCACGCAGACC
3' ss Score
8.41
Exon sequences
Seq C1 exon
AATCAGCTCAGCCTCACCCATGGGCTCAGCCGGACATCCATGAGGCCCCGCTCCAGCCGAGGGAGCATTTTCACATTCCGGCGACGGGACCAAGGCTCCGAGGCAGATTTTGCAGATGACGAGAACAGTACAGCAGGAGAGAGCGAGAGCCACCGCACATCGCTGCTGGTGCCCTGGCCCCTGCGCCGTCCCAGCACCCAAGGGCAGCCCGGCTTTGGAACCTCAGCTCCTGGTCATGTCCTCAATGGCAAAAGAAACAGCACCGTGGACTGCAATGGGGTGGTTTCCTTGCTGGGGGCAGGGGACGCAGAGGCCACCTCTCCAGGGAGCCACCTTCTCCGCCCTATAGTGCTGGACAGACCCCCAGACACG
Seq A exon
GTGAGCCACCCCCACCTGATGAGCACCAGTCCAGATCTATCTCCCAAACTGGTGATAGGTACCAGGCTCAAAACTACTTGCTAAATGTTGATCAAGCACCTACTGTGTGCCCCACTCCCAGAACATCTCTCCCCTTATAGTTTCCATGCCAACTGGGCAGGCAGTCAAGTCAAGAGAAAAAAAGAGAAGATGGAAAGAAAAGTGTCTGTGTAAACACATTTGGTGTAGTGATGAGAGAGTCAGATTTCATACCTGGTGCATTGTCCATGCTGAAGTGCCACAGCAGACCAGTGTCCCGGAGGCCACGTGCTGTATCAAGTGCCTTCTGCATCAGCCAGACAGGAACAAGCCATCCCGGCAAGCCTGGGACAAGGGCTAGGTGGCAAAGGGGCCCTCAGAGGATTCCAGACAGCACTCACTAAGTGAGTCAGAGATAGTCCAGTACTTTACTCACTTGTGATGGACACAGTGCCAGCCAGGGTCGTAAGTGTTGGGAGTGGGGAGCAGGATGAGTGGAGAGGAACCCCTAAAAACATATGTTAGGAAGCATTTAAGCAGCAACCACAAGAAGAGGAGCCAGGCTGCTTTCTACATCTGGAGGGCTAGTGTGCAGAGTGGTTAGTGCCCAAGCTCTCGACATTAGCCTAGGTTTGGATTCTAGATCGCAGCTTACCAGCTTAGACAGCTGTTGGCACGTCTTTTTGCTCCTCTGCACTTTAAGTGTCTCATCTGTATAATGGGCGAAAATTACCCAAAGTGGCTAATATAGACAGGACCAAAGACATACAGGAACATGGTCGGCACTGTTAAAATGTCACGGTACCATGCTTCCCATACCAAAGTGTGTCACACACAGCCAAAGGGCAGACAGCCCGGGGAAGAGCCTATCTGGCACTGTGAGGTCAGTGGGGCTGGAACAGAGGGAAGCAAGGTGTTTACAATCACGGAAGGTCTCTTGTGGCACACTGGTGACTGCCCGGTTGGCCCCTGCAAGTCCACATACCCTCTCAGGAACACATATACAGACAGGAAAGCCAAGATGGAGAAACCACTGGACAATGGGATCTTGGTCAGGAAGGTAGTGTGAAGAGGGAGGGCCCAGTCCACATGGCCAATAGCTGTGGATCTTTATACGGGCTAATCATCTGGAGCCACAATTTCCTGCAAAGTGGAAATCAGATTTAACACGTACGTCAGCATGTGGTAGTGGGACCGAGGGAGCTGAAACAGGTCCAGGGCTTAGGCCAGATCTTGCCACTTGAGCATGTTACTGGTTACTGTTACTAGGTGCTGTTGACACCAGCAAGTAGAGGCTTCTGGGATGCATTGCCAAGAGTCCAAGCCCTATATAGGGAGTGAAGGGGAAGAACTTCAAGACCCCTAAGGGCTGCAGAGTCGTCTGTGTTCTTTAGGACCTGTCACCTGGAGGGTAGGGTATCTGGCTTCCAGTCGGGCTCTGGATCCCCAGCCTTAGGCAGGCAGAGCTGGAGCGCTAATAGAATTTCCTAATCCCATTAGGGAGAAAATCATCTCATTGTGCTGCACATGTCGGGAGGAATCCAAGTTCACACACTTCATTACCGGGAACTCTGACTTCACCCATTCTCACTTCTGCAGGGCCCATTTGTAACTTTAAAGGGATTAGCTGGCCTAGGCGGAGTCGTTTGTAAGGTTAAAGGAATTAGCATCCAAGATGGAGACGTTTGAAAAGTCAAAGAGATTAGCCGGGCAGAAGCCCCTGGGAATGCCTTCCCCACTCTGCTGGTCCCCTGTGAGCCCTTTTCTAGTCTGCAAACAGGGCCCTGGGTTGGGTACAGGGCCCCTGTCAGTGTTGGGGAGTGGGGGTGGGGAGTGGGAGGAGGCCTCTCTGGTTCAGGGTGGGTTAGGGGAAGGAGCCTAGAGAGGGCACGCCTGCTGCCACCAGTTAGCCAGAGCTGTCTTTCTACTTGCTCTTGGTTATTGGAGAGCAACCCAAAGAAGTTGAAGCTCGAGAAGTGAGCAGGGACTGTCACTTTCCACTGTGCCTGGTCCCTGTTCCACAAGTATCTGCACGTTGACAATTGGGTATTCATTCTCCAGATCTTTGACTGGCTCTTACATCTGTCTCGGGGATATGCCCAAGGGAGTATACCCAGAGCAGCTTCTCACTGTTGTCTGTATCAGAGTTCAGGGTTGGGTAGAGCCATGATTGATTTTAATATTCTCCCTAGTAGGCTAGACATTTAGTTACGGGGAACAGTGCCGCAAAGCAAAGTCTCTCTCTCTGCATTCTTGGTGTGTGTATAAAAGTGTTTATGAGTCGGGCGGTGGTGGTGCACGCCTTTAATCCCAGCACTTAGGAGGCAGAGGCAGGCGGATTTCTGAATTCGAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGAGCTACACAGAGAAACCCTGTCTCGAAAGTGTTTATGAGGGTGGATTGAAAGACAAGGAATCTCGGAATCATTTAAAAAATAATAAGTGGAGGCTGGAGAGATGACTCAGTGGGCACAAGCACTGGCTGCTCTTTCAGAGGACTAGAGTTTGATTCCAAGCACGCATATGGAGGCTCACAACTGTCTGCAACCCCAGTTCCAGGGATCCAGTCGTGTTTATGGGCACCAAGCACACACATGTGCACCAACATTTACACTCAGGCAAAACACTCACGCATATAAGGTATGGTTATTTAAAAAAAATGAAAGTTTTCTGATTTAGACCCAAGCATACCTCCTCTGTATGACATGGTCTGCCACTGTCCTCATCTAAGCACCGTGTAGGTGTCGTGTTTCTCTGAAGGTCATCCTAGAGCATGTCAGACCTTTTCAGCCTCTCCGTCCTTGACAATAGAGAGCTTTAGTGAGGATCACTGTTGTGTGTGCTAACGTATGTCGTGTGCTGGTACTGGAGGGGCCTGTGTGGTGTGTGTATGCTGAGAACAGGGAAGGAAGGAGATGGTGGTGGATGGAAGATGCAAGGATCAGGGAGTTGTCAGCTTCTCCAAGTCCAGCATTCCTTATCCCAGCAAAACCTCTATGCTTGGGGCTATGATGTAGCTCAGTAGGAAGAGAGGTCAGAATGCTTGTCTAGCATGCATGGAGTCCTGGGTATGATCCCCAGCAGAGCATGAACTAGACGTGATGGCACACACCTGCAACCCCGACAGCACTTGGGAGGTAAAGACATAAGGATCAGGAGTTCAAGGACATCTTCAGACTCATGTTAAGTTCAAGGCCAGCCTGGCCTACATGAGACTATATATAAATCAATCAATCAATCAATCAATCAATCAACAAGGGCTAGCGAGATGGTTACGTAGGCAAAGGCTGCAGCTGCCAACTTTAGAACCTGGGTTCAGTCCCTGAGATGCCCATGGCAGGGGAGACGGCCAATGCCCGCTGGCCAAACTCTAACCTCCACATGTGCAAACACCCACAAGAATGAATGGATGAATGTGTGAATGCATTTTTAAAATTAAAGACCAAAACACAGAAACAAGACTGCCACTCTGTCTTCCTGAGTCCTCCCGGGCTGACGCATGTCTCCTGGTTGCACGCAG
Seq C2 exon
ACCACGCCGTCAGAGGAGCCGGGTGGGCCCCAGATGCTGACACCGCAGGCTCCATGTGCAGATGGCTTTGAGGAGCCCGGGGCACGGCAACGGGCACTCAGCGCCGTCAGTGTCCTCACCAGCGCTCTGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032511:ENSMUST00000117911:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.895 A=NA C2=0.533
Domain overlap (PFAM):
C1:
PF119333=DUF3451=FE(59.1=100)
A:
NA
C2:
PF119333=DUF3451=PD(17.8=82.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
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
- 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