MmuINT1030762 @ mm10
Intron Retention
Gene
ENSMUSG00000032511 | Scn5a
Description
sodium channel, voltage-gated, type V, alpha [Source:MGI Symbol;Acc:MGI:98251]
Coordinates
chr9:119515903-119517791:-
Coord C1 exon
chr9:119517348-119517791
Coord A exon
chr9:119516065-119517347
Coord C2 exon
chr9:119515903-119516064
Length
1283 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGC
5' ss Score
7.16
3' ss Seq
TGCTCATGGGGTCTTTTCAGCAG
3' ss Score
4.56
Exon sequences
Seq C1 exon
GTCCTGAATCTCTTCTTGGCCTTGCTGCTCAGCTCCTTCAGCGCAGACAACCTCACAGCCCCTGACGAGGATGGGGAGATGAACAACCTCCAGCTGGCCCTGGCTCGCATCCAAAGGGGCCTTCGCTTTGTCAAGCGGACCACCTGGGACTTCTGCTGCGGGCTCCTGCGGCGGCGACCTAAGAAGCCCGCGGCTCTTGCCACCCACAGCCAGCTGCCCAGCTGTATCGCCGCTCCCAGGTCCCCACCACCCCCAGAGGTGGAGAAGGCGCCCCCAGCCCGCAAGGAAACACGGTTCGAGGAAGACAAGCGGCCGGGCCAGGGCACCCCTGGGGATACCGAGCCTGTGTGTGTTCCCATCGCAGTGGCTGAGTCAGACACTGATGACCAGGAAGAGGATGAGGAGAACAGCCTTGGCACGGAGGAGGAAGAGTCCAGCAAACAG
Seq A exon
GTCAGCCATCTCCCCACCCGTCCTGACGGGACAGCCACCTGCTTGTATGGAGTCCAGAGAGCAGCTCCTAGCCTCACCCAGACTACCTCAGCAATGACACGGGGAGAGAGGAAGCCCCACGGCAGCTGGCCCCTCAGAAGGTGCCAACTCCAGCTTGTCCGTTTATGCCGTTAGTTAGTATTCATCCCTGGCTGACCTTACAGCCAGGGAACATGAGGCATAGCTCAGTATTCTTGATGAATACTTCCACCCCCACCCCCAGCTCTGCACATTGTCCAGCACCAGGACCAGCAGAGACAGATGTCCGGGAGAGAGAGGGCTACAGTTTGGTGTCCTTGCCACCCTCTCCTCCCCTCCTCCCATGACTGAGGCTAATTCTGAGATTTAAAAATAAGTATCCCTGAGATGGAGGTGTCGGAGACACCACTATCTTATCTCTCAACCTGTTACTTTTAACACTTAGGACCAGGGTCTGGCTAAGGCAGGGTGTCTGTCCCTCAGGTTTCCCTTGACCTGAGCTGGGCTCCGTATAGCTCCTGAGGTCCCTCGGTCAGGCGTAACCAGGTCCCCTCCATGTTGGTGGCCCTTCCTGACTGCTTCCTTAGCTAGCAGTAGCTGGGCCCAGCTCCGGGGTTCTGCTTTCTCCTGCCTCAGTTGGCCTTGTTGTAGGGGCGGTTGAGGGAGGGAGGGCTGGGATTATAGGACCACAGCTTCCGGTGTCTCCTGCACAGGAGATGAGAATTGGTTTCTGGCTGTTCCTTCTCTTCCTCGTCCCCTGGGACCAGAACAAACATGCCTGTGCACTTGTGCGGGTGCACGTGTGTGCATGAGTATGCTTGAGCGTGAGCGTGGGCGTGTGTGTGCTCGTGTGTGTGTGTGTGTTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAATCGGTCCAGGCTAACTGCAGTATCTTCAGACTTTGAGAAGTCAGAGCATCCTCCTGAGGAGAGTTGATAGCAATCATAAGATGGGTATCGAGGGCCAGCTGCTCCCTTTCAGGGAGTCTTAAATATGCTGAGCTTTGGCTACGGGTCCTTTGCCCATACTTACCAGGAACCTCTCACTTACTGACCCAAGTCAGCAGAGGATGGGACCTTTAGTAGGTGGAGGTTCATGAAGAGGCCAGGAAGCAGTGGGCAGGGGCTGCAGCCCACAAGACTAGGGCCCTGGAGACCCCCTGCCCGGGTGTCTGGGCTCTGCTCATGGGGTCTTTTCAG
Seq C2 exon
CAGGAATCCCAAGTTGTGTCTGGTGGCCACGAGCCCCCCCAGGAGCCCAGGGCCTGGAGCCAGGTGTCAGAGACCACATCCTCTGAAGCCGAGGCCAGTACGTCTCAGGCAGACTGGCAGCAAGAGCGGGAAGCGGAGCCCCGGGCCCCGGGGTGCGGTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032511:ENSMUST00000117911:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.538 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=5.4),PF065128=Na_trans_assoc=PU(47.0=83.8)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(20.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTTGTCAAGCGGACCACCTG
R:
CCACCAGACACAACTTGGGAT
Band lengths:
345-1628
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