MmuINT0139718 @ mm9
Intron Retention
Gene
ENSMUSG00000001027 | Scn4a
Description
sodium channel, voltage-gated, type IV, alpha [Source:MGI Symbol;Acc:MGI:98250]
Coordinates
chr11:106205528-106207043:-
Coord C1 exon
chr11:106206729-106207043
Coord A exon
chr11:106205592-106206728
Coord C2 exon
chr11:106205528-106205591
Length
1137 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
GTGACCTCTGATTCCCAAAGGGA
3' ss Score
5.49
Exon sequences
Seq C1 exon
GGCTGAAGACGATCGTGGGAGCCCTGATCCAGTCTGTGAAAAAGCTCTCGGATGTGATGATCCTCACTGTCTTCTGCCTGAGCGTCTTTGCCCTGGTGGGGCTGCAGCTTTTCATGGGAAACCTGCGTCAGAAGTGCGTGCGTTGGCCCCCGCCCATGAATGACACCAACACCACGTGGTATGGTAATGATACGTGGTACGGCAATGACACCTGGTACGGCAATGACACCTGGTATGGCAATGACACTTGGAACAGCCAGGAGAGCTGGGTCAGCAACTCTACCTTTGACTGGGAGGCCTACATCAATGACGAAG
Seq A exon
GTGAGAAGGGAGGTAGACGGGCTAGAGGAGATACCTGGCTCCTCAGGTACCCATTGTCTCAGCTGCTTCTTCAGAGAAGACATAGCTTATGTCCATCCCTCTCCAGCTTGGGTAGCAGCCTCTAGCAGGTCTCTCAGCCATGACCCTTAGAACTGTTTCGTATTAAATGGAGTATGGCAAAACCTCCCTCAAAGGGTTAATGTGATGACGACAGACAGACCATTTTAAAATCCTGCATCTGTCAGGCTGAGAGAGCTCAATCCACAAAGTGCTTGCCCCACAAAGCTGAGGACTCAAGGTTAATCCCCAGAGCCTGTGTAAACAACCAGGCACAATGGCACATGTCTGTAGTTCCAGCTCTGGGGGAGTGGAAGCAGGCAGGTCCCAGGAGCTCGCTGTGCAGCGAGCCAACCCTGCTTCATTGGCAAGCCCCAGATCGTAAGGAGAGAATTCTGAAAAAAGTGTACCATTGGTCCTGAGAAACAGCACCCGAGGTTGCCCTGGGAGATACACACACACACACACACACACACACACACGCACACACACACACACGAACGCACACACGTGTGTGCTAAGGCTCTCACTGTACAAAGAGACAGTCTATCATCCTTCTATAGCCTAAGCATATTCTCCTTTCCCACATTCTGTGTGCCCTCCCTGGTAGAGCTGTTGCCAGTCACATCCCATTTGCGTGGTTGTCCTTTACAGCACACACAACACACATACACAGTCTCACGCAGTCACTATTACACACAGTGTCCTCATGGGAATAGTGTCCTTCCTTCACTGTGGTCTCTAGATTCCAACCCCAACCCCTCCCCAGTGCACACACAGAAACATGCCTTTTTGACCATTGGGCCTTATTAGGGCTCTGGTGAATCCTGACTTCATAACCACAGCAGGTACCAAGCTGATGTGGCTTAGCGCTGAGCCCATGCAGTTTATCCACTGGAGACCCTGGAGTTCGGAACTGTTCGTAAAAGACGGGGCTGAGGGGGGCAGGGAGTGTCTGTGTGGCCTCTTTGGGCACACAGATCTGTTGATGTGTACATGTGATAGATATGTGATGTGTACATGTGTTTCCTGGGCTTCTGTGTGGTAACATGTCTTCTTTGTGACCTCTGATTCCCAAAG
Seq C2 exon
GGAACTTCTATTTCTTGGAGGGCTCCAATGATGCCCTGCTCTGTGGGAATAGCAGTGATGCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001027-Scn4a:NM_133199:6
Average complexity
IR-S
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(37.4=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(7.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCCCTGATCCAGTCTGTGAA
R:
TATTCCCACAGAGCAGGGCAT
Band lengths:
347-1484
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: