MmuINT0139706 @ mm9
Intron Retention
Gene
ENSMUSG00000001027 | Scn4a
Description
sodium channel, voltage-gated, type IV, alpha [Source:MGI Symbol;Acc:MGI:98250]
Coordinates
chr11:106188020-106188979:-
Coord C1 exon
chr11:106188825-106188979
Coord A exon
chr11:106188194-106188824
Coord C2 exon
chr11:106188020-106188193
Length
631 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGC
5' ss Score
6.99
3' ss Seq
GGTTATACTGGTGTCCCCAGGCC
3' ss Score
7.2
Exon sequences
Seq C1 exon
CCTGTGTGAAGCGCTGCCCCTGCCTCTATGTGGACATCTCCCAGGGCCGCGGGAAAATGTGGTGGACACTCCGCAGGGCCTGCTTCAAGATTGTTGAGCACAACTGGTTTGAGACCTTCATCGTCTTCATGATCTTGCTCAGCAGCGGGGCCCTG
Seq A exon
GTAGGCACCCTCCCCCAGGGGACAGGGCGGGAGCAGGAATGGGTGCCTTGCTTCCTAAGGCTTCCATATCATGTCTTTCTCAATTGTTCTCCATCTTTTGCATTAAGGCAGGGTTTCTCACTGAACTCAGAGCTCGATGTTTGGGCTGTTTAAGGGATTCCCTGTCTCTGTCTCCTGTAAGCCTGGGGTTTCAGGCAGGCTGCTGCTGCCACCCGGCTTCCATACAGGTTCTGGGGATCCAAACTTCAGCTCTCATGCTTGCACGACAGATAAGGCATTTCCCCACTCAACGTCAGTTTCTTAAAGTAAAAGATTGGTCCCTTTGTTTTGAAAACCCTGTCCCCTCAGCCAATAGGAAGGTAGGTGGGCCCTGGGAATTTGGAGTTAAGGGCGGTCAGAACTGAAGATAACGTTATTGTGGACCCCCAGCAGAGAGTTGAGAGCTAAGCCTCCTTCCCTACCAGGCATCTTGCCCCTCCCCCTCCTGATGATAGGGCTGGGAATGGAAGATTCCCAGAGGTGCTACAGCCTATGTCCCGTGAAACCAGCAACAGCAGGCAGGATGGGGAACAGAGCTTGCTGCCCCAGCTGCTGAGCCCCTGGTCATTGTGGGTTATACTGGTGTCCCCAG
Seq C2 exon
GCCTTCGAGGACATCTACATTGAACAGCGGCGAGTCATCCAAACCATCCTGGAATATGCTGACAAGGTCTTCACCTACATCTTCATCCTGGAGATGCTGCTAAAGTGGGTGGCCTACGGCTTCAAGGTGTACTTCACCAACGCCTGGTGCTGGCTCGACTTCCTCATTGTGGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001027-Scn4a:NM_133199:16
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:
PF065128=Na_trans_assoc=PD(19.5=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(17.1=67.2)
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:
CTGTGTGAAGCGCTGCCC
R:
CCACAATGAGGAAGTCGAGCC
Band lengths:
326-957
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: