MmuINT0139659 @ mm9
Intron Retention
Gene
ENSMUSG00000075318 | Scn2a1
Description
sodium channel, voltage-gated, type II, alpha 1 [Source:MGI Symbol;Acc:MGI:98248]
Coordinates
chr2:65520054-65520651:+
Coord C1 exon
chr2:65520054-65520182
Coord A exon
chr2:65520183-65520559
Coord C2 exon
chr2:65520560-65520651
Length
377 bp
Sequences
Splice sites
5' ss Seq
TGCGTAAGT
5' ss Score
9.73
3' ss Seq
ACTCTGATTTAATCCTACAGGTA
3' ss Score
9.61
Exon sequences
Seq C1 exon
GTATACTTTTACAGGAATTTATACTTTTGAATCACTTATTAAAATACTTGCAAGGGGCTTTTGTCTAGAAGATTTCACATTTCTACGGGATCCCTGGAACTGGCTGGATTTCACAGTCATTACCTTTGC
Seq A exon
GTAAGTATTTTTATGATACTTTCTACCCTGGCAGAGGTAATACAATGGAATCTATACTGTAGTTCTCAGTGTTGGCTTCCTTTGACTCATAAAGCATTTTAATTAGTTATCATATGGATTTAAAGTACCTTTTCCAATCAAATTATTCAGTCTGGAGAAATTAGGAATGATCCTAATAAGTTATATGGTGTTGGTTTCGATTAGCTTTTAGGTAATAACAATAACTCCCAATAGCAGCTCAGTTGGTGTCAATGCCATTCTCCCCTTAACTGGGAAATCTGGTGACAACACTCACTGAAGTTGAAATGATCTTGATTCAAGACCAACACAGATGTAGATTTCCCCAAATTCTGAATAACTCTGATTTAATCCTACAG
Seq C2 exon
GTATGTAACAGAATTTGTAAACCTAGGCAATGTTTCAGCTCTTCGAACTTTCAGAGTCTTGAGAGCTTTGAAAACTATTTCTGTAATTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075318-Scn2a1:NM_001099298:4
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(16.0=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(11.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACTTATTAAAATACTTGCAAGGGGC
R:
TACAGAAATAGTTTTCAAAGCTCTCA
Band lengths:
182-559
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: