MmuINT0139640 @ mm10
Intron Retention
Gene
ENSMUSG00000075318 | Scn2a
Description
sodium channel, voltage-gated, type II, alpha [Source:MGI Symbol;Acc:MGI:98248]
Coordinates
chr2:65670445-65671720:+
Coord C1 exon
chr2:65670445-65670762
Coord A exon
chr2:65670763-65671601
Coord C2 exon
chr2:65671602-65671720
Length
839 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
TGTTGTGTTCTCTTTTTCAGACC
3' ss Score
12.84
Exon sequences
Seq C1 exon
CACTTTCTTATGCGAGGAGCTAAACAGTGATTAAAGAAGCAGGATGAAAAGATGGCACAATCAGTGCTGGTACCGCCAGGACCTGACAGCTTCCGCTTCTTTACCAGGGAATCCCTTGCTGCTATTGAACAACGCATTGCAGAAGAGAAAGCTAAGAGACCCAAACAGGAACGCAAGGACGAAGACGACGAAAATGGCCCAAAGCCAAATAGTGACTTGGAAGCAGGAAAATCCCTTCCTTTTATTTATGGAGACATTCCTCCAGAGATGGTGTCAGAGCCCCTGGAGGACCTGGACCCCTACTATATCAATAAGAAA
Seq A exon
GTGAGTTTTTAGACCAGTTGCTTTTATTTCCTCGATTTCTTTAAGATGGTGAAGAGGGTGCCTCTTTTCATCTCTTAAGATATCTGTAGAATATTGGGTAGGTCTGATAAGGGAATGGAGCCATTATTCCAGAAGTGTTTTGAAAGCATTTGGTTGAGCCTGTGTTCTTGGGACAGTCATATTTTGAAGAGGCATCCTGCAAGGGGGCATGTGAAGAAGACAAAGCCAATTTATTTTCCTGAGTACTCATTATACCATAAATTGAATGCAGATTCACCCTGGTGCTACTGACATTGTGATAAAGGGAAAAGTAGAGAAAGGATCTGTGTGTGTGTTTTATACTTCTAAGAGCAGTGTCTCAGATCCCCTATTGCTTTGAATTTGATCTTAGGCTTTGGGGTCCTCCACAGGCTTAATTATGCCTTTACACCACAGACTGTTATTTCCCCATGGCTCCCTGCAGAAGAAATAACAGCAGAACACGTGTAAGGGGAAAAAAGTTCTAACAGTTTTCATGAGAAAATTACCTAAATGAAGAAGTTGCTGAAACCTCACTTTTAAGCTGTGTAAAAATTACAGACATGGCGGAAAACATGAGTAAAAGACTCGGCAAAGTTACCAAGAAGTCTGTGGTCCTAATCACAAAATTGTCTTTGTATTCCTTACCTCCTGAAGGTCCTTATCAAATTTTGAATGGTTTGCAAGAAAAAAGACCCGTGTCCTGTCCTTTGTTTGTAACAGTTGCAACACTTGATATTTTAGAGGGGTCTTTTACTCTCTTCAAACGTCCTTGATGTGGTCTGTAAATTCTGTTTCACCTGTTGTGTTCTCTTTTTCAG
Seq C2 exon
ACCTTTATAGTATTGAATAAAGGGAAAGCAATCTCTCGGTTCAGTGCCACCTCCGCCCTGTACATTTTAACTCCCTTCAACCCCATTAGAAAATTAGCTATTAAGATTTTGGTACATTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075318:ENSMUST00000028377:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.360 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
AGCAGGATGAAAAGATGGCAC
R:
AAAATGTACAGGGCGGAGGTG
Band lengths:
349-1188
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