MmuEX0041257 @ mm10

Exon Skipping

Gene

ENSMUSG00000064329 | Scn1a

Description

sodium channel, voltage-gated, type I, alpha [Source:MGI Symbol;Acc:MGI:98246]

Coordinates

chr2:66327651-66329094:-

Coord C1 exon

chr2:66329031-66329094

Coord A exon

chr2:66328405-66328546

Coord C2 exon

chr2:66327651-66327857

Length

142 bp

Sequences

Splice sites

3' ss Seq

TTCTTTTTCCCCATTTGCAGCCA

3' ss Score

10.19

5' ss Seq

CTGGTGAGA

5' ss Score

7.54

Exon sequences

Seq C1 exon

GATATCATTATTTCCTGGAGGGTGTTTTAGATGCACTGCTGTGTGGAAATAGCTCTGATGCAGG

Seq A exon

CCAATGTCCAGAAGGATATATGTGTGTAAAAGCTGGTAGAAACCCTAATTATGGTTACACAAGCTTTGATACCTTCAGTTGGGCATTTTTGTCCCTGTTTCGACTGATGACTCAGGACTTCTGGGAAAATCTATACCAACTG

Seq C2 exon

ACATTGCGTGCTGCTGGCAAAACCTACATGATATTTTTTGTGCTGGTCATTTTCTTGGGCTCATTCTACCTGATAAACTTGATCCTGGCTGTGGTGGCCATGGCCTATGAGGAGCAGAATCAGGCCACACTGGAGGAGGCTGAACAGAAAGAGGCAGAATTTCAGCAGATGTTGGAGCAACTTAAGAAGCAGCAAGAGGCTGCACAG

VastDB Features

Vast-tools module Information

Secondary ID

ENSMUSG00000064329_CASSETTE2

Average complexity

S

Mappability confidence:

100%=100=100%

Protein Impact

ORF disruption upon sequence exclusion

No structure available

Features

Disorder rate (Iupred):

C1=0.000 A=0.000 C2=0.220

Domain overlap (PFAM):

C1:

PF0052026=Ion_trans=FE(7.9=100)

A:

PF0052026=Ion_trans=FE(17.6=100),PF0253517=Zip=PU(16.2=43.8)

C2:

PF0052026=Ion_trans=PD(11.6=44.9),PF0253517=Zip=FE(52.3=100)

Main Inclusion Isoform:

ENSMUSP00000107985

Main Skipping Isoform:

NA

Other Inclusion Isoforms:

ENSMUSP00000076697, ENSMUSP00000092558, ENSMUSP00000107990, ENSMUSP00000116881

Other Skipping Isoforms:

NA

Associated events

Other assemblies

mm9

Conservation

Human

(hg38)

chr2:166047627-166047768

HIGH PSI

HsaEX6016400

(SCN1A)

Human

(hg19)

chr2:166904137-166904278

HIGH PSI

HsaEX6016400

(SCN1A)

Rat

(rn6)

chr3:52440181-52440322

HIGH PSI

RnoEX0078531

(Scn1a)

Cow

(bosTau6)

chr2:30355273-30355414

HIGH PSI

BtaEX6009371

(SCN1A)

Chicken

(galGal4)

chr7:19113312-19113453

Chicken

(galGal3)

chr7:21089709-21089850

HIGH PSI

GgaEX6042500

(E1C4S3_CHICK)

Zebrafish

(danRer10)

chr9:50264625-50264766

HIGH PSI

DreEX6038636

(scn1a)

Fruitfly

(dm6)

No conservation detected

Primers PCR

Suggestions for RT-PCR validation

F:

CCTGGAGGGTGTTTTAGATGCA

R:

TGCTGCTTCTTAAGTTGCTCCA

Band lengths:

245-387

Functional annotations

(Submit an annotation)

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

Special

MmuEX0041257 @ mm10

GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]

SPECIAL DATASETS