BtaEX0031587 @ bosTau6
Exon Skipping
Gene
ENSBTAG00000021339 | SCN8A
Description
sodium channel, voltage gated, type VIII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10596]
Coordinates
chr5:28286100-28299511:-
Coord C1 exon
chr5:28299383-28299511
Coord A exon
chr5:28297494-28297585
Coord C2 exon
chr5:28286100-28286321
Length
92 bp
Sequences
Splice sites
3' ss Seq
CGTGACCTCCCTTACTACAGATA
3' ss Score
7.66
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
Exon sequences
Seq C1 exon
GTACACGTTCACAGGGATTTATACATTTGAATCACTAGTGAAAATCATTGCAAGAGGTTTCTGCATAGATGGCTTTACCTTTTTACGGGATCCATGGAACTGGTTGGATTTCAGTGTCATCATGATGGC
Seq A exon
ATATGTGACAGAGTTTGTGGACCTGGGCAATGTCTCAGCGCTGAGAACATTCAGGGTTCTCCGAGCTTTGAAAACTATCTCTGTAATTCCAG
Seq C2 exon
GCCTGAAGACCATCGTGGGCGCCCTGATTCAGTCCGTGAAGAAGCTGTCAGACGTGATGATCCTGACAGTGTTCTGCCTGAGTGTCTTTGCCTTGATCGGACTGCAGCTCTTCATGGGAAACCTGCGAAACAAGTGTGTGGTGTGGCCCATCAACTTCAACGAGAGCTATCTTGAAAACGGCACCAAGGGCTTTGATTGGGAAGAGTACATCAACAATAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021339_MULTIEX1-2/2=C1-C2
Average complexity
ME(1-2[100=100])
Mappability confidence:
100%=100=100%
Protein Impact
In the CDS, with uncertain impact
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(17.1=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(29.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGGATCCATGGAACTGGTTG
R:
GGTTTCCCATGAAGAGCTGCA
Band lengths:
167-259
Functional annotations
There are 1 annotated functions for this event
PMID: 15664175
Mutually exclusive exons 5A and 5N alter voltage-dependent gating and/or interactions with a blocking subunit. From Vuong et al, Nat Rev Neurosci 2016.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development