BtaALTD0019212-2/2 @ bosTau6
Alternative 5'ss
Gene
ENSBTAG00000021339 | SCN8A
Description
sodium channel, voltage gated, type VIII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10596]
Coordinates
chr5:28256627-28270758:-
Coord C1 exon
chr5:28270396-28270758
Coord A exon
chr5:28270363-28270395
Coord C2 exon
chr5:28256627-28256759
Length
33 bp
Sequences
Splice sites
5' ss Seq
AGTGTAAGG
5' ss Score
5.2
3' ss Seq
TTGTTTTCTTTTTTTTTAAGGCT
3' ss Score
9.69
Exon sequences
Seq C1 exon
TCACTGCTCAGCATTCCAGGCTCCCCATTCCTCTCCCGCCACAACAGCAAGAGCAGCATCTTCAGCTTCAGGGGGCCCGGGCGGTTCCGGGACCCGGGCTCGGAGAATGAGTTTGCAGACGACGAGCACAGCACGGTGGAGGAGAGCGAGGGCCGCCGGGACTCGCTCTTCATCCCCATCCGGGCGCGCGAGCGCCGCAGCAGCTACAGTGGCTACAGCGGCTACAGCCAGGGCAGCCGCTCTTCGCGCATCTTCCCCAGCCTGCGGCGCAGCGTCAAGCGCAACAGCACAGTGGACTGCAATGGCGTGGTGTCCCTCATCGGCGGCCCCGGCTCCCACATCAGCGGGCGTCTCCTGCCAGAG
Seq A exon
GTGAAAATAGATAAGGCAGCTACTGATGACAGT
Seq C2 exon
GCTACAACTGAGGTGGAAATTAAGAAGAAAGGCCCTGGATCTCTCTTAGTTTCTATGGACCAACTGGCTTCCTATGGACGAAAGGACAGGATCAACAGTATATTGAGTGTTGTTACAAATACACTGGTGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021339-11-15,12-15-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.397 A=NA C2=0.022
Domain overlap (PFAM):
C1:
PF0310514=SPX=PD(28.9=46.3),PF119333=DUF3451=FE(52.6=100)
A:
NA
C2:
PF119333=DUF3451=PD(16.7=84.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTGGACTGCAATGGCGTG
R:
AGAGAGATCCAGGGCCTTTCT
Band lengths:
119-152
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development