BtaALTD0019213-3/3 @ bosTau6
Alternative 5'ss
Gene
ENSBTAG00000002425 | SCN9A
Description
sodium channel, voltage gated, type IX alpha subunit [Source:HGNC Symbol;Acc:HGNC:10597]
Coordinates
chr2:30120058-30123356:+
Coord C1 exon
chr2:30120058-30120396
Coord A exon
chr2:30120397-30120453
Coord C2 exon
chr2:30123227-30123356
Length
57 bp
Sequences
Splice sites
5' ss Seq
CAGGCATGG
5' ss Score
2.23
3' ss Seq
ATCATCTTTTTTTTTTTCAGGGT
3' ss Score
11.86
Exon sequences
Seq C1 exon
TCACCACTGAGCATCCGTGGCTCCTTGTTTTCTGCAAGGCGGAGCAGCAGAACAAGTCTTTTCAGCTTCAAAGGTCGAGGAAGAGATATTGGATCTGAGACTGAATTTGCCGACGACGAGCACAGCATCTTTGGTGACAACGAGAGCAGAAGGGGCTCCCTGTTTGTGCCCCACAGACCTCGGGAGCGGCGCAGCAGTAACATCAGCCAAGCCAGTAGGTCTCCCCCAGTGCTGCCAGTGAACGGGAAGATGCACAGCGCTGTCGACTGCAATGGCGTGGTCTCCTTGGTGGATGGACCCTCCGCCCTCATGCTACCCAATGGACAGCTCCTGCCAGAG
Seq A exon
GTGATAATAGATAAGGCAACTTCTGATGACAGCGTAAGGACGTTTTAAATAGCTCAG
Seq C2 exon
GGTACAACCAATCAAATACACAAGAAAAGACGTCACAGTTCTTACCTCCTTTCTGAGGATATGTTGAATGACCCCAATCTCAGACAAAGGGCAATGAGTAGGGCAAGCATATTAACAAACACTGTAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002425-13-12,14-12,15-12-3/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.581 A=NA C2=0.136
Domain overlap (PFAM):
C1:
PF119333=DUF3451=FE(52.8=100)
A:
NA
C2:
PF119333=DUF3451=PD(15.5=81.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCTCATGCTACCCAATGGAC
R:
ATGCTTGCCCTACTCATTGCC
Band lengths:
145-202
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development