BtaALTA0026200-2/2 @ bosTau6
Alternative 3'ss
Gene
ENSBTAG00000004770 | SCN4A
Description
sodium channel, voltage gated, type IV alpha subunit [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr19:48798842-48800674:-
Coord C1 exon
chr19:48800552-48800674
Coord A exon
chr19:48799038-48799120
Coord C2 exon
chr19:48798842-48799037
Length
83 bp
Sequences
Splice sites
5' ss Seq
AGGGTGGGT
5' ss Score
5.37
3' ss Seq
TCCCCACCCCCGGCCCCCAGGTG
3' ss Score
9.73
Exon sequences
Seq C1 exon
GTCTCCATCATCAGCCTGGTGGCCAACTGGCTGGGCTACTCGGAGCTGGGACCCATCAAATCCCTGCGGACGCTGCGGGCCCTGCGCCCCCTGAGGGCACTGTCTCGATTCGAGGGCATGAGG
Seq A exon
GTGGTGGTGAATGCCCTCCTGGGAGCCATCCCCTCCATCATGAACGTGCTGCTCGTCTGCCTCATCTTCTGGCTCATCTTCAG
Seq C2 exon
CATCATGGGTGTCAACCTGTTTGCCGGCAAGTTCTACTACTGCATCAACACCACCACCTCCGAGAGATTCGACATCACCGAGGTCAACAACAAGTCCGAGTGCGAGAGCCTGATGCACACGGGCCAGGTCCGCTGGCTCAACGTCAAGGTCAACTACGACAACGTGGGCCTCGGCTACCTCTCGCTCTTGCAGGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004770-18-21,18-20-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(17.5=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(40.4=100)
Main Skipping 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:
GAGCTGGGACCCATCAAATCC
R:
TTGTTGACCTCGGTGATGTCG
Band lengths:
171-254
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development