BtaALTA0026192-2/2 @ bosTau6
Alternative 3'ss
Gene
ENSBTAG00000046911 | SCN10A
Description
sodium channel, voltage gated, type X alpha subunit [Source:HGNC Symbol;Acc:HGNC:10582]
Coordinates
chr22:12168109-12169963:-
Coord C1 exon
chr22:12169826-12169963
Coord A exon
chr22:12168233-12168334
Coord C2 exon
chr22:12168109-12168232
Length
102 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGT
5' ss Score
9.65
3' ss Seq
GGGCTCTCTCTGTATCTCAGGGC
3' ss Score
7.62
Exon sequences
Seq C1 exon
GAGCAGCTGCAGCAAGTTGGGAAGTATGAGGACCACCTGCCACCCAGGAGCCCAGGGTCTGGAATATCCTCTGAAGACCTGACTCCAGGCCTAGGTGAGAAGTGCAAAGGCGAGGCTCCTGCTCAGGGCCCTGCAGAG
Seq A exon
GGCATCTTGGAACTCCAGGCCCGTTGGGCCGATGGTGACCGTGTGCAGATTCACGGGGCCCCACGGAGAGCTGGGTTCACTGCTGGGGCTTTTGCCCTGCAG
Seq C2 exon
GGAGCGGATGACACGAGCTCCTCGGAAGGCAGCACTGTGGACTTCCTGGACCCTGAGGAGATCCTGAGGAAGATCCCTGAGCTGGCAGATGACCTCGATGAGCCAGATGACTGCTTCACGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000046911-19-17,19-16-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.381
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(17.4=100)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(15.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
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:
GCTGCAGCAAGTTGGGAAGTA
R:
GCAGTCATCTGGCTCATCGAG
Band lengths:
247-349
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development