BtaEX6093438 @ bosTau6
Exon Skipping
Gene
ENSBTAG00000009155 | SCN5A
Description
Bos taurus sodium channel, voltage-gated, type V, alpha subunit (SCN5A), mRNA. [Source:RefSeq mRNA;Acc:NM_174458]
Coordinates
chr22:12025487-12029213:-
Coord C1 exon
chr22:12028932-12029213
Coord A exon
chr22:12026243-12026296
Coord C2 exon
chr22:12025487-12025624
Length
54 bp
Sequences
Splice sites
3' ss Seq
CTCTTGTCTCTTTCTTCCAGGCA
3' ss Score
11.69
5' ss Seq
GGGGTAGGT
5' ss Score
6.59
Exon sequences
Seq C1 exon
GTTGTGGTTAACGCCCTGGTGGGCGCCATCCCATCCATCATGAACGTCCTCCTCGTCTGCCTCATCTTCTGGCTCATCTTCAGCATCATGGGCGTGAACCTCTTCGCGGGGAAGTTTGGGAGATGCATCAACCAGACCGAGGGAGACCTGCCCTTGAACTATACCATCGTGAACAACAAGAGCGACTGTGAGTCTTTCAACGTGACTGGCGAATTGTACTGGACCAAGGTGAAGGTCAACTTTGACAACGTGGGGGCCGGGTACCTGGCCCTTCTGCAGGTG
Seq A exon
GCAACATTTAAAGGCTGGATGGACATCATGTATGCAGCTGTAGACTCCAGGGGG
Seq C2 exon
TACGAGGAGCAGCCCCAGTGGGAATACAACCTCTACATGTATATCTATTTTGTCATCTTCATCATCTTTGGGTCTTTCTTCACCCTGAACCTGTTCATCGGTGTCATCATTGACAACTTCAACCAGCAGAAGAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000009155-'26-31,'26-30,27-31=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=0.000 C2=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(40.6=100)
A:
PF0052026=Ion_trans=FE(7.4=100)
C2:
PF0052026=Ion_trans=PD(15.3=76.1)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Primers PCR
Suggestions for RT-PCR validation
F:
TCAACTTTGACAACGTGGGGG
R:
CAGGTTCAGGGTGAAGAAAGACC
Band lengths:
140-194
Functional annotations
There are 1 annotated functions for this event
PMID: 20398673
HsaEX0056554 encodes 18 amino acids in the D3 pore region. Isoforms lacking HsaEX0056554 were tested by exogenous expression in Xenopus oocytes and HEK293 cells. Electrophysiological recordings of these cells suggest that the isoform is non-functional. Skipping this exon is speculated to be relevant for limiting Nav1.5 sodium currents in several tissues, including brain.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]