DreEX6029430 @ danRer10
Exon Skipping
Gene
ENSDARG00000090724 | scn12aa
Description
sodium channel, voltage gated, type XII, alpha a [Source:ZFIN;Acc:ZDB-GENE-060908-2]
Coordinates
chr2:52297360-52302601:-
Coord C1 exon
chr2:52302329-52302601
Coord A exon
chr2:52298354-52298407
Coord C2 exon
chr2:52297360-52297501
Length
54 bp
Sequences
Splice sites
3' ss Seq
TGATTTATTCTGTTTTTCAGGCT
3' ss Score
9.56
5' ss Seq
GGAGTAAGC
5' ss Score
5.07
Exon sequences
Seq C1 exon
GTTGTAGTGAATGCACTGATCGGGGCCATCCCGTCCATCATGAATGTACTGCTGGTGTGTCTGATCTTTTGGCTCATATTTAGTATCATGGGCGTCAATCTCTTTGCTGGGAAATTTGGCAAATGTGTCAATAGGACAGGATTCATCCACAATGCAAGCATTGTCAACAACAAGACAGAGTGCCTGTCCATGAATGATACACAGTTCTACTGGACCAAGGTGAAAGTCAACTTCGACAACGTGGGACTCGGATACCTCTCACTTCTGCAGGTG
Seq A exon
GCTACATTCAAAGGCTGGATGGAAATCATGTATGCCGCCGTTGATTCCCGTGGA
Seq C2 exon
GTTGAGGACCAGCCCATCAAAGAGATAAACCTCTACATGTACCTCTACTTTGTCATCTTCATCATCTTTGGATCATTCTTTACCCTGAATTTGTTCATCGGTGTCATTATCGACAATTTCAATCAACAAAAAAGAATGATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000090724-'25-23,'25-22,26-23=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (No 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(39.8=100)
A:
PF0052026=Ion_trans=FE(7.5=100)
C2:
PF0052026=Ion_trans=PD(15.5=72.9)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Primers PCR
Suggestions for RT-PCR validation
F:
TCAACAACAAGACAGAGTGCCT
R:
TCTTTGATGGGCTGGTCCTCA
Band lengths:
133-187
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]