DreALTD0016486-1/2 @ danRer10
Alternative 5'ss
Gene
ENSDARG00000090724 | scn12aa
Description
sodium channel, voltage gated, type XII, alpha a [Source:ZFIN;Acc:ZDB-GENE-060908-2]
Coordinates
chr2:52295271-52297077:-
Coord C1 exon
chr2:52296807-52297077
Coord A exon
NA
Coord C2 exon
chr2:52295271-52296496
Length
0 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
TCATGTGCCTTTTTTCACAGGAA
3' ss Score
9.89
Exon sequences
Seq C1 exon
AATATTCTACAAGGATTCTTCTTCGACTTGGTGTCCAAGCAAGCCTTTGATATAACCATTATGATGCTCATTATCCTCAATATGATAACCATGATGGTTGAGACTGATGAACAATCTGCTCGCATGGAGACCATCCTCAATAACATCAACTTGGCCTTCATTGTCATCTTCACTACTGAATGCCTCATCAAGATTTTTGCCCTCCGCTGTTATTTCTTCACCATTAGTTGGAACATATTTGATTTTGTAGTCGTCATTCTGTCCATCGTTG
Seq A exon
NA
Seq C2 exon
GAATTGTCCTGGCGGATATAATTGAAAAGTACTTTGTCTCCCCAACTCTTTTTCGAGTCATCCGGTTGGCAAGAATAGGACGAGTTCTTCGACTGATACGAGCAGCTAAGGGAATAAGGACTTTACTTTTTGCCTTAATGATGTCATTACCAGCATTGTTCAACATCGGTCTCCTACTGTTTCTGGTCATGTTCATCTATGCCATTTTTGGCATGGCAAACTTCGCTTATGTGAAGAAGCAGGGTGGGATTGATGACATGTTCAACTTTGAGACCTTCGGGAACAGCATGATCTGCCTTTTCCAGATCACCACATCGGCCGGTTGGAATAACCTGCTGGATCCTATCCTGAACAACTCTCCGGAAGAGTGTAGCTCCAGTTTTGCGAACACCGGAACAAATACTAAGGGCAACTGTGGTCACCCCTCAGTAGGGATCACTTTCTTTGTCAGCTACATCATCATTTCCTTCTTGATCGTCGTCAACATGTACATCGCCATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000090724-29-26,30-26-1/2
Average complexity
Alt5
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=0.159
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.4=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.1=40.8),PF0061222=IQ=WD(100=5.1)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTCGTCATTCTGTCCATCGT
R:
CGTCCTATTCTTGCCAACCGG
Band lengths:
105-129
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]