DreALTD0016486-2/2 @ 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
chr2:52296783-52296806
Coord C2 exon
chr2:52295271-52296496
Length
24 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
TCATGTGCCTTTTTTCACAGGAA
3' ss Score
9.89
Exon sequences
Seq C1 exon
AATATTCTACAAGGATTCTTCTTCGACTTGGTGTCCAAGCAAGCCTTTGATATAACCATTATGATGCTCATTATCCTCAATATGATAACCATGATGGTTGAGACTGATGAACAATCTGCTCGCATGGAGACCATCCTCAATAACATCAACTTGGCCTTCATTGTCATCTTCACTACTGAATGCCTCATCAAGATTTTTGCCCTCCGCTGTTATTTCTTCACCATTAGTTGGAACATATTTGATTTTGTAGTCGTCATTCTGTCCATCGTTG
Seq A exon
GTAAGTGCACGACTTTCCAGTCTG
Seq C2 exon
GAATTGTCCTGGCGGATATAATTGAAAAGTACTTTGTCTCCCCAACTCTTTTTCGAGTCATCCGGTTGGCAAGAATAGGACGAGTTCTTCGACTGATACGAGCAGCTAAGGGAATAAGGACTTTACTTTTTGCCTTAATGATGTCATTACCAGCATTGTTCAACATCGGTCTCCTACTGTTTCTGGTCATGTTCATCTATGCCATTTTTGGCATGGCAAACTTCGCTTATGTGAAGAAGCAGGGTGGGATTGATGACATGTTCAACTTTGAGACCTTCGGGAACAGCATGATCTGCCTTTTCCAGATCACCACATCGGCCGGTTGGAATAACCTGCTGGATCCTATCCTGAACAACTCTCCGGAAGAGTGTAGCTCCAGTTTTGCGAACACCGGAACAAATACTAAGGGCAACTGTGGTCACCCCTCAGTAGGGATCACTTTCTTTGTCAGCTACATCATCATTTCCTTCTTGATCGTCGTCAACATGTACATCGCCATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000090724-29-26,30-26-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No 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 Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
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]