BtaEX6009366 @ bosTau6
Exon Skipping
Gene
ENSBTAG00000018520 | SCN1A
Description
sodium channel, voltage gated, type I alpha subunit [Source:HGNC Symbol;Acc:HGNC:10585]
Coordinates
chr2:30370136-30389703:+
Coord C1 exon
chr2:30370136-30370492
Coord A exon
chr2:30371671-30372153
Coord C2 exon
chr2:30389583-30389703
Length
483 bp
Sequences
Splice sites
3' ss Seq
ATGTTTGTGTTATTTTTAAGGTC
3' ss Score
11.2
5' ss Seq
GAGGTAAGA
5' ss Score
10.06
Exon sequences
Seq C1 exon
CTTCGAGTTTTCAAGTTGGCAAAATCTTGGCCAACATTAAATATGCTAATAAAGATCATCGGCAATTCAGTGGGGGCTCTGGGAAACCTAACCTTGGTGTTAGCCATCATCGTCTTCATTTTTGCTGTGGTTGGCATGCAGCTCTTTGGTAAAAGTTACAAAGATTGTGTCTGCAAGATCAACAGTGAGTGTAAACTCCCACGCTGGCACATGAATGACTTCTTCCACTCCTTCCTGATTGTGTTCCGGGTGCTGTGTGGAGAGTGGATAGAGACCATGTGGGACTGCATGGAGGTCGCCGGTCAAGCCATGTGCCTTACTGTCTTCATGATGGTCATGGTCATTGGAAACCTGGTG
Seq A exon
GTCCTGAACCTCTTTTTGGCCTTGCTTCTGAGCTCATTTAGTGCAGACAACCTTGCGGCCACTGATGATGATAATGAAATGAACAATCTCCAAATTGCTGTGGATAGGATGCACAAAGGAATAGCTTATGTGAAGAGAAAAATATATGAATTTATTCAGCAGTCCTTTGTTAGAAAACAAAAGATTTTAGATGAAATTAAACCACTTGATGATCTAAACAACAGGAAAGACAATTGTATGTCCAATCATACAACAGAGATTGGGAAAGACCTTGACTATCTTAAAGACGTAAATGGAACCACAAGTGGAATAGGAACCGGCAGCAGTGTTGAAAAGTACATTATTGATGAAAGTGATTACATGTCCTTCATAAACAATCCCAGTCTTACTGTGACTGTACCAATTGCTGTAGGAGAATCTGACTTTGAAAATTTAAACACAGAGGACTTCAGTAGTGAATCAGATCTGGAAGAAAGCAAAGAG
Seq C2 exon
AAGCTTAATGAAAGCAGTAGTTCATCTGAAGGTAGCACTGTAGACATTGGAGCACCTGCCGAGGAACAGCCTGTGGTGGAACCCGAGGAAACCCTTGAACCTGAAGCCTGTTTCACTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018520-'18-16,'18-15,19-16=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=0.149 C2=0.756
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(62.1=100)
A:
PF0052026=Ion_trans=PD(4.2=5.0),PF065128=Na_trans_assoc=PU(61.4=85.1)
C2:
PF065128=Na_trans_assoc=FE(17.9=100)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTTTGCTGTGGTTGGCATGC
R:
CAGGTTCAAGGGTTTCCTCGG
Band lengths:
342-825
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]