BtaEX6009342 @ bosTau6
Exon Skipping
Gene
ENSBTAG00000002425 | SCN9A
Description
sodium channel, voltage gated, type IX alpha subunit [Source:HGNC Symbol;Acc:HGNC:10597]
Coordinates
chr2:30170331-30180355:+
Coord C1 exon
chr2:30170331-30170464
Coord A exon
chr2:30178629-30178733
Coord C2 exon
chr2:30180085-30180355
Length
105 bp
Sequences
Splice sites
3' ss Seq
ATTTATTTTTATTTCTTTACCTT
3' ss Score
-0.36
5' ss Seq
GGGGTAAAA
5' ss Score
2.56
Exon sequences
Seq C1 exon
ACAAGCAGCCCATTTATGAATACAGCCTCTACATGTATATTTATTTTGTCATCTTCATCATCTTTGGGTCATTCTTCACTTTGAACTTGTTCATTGGTGTCATCATAGATAATTTCAACCAACAGAAAAAGAAG
Seq A exon
CTTGGAGGTCAAGATATCTTTATGACAGAAGAACAGAAGAAATATTATAATGCAATGAAAAAGCTGGGATCCAAGAAACCACAAAAGCCAATACCTCGGCCAGGG
Seq C2 exon
AACAAATTCCAAGGATGTATCTTTGACCTAGTAACAAACCAAGCTTTTGATATAGCCATCATGGTTCTGATCTGCCTCAACATGGTAACCATGATGGTGGAAAAAGAGGGACAAAGTGACTACGTGACTGAAGTTTTAAATTGGATCAATGTGGTTTTTATTATCCTGTTCTCTGGAGAATGCGTGCTGAAACTGATCTCCCTCAGATGCTACTACTTCACTGTAGGCTGGAACATCTTTGATTTTGTGGTTGTAATTCTCTCCATTGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002425-'33-29,'33-27,34-29=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=0.057 C2=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(14.8=75.6)
A:
NO
C2:
PF0052026=Ion_trans=PU(20.4=47.3)
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:
GCAGCCCATTTATGAATACAGCC
R:
TCACGTAGTCACTTTGTCCCTCT
Band lengths:
257-362
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]