BtaINT0129438 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004770 | SCN4A
Description
sodium channel, voltage gated, type IV alpha subunit [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr19:48825171-48825660:-
Coord C1 exon
chr19:48825388-48825660
Coord A exon
chr19:48825299-48825387
Coord C2 exon
chr19:48825171-48825298
Length
89 bp
Sequences
Splice sites
5' ss Seq
AAGGTCCGC
5' ss Score
5.01
3' ss Seq
CAGCTCTCTCCCTGCCGCAGACC
3' ss Score
8.24
Exon sequences
Seq C1 exon
ATGGCCAAGGCGTCTCTGCCCACGGTGGTGCCTCTGGGCCCCGAGAGCCTACGCCCCTTCACCCGGGAGTCCCTGGCAGCCATAGAGCGCCGGGTGTTGGAGGAGGAGGCCCGGCAGTTGCGGAACAAGCAGATGGAGATCGAGGAAACCGAGCAGAAGCCGCGCAGCGACATGGAGGCTGGCAAGAACCTGCCGCTCATCTACGGGGACCCCCCGCCGGAGCTCATTGGCATCCCCCTGGAGGATCTGGATCCCTACTACAGCGACAAGAAG
Seq A exon
GTCCGCGCCGGGGAGGCCTCCCTCCACCTGTCTGTCTCTGATCCATCCGTCTGCCTGTCCCAGGCCTCACAGCTCTCTCCCTGCCGCAG
Seq C2 exon
ACCTTCATCGTGCTCAACAAGGGCAAGTCCATCTTCCGCTTCTCAGCCACTCCTGCTCTCTACATCCTGAGCCCCTTCAGCATCGTCAGACGCTGCGCCATCAAGGTGCTCATCCACTCATATCCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004770:ENSBTAT00000006265:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.253 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion 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:
AGATCGAGGAAACCGAGCAGA
R:
ATGGACTTGCCCTTGTTGAGC
Band lengths:
169-258
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]