BtaINT0129449 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004770 | SCN4A
Description
sodium channel, voltage gated, type IV alpha subunit [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr19:48824941-48825298:-
Coord C1 exon
chr19:48825171-48825298
Coord A exon
chr19:48825022-48825170
Coord C2 exon
chr19:48824941-48825021
Length
149 bp
Sequences
Splice sites
5' ss Seq
TGGAGGAGT
5' ss Score
-7.1
3' ss Seq
CTCCCCCCAACGCTGTTCAGCAT
3' ss Score
3.73
Exon sequences
Seq C1 exon
ACCTTCATCGTGCTCAACAAGGGCAAGTCCATCTTCCGCTTCTCAGCCACTCCTGCTCTCTACATCCTGAGCCCCTTCAGCATCGTCAGACGCTGCGCCATCAAGGTGCTCATCCACTCATATCCTGG
Seq A exon
AGGAGTGGGGCGAGCGCAGGGGCGGGGAAAGGCAGGCAGGGGTCAGGGATGGGCAAGAACGGGGCGCTCTGGGTGAGGAGGCCCTCTGTCCTCCTCTCCTCCCCACCTGCTCCCTCACTTTCCTTGACCCTCCCCCCAACGCTGTTCAG
Seq C2 exon
CATGTTCATTATGATCACCATCCTGACCAACTGCGTGTTCATGACCATGAGTGACCCGCCTTCCTGGTCCAAGCACGTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004770:ENSBTAT00000006265:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(0.7=7.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCATCGTGCTCAACAAGGGC
R:
CACGTGCTTGGACCAGGAAG
Band lengths:
204-353
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]