BtaINT0129448 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004770 | SCN4A
Description
sodium channel, voltage gated, type IV alpha subunit [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr19:48798502-48799120:-
Coord C1 exon
chr19:48798842-48799120
Coord A exon
chr19:48798556-48798841
Coord C2 exon
chr19:48798502-48798555
Length
286 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
ACCCAACCACACTCTCGCAGGCC
3' ss Score
5.69
Exon sequences
Seq C1 exon
GTGGTGGTGAATGCCCTCCTGGGAGCCATCCCCTCCATCATGAACGTGCTGCTCGTCTGCCTCATCTTCTGGCTCATCTTCAGCATCATGGGTGTCAACCTGTTTGCCGGCAAGTTCTACTACTGCATCAACACCACCACCTCCGAGAGATTCGACATCACCGAGGTCAACAACAAGTCCGAGTGCGAGAGCCTGATGCACACGGGCCAGGTCCGCTGGCTCAACGTCAAGGTCAACTACGACAACGTGGGCCTCGGCTACCTCTCGCTCTTGCAGGTG
Seq A exon
GTGAGTGTGACATGCGGCCCCTGCATGAGGCAGGGGTGGAGACGCCCCTGGAATCTCACTGGGACTGAGCCCACGGCCACTCCTCGTTAGGGAACCTCCCACCTGCCTCCAGGGCTGGAGGACCCAGAGGTCGTGTCCATACCTGTCTGTATTTTGATTGTCTGTACTTGATGCCTGCCCAGTGGGACTCGGAGCAGGCAGCTTCTGGGGTGGGCAGGGAGGGAAACTCATGGATGGTGGAAGCAGCTAGCAGCCCCTCCCCTCACACCCAACCACACTCTCGCAG
Seq C2 exon
GCCACCTTCAAGGGCTGGATGGACATCATGTATGCTGCCGTGGACTCCCGGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004770:ENSBTAT00000006265:19
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:
PF0052026=Ion_trans=FE(40.4=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(7.5=100)
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:
AGCCATCCCCTCCATCATGAA
R:
CCACGGCAGCATACATGATGT
Band lengths:
299-585
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]