BtaINT0129452 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004770 | SCN4A
Description
sodium channel, voltage gated, type IV alpha subunit [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr19:48796648-48797636:-
Coord C1 exon
chr19:48797532-48797636
Coord A exon
chr19:48796919-48797531
Coord C2 exon
chr19:48796648-48796918
Length
613 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCA
5' ss Score
7.88
3' ss Seq
CACCCCCACCCCTGCTGCAGAAC
3' ss Score
7.48
Exon sequences
Seq C1 exon
TTTGGAGGGAAAGACATCTTCATGACAGAGGAACAGAAGAAATACTATAACGCCATGAAGAAGCTTGGCTCCAAGAAGCCTCAGAAGCCAATTCCCCGGCCCCAG
Seq A exon
GTACCAGCCCTCTGGGCCCCTCCCGCTACAGCCCATATAAGGCTCCTGCCCAAGGGGGCCCTGTGCGGGGGATGCAGAAGGCAGGCTGCTCTCTGCCCACCAGGCTGTGTCCCTGGTGTGAGGCTGGGGCCCCCTGCAGGAAGGTTGTGCCCACCTGATGGGAGGGGCACCTCTCCATAACGCCACACTTCATGTGCAAGCAAGAGCAGCCTGACAAACTCCAGTCACTGGTTTACCCCTTGCCTGACCCGCCCAGCGCCCCCAGCGTCCATTCAGCTCCTTAGCTGGTGGCCTCTGGGGGCAAGGGCCCCTGGAGAGGGGAGGAAGAGGATGTCCAGACAGGTCCCCCAGTGAGCAGCCACTTCGGGAGAAGGAGGAGGGGTTGCTGAGGGCCCTTAATTCGGGAAGAAGTTCCCAGAGAGAGGAAGGAGGCCCACAGACCCCACAGAGTGGCCCGTCTCCATGGGTCTCCCTGCCTCCCGAGGATGCCCTGATGCCTTCATTCTCTCTCTCTCGCCTCCCCACCCCCACACTCCTGTGTCGTGTCCTCTCGCCTCTCCTGCCGGTGCATGTCCTGCTCTGACCGCTGCCCGCACCCCCACCCCTGCTGCAG
Seq C2 exon
AACAAGGTCCAGGGCATGGTGTACGACCTGGTGACCAAGCAGGCGTTCGACATCACCATCATGATCCTCATTTGCCTCAACATGGTCACCATGATGGTGGAGACGGACGACCAGAGCCAGCTCAAGGTGGACATCCTGTACAACATCAACATGGTCTTCATCATCATCTTCACGGGCGAGTGCGTGCTCAAGATGCTGGCCCTGCGCCAGTACTACTTCACCGTCGGCTGGAATATCTTCGACTTTGTGGTCGTCATCCTGTCCATTGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004770:ENSBTAT00000006265:22
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.057 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(20.4=47.3)
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:
GGAGGGAAAGACATCTTCATGACA
R:
CGAAGATATTCCAGCCGACGG
Band lengths:
343-956
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]