BtaINT0129527 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021339 | SCN8A
Description
sodium channel, voltage gated, type VIII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10596]
Coordinates
chr5:28234686-28235794:-
Coord C1 exon
chr5:28235640-28235794
Coord A exon
chr5:28234860-28235639
Coord C2 exon
chr5:28234686-28234859
Length
780 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGG
5' ss Score
8.3
3' ss Seq
AGCTGCTGCCTCTCTTCCAGGCC
3' ss Score
8.89
Exon sequences
Seq C1 exon
GTTGTGTCCAGAGATTTAAGTGCTGCCAGGTCAACATTGAGGAGGGACTGGGCAAGTCTTGGTGGATCCTGCGGAAAACCTGCTTCCTCATCGTGGAGCACAACTGGTTCGAGACCTTCATCATCTTCATGATTCTACTCAGCAGTGGTGCCCTG
Seq A exon
GTGAGGTCTGGGGAGAATCTGCTGGGGGATTGACTGGGCAGGGGTATAGGGACCAGCAGGAAAGACTGGGTGGCCTGAGCCCAGTTTCTCAAACAACACAGCCTGGCTGAAGACCAAGAGTAACGATCTACTCCGGTGCTTCGGGCTGGTGTTTTGAGTCCTGGGGATTAGAATTCACACTTGTCTGTATCTTCATCCTAGACCTCAGCATGATCCCACTTGAGCCCAAGGCCCCCTTTTCATCAGGATAAGAATACGAATGACCAAGTATCTTCACTGCTTAGCTTGCCTCATTCAAAGCAACTTCCCTTACTTCCCTAAACCCCTGATTCACAAAGGACCACATGTTATATGATTCAGTTTATACAAAATGTCCAGAAGGAGCTGGTCTCTGGAGACAGAAAGCAGATTGGTGGTTGCCAGGACTAGGAGGAGATCGGGAGACTAGAGGGTGACAGCTGGAGGGTGTGGGGTTTCTTTGGAGGGTAATGAAAATATTCTAAATTCGACTGAGGTGATGAATATATGACTCTGAATGCATTAAGAGCTATTGCGCTGTAAACTTTAAGTAGCTGAATTATGAGGTATGAAAATTACATCTCAAGAAAAGTTTTTTACAAAGAAAAGCCATGTGTAGCAAGGGACAGTGAAGGGAGACGGGGAGCTGATGACCCGCCAGCACAGGTGGGAAGGCTGCGGGGGGTTGCGGGGGTGGGGGTGGTACTTCCGTGTTGCTCATTTCCCTGTAGGCGCTATAGGCAGCTGCTGCCTCTCTTCCAG
Seq C2 exon
GCCTTCGAGGACATCTACATCGAGCAGAGGAAGACCATCCGTACCATCCTGGAGTATGCTGATAAAGTCTTCACCTACATCTTCATCCTGGAGATGTTGCTCAAGTGGACAGCCTACGGCTTCGTCAAGTTCTTCACCAATGCCTGGTGCTGGCTGGACTTCCTCATCGTGGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021339:ENSBTAT00000061543:18
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:
PF065128=Na_trans_assoc=PD(20.2=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(17.0=67.2)
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:
GTGTCCAGAGATTTAAGTGCTGC
R:
AGCCACGATGAGGAAGTCCAG
Band lengths:
326-1106
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]