BtaINT0129526 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021339 | SCN8A
Description
sodium channel, voltage gated, type VIII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10596]
Coordinates
chr5:28235640-28236418:-
Coord C1 exon
chr5:28236301-28236418
Coord A exon
chr5:28235795-28236300
Coord C2 exon
chr5:28235640-28235794
Length
506 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAAA
5' ss Score
4.51
3' ss Seq
GCCTCTCCCGCCGGTGCCAGGTT
3' ss Score
7.36
Exon sequences
Seq C1 exon
AAACTGGACGACACCAGCTCCTCTGAAGGAAGCACCATTGACATCAAACCAGAAGTAGAAGAAGTCCCTGTGGAGCAGCCTGAGGAATACTTGGATCCAGATGCCTGCTTCACGGAAG
Seq A exon
GTGAAAGGGGGCCAGGAGAGCGGATGGCATGTAGCACTTGCATGGCTTGCAGACAACGTTTATGCTAGGGTCCGTGGTTGGCCGGGGAGAAGGGGGCTCTGTGGGTATCTGCAGGAACTTTGTTCCCTGCCTCATCAGTTTCAGGGAGGCTGATACCATTTTCCCCATTGGATGCTCAGCTGTAACAAGTTTTTATTCTCAAACTTTTCTTTGTCCATTTTTCTCAACATCAGCCCCAAGACTTCCACTGTGTCTGCCTCCTGACTACCCTCTTCTCCTCCCGCTCACTGCTTCTTTATAGGATATCTTCCCATCACCAGAGGGCCTTGCCCTGGCTGCCTGGCAGCATAGCTTCAGCCCCACCACCCTCTCCACTTCTGAGTCAAAGATTCTGAGTCAGCCGCTGAACTCCCGTTGTGCTGTGTGGTGGGGCAGCACCTGGGGGGCCCGGGCGCTCTGGGCGGGGCACGTCCCACAGTCTGATCTGCCTCTCCCGCCGGTGCCAG
Seq C2 exon
GTTGTGTCCAGAGATTTAAGTGCTGCCAGGTCAACATTGAGGAGGGACTGGGCAAGTCTTGGTGGATCCTGCGGAAAACCTGCTTCCTCATCGTGGAGCACAACTGGTTCGAGACCTTCATCATCTTCATGATTCTACTCAGCAGTGGTGCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021339:ENSBTAT00000061543:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.575 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(17.9=100)
A:
NA
C2:
PF065128=Na_trans_assoc=PD(20.2=84.6)
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:
GACGACACCAGCTCCTCTGAA
R:
GGCACCACTGCTGAGTAGAAT
Band lengths:
264-770
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]