BtaINT0129428 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019385 | SCN3A
Description
sodium channel, voltage gated, type III alpha subunit [Source:HGNC Symbol;Acc:HGNC:10590]
Coordinates
chr2:31209349-31210061:+
Coord C1 exon
chr2:31209349-31209477
Coord A exon
chr2:31209478-31209969
Coord C2 exon
chr2:31209970-31210061
Length
492 bp
Sequences
Splice sites
5' ss Seq
GGCGTGAGT
5' ss Score
7
3' ss Seq
ACTCTGATTTAATTCTACAGGTA
3' ss Score
9.49
Exon sequences
Seq C1 exon
GTACACATTCACTGGAATCTATACCTTTGAGTCACTTATAAAAATCTTGGCAAGAGGGTTTTGCTTAGAAGATTTTACATTCCTTCGTGATCCATGGAACTGGCTGGATTTCAGTGTCATAGTCATGGC
Seq A exon
GTGAGTATTTTTAAAAACATGTTAAGCTCAAAGGCATGAAACAGTTGTAGCATAAAACAGGTTGTTGTGACATATTTTAAATGTAGAGTTTGCTTGTTAGCCAAATTAACTATATGCCGCATATATTTTGAGAATACATATTAGAATATATATTGCAAGGTAAATGTATCTGATAAATGAGCAATAAATGGAATCACTTTCATGTCATAGTCTTCTACTTCATCAAAATGAAGTTATTCATTGACTATAAATTTAATACCACCAACTGTACTTTAATTAGTTTTGCAAACAAACGTTCATATTAGTGAAAACTGTATTGAAATAAAGCAACAAAATTTTATTCCTTAAAGGCAGCTTTTAGCACATGGCACCCTGAAGTCTAGCATTTCCGTAAAATTCAAGGGGCTCTATATGCCAAACCAACCCACTTTTCATTCTTTATGTAGTATAAACTTTGCCAAAACTATCAGTAACTCTGATTTAATTCTACAG
Seq C2 exon
GTATGTAACAGAATTTGTAAACCTAGGCAATGTTTCAGCTCTTCGAACTTTCAGAGTCTTGAGAGCTCTGAAAACTATTTCTGTAATTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019385:ENSBTAT00000025829:4
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(16.0=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(11.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTACACATTCACTGGAATCTATACCT
R:
TACAGAAATAGTTTTCAGAGCTCTCA
Band lengths:
214-706
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]