DreINT0131574 @ danRer10
Intron Retention
Gene
ENSDARG00000018032 | scn8ab
Description
sodium channel, voltage gated, type VIII, alpha subunit b [Source:ZFIN;Acc:ZDB-GENE-060906-2]
Coordinates
chr6:39397433-39399285:-
Coord C1 exon
chr6:39399181-39399285
Coord A exon
chr6:39397704-39399180
Coord C2 exon
chr6:39397433-39397703
Length
1477 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGC
5' ss Score
8.69
3' ss Seq
GTGTGTTTTCTTTCTCATAGAAC
3' ss Score
10.19
Exon sequences
Seq C1 exon
TTTGGAGGTCAGGATATCTTCATGACAGAAGAACAGAAAAAATACTACAATGCTATGAAGAAACTGGGCTCAAAGAAGCCACAGAAACCCATCCCTAGACCTCTG
Seq A exon
GTAAGCACACAGATATACAATGTTTATTGTAATTCCCCCTGAATTATAAGCGCTCCTGTTTATTTTTTTCCCTAATTTCTGTTAAATGAAGTAAAGATTGTTTCAGCACATTTCTAAGCATAAAAGTTTTAAAAACTTATTTCCAATAACGGATTTATTTTATCTTTGCCATGATGACAGTAAATAATATTTTACTACATATTTTTCAAGACACTTCTATACAGCTTAAAGTGACATTTAAAGACCTAACTAGGTTAATAAGGTGAACTAGGCAGGTTAGGGTAATTAGGCAAGTTATTGTTAACTTGCCTAATTACCCTAACCTGACTAGTTAACCTAATTAACCTAGTTAAGCTTTTAAATGTCACTTTAAGCTGTTTAGAAGTGTCTTGAAAAATCTAGTAAAATAGTATGTACTATTATAATGGCTAAGGTAAAATAAATCAGTTATTAGATATAAGTTATAAAAACTATTATTTTTAGAAATGAGTTGAAAAAATATTCTCTCCAGTAAACACAAATTAGACAAAAAAAAAAAAAAAAAAAAATATATATATATATATATATATATATATAAATATATATATATATATATATATATATATATATATATATAAAGCCCTCATAGTTTACTGACAAGCTTTGTACTGTAAATATTGCTTGATTTTAAAATAATTAAAGGAAACAAACACTGCCTACTATCTATGATTATTTATTAACATCAACGTTAAATAACTAAAATTAAAACATACATTACCTAAAATCAACAGCCACTTTTTTCTAATAAAAAAGTAAAAATAAATAGCTTGCACGTTTGGAAATAAATTTAATTATTTTCAAGTATAAAATAAATAAAATAACTCTTGTATATCCTGTAAATAATATTTTAAATTTTGCATTAACTGCATTTTATGTAAACAAATATTTTAATGTAAATAATAATTATAATGTAATGGAAAATATGCCCTCTTAAGGCATCTCTGGCGCAGCTTCCAATTATCGTCAATGTAGTGTAAAGAAAGGCTCAAGAGTGGGTCCATCGTCCTACTTAACCAGAGATCAGATGTGGCTGCAAAATGGCTGGATGAGTTTAAAACAGCCATTAAAAAAAGGCTTAAAAGAGCGGTTCATGTAATTCCATGTACGGTAGGAAAAGTAAGTTAAAAACTAGATTGATTCTAGGTTCTGAATGTCGATTTCGATTACTTTTTAATTAATCGTCCAGCCCTATTTACATTTGAATACATTTTAAAATATTAATTCAACAGTTTTACATTTTCATTTGTCAATTGACTAAATTTATTTATTATATTACATTTAGCTACATTTATAAAAGTTTAAAATGGTATTTTAACTATTGATTTGTAATGTCATTTTTTATTTTATGAATTTCTTTAGCTTTTTTTATTATTAGATGAAGTCGCACTTCTAGTCCACTGTTGTAATTGTGCGCCAATGTGTGTTTTCTTTCTCATAG
Seq C2 exon
AACAAAATCCAGGGGATGGTATTTGACTTTGTCACTCAGCAGGCCTTTGATATTTCCATCATGATGCTCATCTGTCTTAACATGGTAACCATGATGGTGGAAACAGATGATCAGTCAGACGAGACAGAGAACATCTTGTATTGGATAAACTTCGTATTCATCGTGGCCTTCACTGGCGAGTTCGTCCTGAAACTCTTTGCGCTGCGACACTATTATTTCACCAATGGCTGGAATGTCTTTGACTGCGTCGTTGTCATTCTGTCCATTGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000018032:ENSDART00000151299:25
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:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(20.5=47.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGAGGTCAGGATATCTTCATGA
R:
CGCAGTCAAAGACATTCCAGC
Band lengths:
350-1827
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]