DreINT0131576 @ danRer10
Intron Retention
Gene
ENSDARG00000018032 | scn8ab
Description
sodium channel, voltage gated, type VIII, alpha subunit b [Source:ZFIN;Acc:ZDB-GENE-060906-2]
Coordinates
chr6:39461795-39462392:-
Coord C1 exon
chr6:39462272-39462392
Coord A exon
chr6:39461883-39462271
Coord C2 exon
chr6:39461795-39461882
Length
389 bp
Sequences
Splice sites
5' ss Seq
CATATCCTT
5' ss Score
-20.06
3' ss Seq
TCCTTAACTAATTCTTACAGTTT
3' ss Score
5.94
Exon sequences
Seq C1 exon
ACCTTTATAGTGCTTAACAAAGGAAAAACAATCTTCCGTTTCAGTGCCACGCCCTCATTATATATCATTAGTCCTTTTAACCTGTTCAGGCAAATAGCAATTAAAATTTTGATACACTCAT
Seq A exon
ATCCTTTTCAATGCTTCAAACTTTGACCATGTGTTTGTGGTTGTTCTTGCTGAAACCTCGGTTGTTCTCGCTGTGATCTGTGTCTGTCTCACTGAGAGCTGACTACCATGCTTTGTAGGATTTTTGTTACATTCTGTTTCAGATTATGTGATTTAACCTTTTCTCAAATGTTAAACTCAGTGATAGTGATAGTGCTGCCTGAAGTAATTTAAAAAGCATTAATCATGGAGATTGATAACACACTATTACTTCCTCATGTAAAGTGTTATCCCTTTTACAGCATGTTCTCAGATTTACCTAATTTCTTGGTATAAGTGTTCCATCATAGCTTTGATATCTGACTAATATTCATGACATCACTACAGGATTTCCTTAACTAATTCTTACAG
Seq C2 exon
TTTTCAGCATGATCATCATGTGTACAATTTTGACAAATTGTGTCTTCATGACATTCAGCAATCCTCCAGAATGGTCCAAACAAGTAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000018032:ENSDART00000151299:3
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(0.8=6.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCTTTATAGTGCTTAACAAAGGAAA
R:
ACTTGTTTGGACCATTCTGGAGG
Band lengths:
206-595
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]