DreINT0131566 @ danRer10
Intron Retention
Gene
ENSDARG00000018032 | scn8ab
Description
sodium channel, voltage gated, type VIII, alpha subunit b [Source:ZFIN;Acc:ZDB-GENE-060906-2]
Coordinates
chr6:39412255-39413217:-
Coord C1 exon
chr6:39413100-39413217
Coord A exon
chr6:39412410-39413099
Coord C2 exon
chr6:39412255-39412409
Length
690 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGC
5' ss Score
8.27
3' ss Seq
ACATGTTTGATGTTTTTCAGCTT
3' ss Score
8.12
Exon sequences
Seq C1 exon
CTGGACGACACTAGCTCTTCTGAAGGAAGTACTATCGATATAAAGCCTGATGAGGAGGAGATGGCTGTGGTGGAGGTGGTGGAAGAGTACTTAGATCCAGAGGCCTGCTGGACTGATG
Seq A exon
GTGAGCAATGCATGTTTGTAAGATCTAATTGGATAGATTCAATATACCTAATATGTATGTGTGTGTATGTATATATTAAATTCAATATCTAGTTTAAGCTACAATCCTAGTATATACTGTATTTCATGGTAGTAGTACGCTGTAAATCCACAGTTTCTGTATTTTATATTTCACAATTGTTTTCTGTTTGTTTACGATTTTAAATTGCATTATGGGATGTTGATTTCTTCTCTGTCAAATTTTGAAGTTGAAAATTCAACTCTACAGTTTAACAAAGTCACTTTTATTGACATTTTAGTACTTTGAAATACTATAAGATTATATACATAATTTATAGAAAAAAATAAGTCCGTAAAACAACAGAAAACGTACTGGCAGCTTATTACAAGGTTTTTGTAACGTAACACACAGCAACAACCCAGGCAATATATGACTTCAAACAATTAAAAATGTTAATAAAAATAACTTTTTTTTCAAACTTTTCAAAGTTAAGTCCCACAATGCAATTTGAAAGCATAAATAAACTGGGAAATATTCAAAATAAATCACAAAATACAGAAAACAGCTAATTTTCAGTTTTTTTTTTTACAGTGTACATCTGTTTTACTTTTAGAACTACTAAAAAACTTACATTTTAAGTCTGGGTATGATGTAAATGTGTATTCAGCTTACATGTTTGATGTTTTTCAG
Seq C2 exon
CTTGTGTGGCGCGCTACAAATGTTGTGATGTGCCTATTACTGAGGGCTGGGGGAAGTACTGGTGGTTTCTGAGGAAAACTTGCTACCTCATTGTTGAGCACAACTGGTTTGAGACGCTCATCATTTTTATGATTCTTCTCAGCTCTGGAGCTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000018032:ENSDART00000151299:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.350 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(17.7=100)
A:
NA
C2:
PF065128=Na_trans_assoc=PD(20.0=84.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGACGACACTAGCTCTTCTGA
R:
CTCCAGAGCTGAGAAGAATCAT
Band lengths:
267-957
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]