DreINT0131540 @ danRer10
Intron Retention
Gene
ENSDARG00000005775 | scn8aa
Description
sodium channel, voltage gated, type VIII, alpha subunit a [Source:ZFIN;Acc:ZDB-GENE-000828-1]
Coordinates
chr23:27348380-27348769:-
Coord C1 exon
chr23:27348652-27348769
Coord A exon
chr23:27348535-27348651
Coord C2 exon
chr23:27348380-27348534
Length
117 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAG
5' ss Score
9.06
3' ss Seq
AAATGTTTGCTGTTTTACAGCTT
3' ss Score
7.72
Exon sequences
Seq C1 exon
TTGGATGACATCAGCTCTTCAGAGGGCAGCACCATAGATATTAAACCAGAGGTAGAGGAAGCAGTGGTGGTGGAGACGGTAGAGGAATATGTCGATCCAGAAGCTTGCTGGACTGAAG
Seq A exon
GTAAAGGGCTTATCGATTGTTGTTTTCTTCTTCCTCTGTTTGGAGACTATTATACATTTTTTAAATGTAGAACATATAAGAATCATAAGATTAATTGAAATGTTTGCTGTTTTACAG
Seq C2 exon
CTTGTATTGCCCGCTACAAGTGTTGCGATGTGCCCATCACGGAAGGCTGGGGCAAGAATTGGTGGTTTCTCCGAAAGACCTGCTATCTGATTGTGGAGCACAACTGGTTTGAAACCCTCATCATCTTCATGATCCTCCTCAGTAGTGGAGCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000005775:ENSDART00000022042:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.150 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:
TTCAGAGGGCAGCACCATAGA
R:
AGTGCTCCACTACTGAGGAGG
Band lengths:
255-372
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]