DreINT0131435 @ danRer10
Intron Retention
Gene
ENSDARG00000086819 | scn1a
Description
sodium channel, voltage-gated, type I, alpha [Source:ZFIN;Acc:ZDB-GENE-040426-751]
Coordinates
chr9:50246329-50246925:-
Coord C1 exon
chr9:50246687-50246925
Coord A exon
chr9:50246506-50246686
Coord C2 exon
chr9:50246329-50246505
Length
181 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGA
5' ss Score
8.24
3' ss Seq
TCCTTTTTTATTGGCCACAGGTT
3' ss Score
8.81
Exon sequences
Seq C1 exon
GTTCAGAGATCTTTAAACAGAGGTGTGAGGAGTGGTGGTTCGAGTTTGCGGAGAATTATTTGATCTGGGATTGCAGTCCCACATGGCTGAGGATAAAGGAGGTCGTCCACATGATTGTGATGGACCCGTTTGCGGATCTGTTTATCACCATCTGCATTGTGATAAACACAGTATTCATGGCCATGGAGTGTTACCCTATGGATGGACCATACTCTAGTATGCTTTCGACTGCTAATGTG
Seq A exon
GTAAGAGCGTTTACTGTATAACAGCATTTTAGGTAAAATTTTATTTTGCTAGATATAATAATTATTAACTAAAGTGTTACTAGTAACTATTAAATAAAAAATATTAACTAAAGTGTTACTAGTAGTTATTAAGTAATAATTATTAACTAAAGTGTTACTAGTCCTTTTTTATTGGCCACAG
Seq C2 exon
GTTTTCATTGGCATCTTCACAGCAGAGATGATATTCAAGGTCATTGCGTTGGACCCGTACAGTTATTTTCTGGAAGGCTGGAATATCTTCGACAGCATCATTGTCACTTTGAGTCTGATGGAACTTTGTCTGGCAAATGTTTTGTCTGGAATTGGATTTCTAAGACCATTTCGACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000086819:ENSDART00000161648:7
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=PU(1.6=3.8)
A:
NA
C2:
PF0052026=Ion_trans=FE(30.9=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:
TGAGGAGTGGTGGTTCGAGTT
R:
CATCTCTGCTGTGAAGATGCCA
Band lengths:
244-425
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]