DreINT0131486 @ danRer10
Intron Retention
Gene
ENSDARG00000098738 | scn4aa
Description
sodium channel, voltage-gated, type IV, alpha, a [Source:ZFIN;Acc:ZDB-GENE-051201-2]
Coordinates
chr12:4851703-4852097:+
Coord C1 exon
chr12:4851703-4851835
Coord A exon
chr12:4851836-4851942
Coord C2 exon
chr12:4851943-4852097
Length
107 bp
Sequences
Splice sites
5' ss Seq
AGGGTTTGC
5' ss Score
0.36
3' ss Seq
GGGTCTCTCTTTAAACTTAGGCT
3' ss Score
6.22
Exon sequences
Seq C1 exon
GCCACTCTTAATGATGGTGACTCTTCGGTTTGTAGCACAGTGGACTACCAGCCTCCAGAACCTGAGCCTGAACCTGAAGAGGTAGAAGAAGAGGAACCAGAACCTGAAGAACCAGAGGCCTGTTTCACAGAGG
Seq A exon
GTTTGCATTCATTTTCCTTCATTTTTGACCATACTGCACTCATCGTATATCAAGGCCATAAATGTCATTTATTATATGTTTATTAATGGGTCTCTCTTTAAACTTAG
Seq C2 exon
GCTGTATTAGGCGATGTGCATGTTTGAGTGTTGACATCACAGAAGGATGGGGTAAAAAATGGTGGAACCTCAGAAGGACATGCTTCACCATCGTTGAGCATGATTACTTTGAGACCTTCATCATCTTTATGATCCTCCTTAGCAGTGGAGCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000098738:ENSDART00000170961:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.778 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(23.4=100)
A:
NA
C2:
PF065128=Na_trans_assoc=PD(23.4=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:
TGGACTACCAGCCTCCAGAAC
R:
CTCCACTGCTAAGGAGGATCA
Band lengths:
243-350
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]