DreINT0131479 @ danRer10
Intron Retention
Gene
ENSDARG00000098738 | scn4aa
Description
sodium channel, voltage-gated, type IV, alpha, a [Source:ZFIN;Acc:ZDB-GENE-051201-2]
Coordinates
chr12:4834291-4834750:+
Coord C1 exon
chr12:4834291-4834542
Coord A exon
chr12:4834543-4834631
Coord C2 exon
chr12:4834632-4834750
Length
89 bp
Sequences
Splice sites
5' ss Seq
AAAGTCAGT
5' ss Score
1.98
3' ss Seq
AACCTCTTTCTCTTTTGCAGACT
3' ss Score
10.9
Exon sequences
Seq C1 exon
ATGGCACGCCTGCTCCCTCCCACAGGCACCAGTGTGTTCCGCCGCTTCACCCCAGAGTCACTGGTGGAGATCGAGAGGCTCATCCAGGAGAAGAGCACCAGGGAGGAACTAGAGGGAGCCGAGGAGGAACCACAGGCACCGAGCAGCGATCTGGAGGCGGGAAAATGCCTGCCGATGATCTATGGCGACCCCCCCGGGGATCTCCTCAACACCCCTCTGGAAGACATCGACCCCTTTTATAAAACACAGAAA
Seq A exon
GTCAGTCTTGTGCCCATTTATGTTAGATGAAGTGATCTCTGTTCATATTGTGTTCTCCAGCTATTTTTTAACCTCTTTCTCTTTTGCAG
Seq C2 exon
ACTTTTATTGTCATAAGCAAGGGAAACACAATCTTCAGGTTCTCTTCTGAACCGGCGATGTTTTGCATCAGTCCTTTTAGTATTGTCAGAAGAGGAGCCATCAAAATTCTTATACATTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000098738:ENSDART00000170961:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.214 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGATCTGGAGGCGGGAAAATG
R:
GATGCAAAACATCGCCGGTTC
Band lengths:
175-264
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]