RnoINT0131627 @ rn6
Intron Retention
Gene
ENSRNOG00000012134 | Scn4a
Description
sodium voltage-gated channel alpha subunit 4 [Source:RGD Symbol;Acc:3636]
Coordinates
chr10:94540517-94540832:-
Coord C1 exon
chr10:94540714-94540832
Coord A exon
chr10:94540607-94540713
Coord C2 exon
chr10:94540517-94540606
Length
107 bp
Sequences
Splice sites
5' ss Seq
CGCATATCC
5' ss Score
-11.86
3' ss Seq
TTCCTTGACCCACCCCCCACGCT
3' ss Score
-0.95
Exon sequences
Seq C1 exon
ACCTTCATTGTGCTCAACAAAGGAAAGGCCATCTTCCGATTCTCTGCCACGCCTGCCCTCTACCTGCTGAGCCCCTTCAGCATCGTCAGGAGGGTGGCTATCAAGGTGCTCATTCACGC
Seq A exon
ATATCCTGCCTAAGTGGGAGAGGGGGGGAGGGTTGGGGCGGGCGGGAGGCCTTCCCATGCCCTCCTCTCCCCAGCGGCTCCGCCTCTTTCCTTGACCCACCCCCCAC
Seq C2 exon
GCTGTTCAGCATGTTTATCATGATCACCATCCTGACCAACTGTGTGTTCATGACCATGAGCAATCCGCCTTCTTGGTCCAAACACGTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000012134:ENSRNOT00000016841:3
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:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(0.7=6.5)
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:
TTGTGCTCAACAAAGGAAAGGC
R:
TCCACGTGTTTGGACCAAGAA
Band lengths:
202-309
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]