RnoINT0131617 @ rn6
Intron Retention
Gene
ENSRNOG00000012134 | Scn4a
Description
sodium voltage-gated channel alpha subunit 4 [Source:RGD Symbol;Acc:3636]
Coordinates
chr10:94515831-94516485:-
Coord C1 exon
chr10:94516350-94516485
Coord A exon
chr10:94515986-94516349
Coord C2 exon
chr10:94515831-94515985
Length
364 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
TGTACCACCCTGCCTCCCAGCCT
3' ss Score
4.48
Exon sequences
Seq C1 exon
AAGCCCCTACAGCCCCTCTACGACGGGAACTCCTCCGTCTGCAGCACAGCTGACTACAAGCCCCCTGAAGAGGACCCCGAGGAGCAGGCTGAGGAGAACCCCGAGGGGGAGCAGCCTGAGGAATGCTTCACGGAAG
Seq A exon
GTGAGATCACACCTACAGACCAGCCCCACACCCAGGTCAGAGGCCAGCAACAGAAACAGTTCTGCTCACTTTGACGGGGGAACCCACACCTGAACCAGAGAGTCATTTGCCAAAGAGCCTAAGCTTGTCGAGATGGTGGCCCGTGGGAATAGCTGACGTCCCGAGCTTGCTTGGGAAGCACTTTTTCTCAGTCTCAACAGCAGTGACATACGGGCTGTGGAGAGCCCCTGAGCTCCTGTGTGAACTAGATGCAGCCACTTGTGGGGAGGAGGTGGGGCCCCAGTCTTGGGTAGCATGGCAGAGGGTGGGGAGGTGTGTTCTGACACAGCCAAAGGCCAGTGACATGTACCACCCTGCCTCCCAG
Seq C2 exon
CCTGTGTGAAGCGCTGCCCCTGCCTCTATGTGGACATCTCCCAGGGCCGTGGGAAAATGTGGTGGACACTGCGCAGGGCCTGTTTCAAGATTGTTGAGCACAACTGGTTTGAGACCTTCATTGTCTTCATGATCTTGCTCAGCAGTGGAGCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000012134:ENSRNOT00000016841:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.696 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(20.0=100)
A:
NA
C2:
PF065128=Na_trans_assoc=PD(19.6=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:
AAGCCCCTACAGCCCCTCTA
R:
GCTCCACTGCTGAGCAAGATC
Band lengths:
287-651
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]