RnoINT0131640 @ rn6
Intron Retention
Gene
ENSRNOG00000015049 | Scn5a
Description
sodium voltage-gated channel alpha subunit 5 [Source:RGD Symbol;Acc:3637]
Coordinates
chr8:128219495-128220587:-
Coord C1 exon
chr8:128220408-128220587
Coord A exon
chr8:128219867-128220407
Coord C2 exon
chr8:128219495-128219866
Length
541 bp
Sequences
Splice sites
5' ss Seq
TTGGTAATC
5' ss Score
3.39
3' ss Seq
CACCATCCCTGTGCCCTCAGAAT
3' ss Score
8.75
Exon sequences
Seq C1 exon
GCTCTCACCATCAGGGGTGTGGATACCGTGTCCCATAGCTCTCTGGAGATGTCTCCTTTGGCCCCAGTAACCAACCATGAGAGAAAGAGCAAAAGGAGGAAACGACTATCTTCGGGGACAGAGGATGGTGGGGATGACAGGCTCCCCAAGTCGGACTCAGAAGATGGTCCCAGAGCATTG
Seq A exon
GTAATCCTGATGTGGTTCTGGCCTCTGCAGAGCCCATCATGGTGGGCCCCGCCCCCCGTGTGGCCACAGCCCTAAGCTTAATCTCCACAAAAGACAGGCTTGGACCCCTCCCATCCCTTTCAGTTTCCTGTAGTCATTCTTAAAGTGGGGGAGAGTTAGGGTGGATTTATGTGTTAATGCTCCTCCTACCTGGAACTAGTCCTCAAGTATGGGGACCAGCACTGGGAGTGGGGGCTTGTGGGGTGGGGTGAAAGGGGCCCAAGTGCTGATCCTAGCTCTCCTGCCCAGCCAAGGCCCCCTCCAGGCCCAGAGCAGCTTCAGAGTCAAACCCAGAGATACAGGGATGAAATGAGCAGAGATCCCACAAGATACAGGGGACACCCCATCTCTTCCTAAGTCCCTACCTCAGCCCTCCCAGGCTCTTGTGGCCAGCAGAAGCCTCGGTGCCCTCAGAACATGAACTGGGCTGACACCAACCATGATAGTTTGGCCGAAGCAGAGTTTGAGCCCTGTGGGTCACGCACCATCCCTGTGCCCTCAG
Seq C2 exon
AATCAGCTCAGCCTCACCCATGGGCTCAGCCGGACATCCATGAGGCCCCGCTCGAGCCGAGGGAGCATTTTCACGTTCCGAAGACGGGACCAAGGCTCTGAGGCGGACTTCGCAGATGACGAGAACAGCACTGCGGGGGAGAGTGAGAGCCACCGCACATCGCTGCTGGTACCCTGGCCCCTGCGCCATCCCAGCGCCCAAGGACAGCCCGGCCCTGGAGCCTCAGCTCCCGGTTACGTTCTCAATGGCAAAAGGAACAGCACCGTGGACTGCAATGGGGTGGTTTCCTTGCTGGGGGCAGGTGACGCAGAGGCCACCTCCCCAGGGAGCTACCTTCTCCGCCCTATGGTGCTGGACCGACCCCCAGACACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000015049:ENSRNOT00000064555:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.767 A=NA C2=0.827
Domain overlap (PFAM):
C1:
PF119333=DUF3451=PU(21.6=75.0)
A:
NA
C2:
PF119333=DUF3451=FE(59.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAGGATGGTGGGGATGACAG
R:
AAGGAAACCACCCCATTGCAG
Band lengths:
351-892
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]