RnoINT0131621 @ rn6
Intron Retention
Gene
ENSRNOG00000012134 | Scn4a
Description
sodium voltage-gated channel alpha subunit 4 [Source:RGD Symbol;Acc:3636]
Coordinates
chr10:94540714-94541978:-
Coord C1 exon
chr10:94541307-94541978
Coord A exon
chr10:94540833-94541306
Coord C2 exon
chr10:94540714-94540832
Length
474 bp
Sequences
Splice sites
5' ss Seq
AAGGTCTGG
5' ss Score
3.93
3' ss Seq
AGTTTCTCTCCCTGCCTCAGACC
3' ss Score
7.51
Exon sequences
Seq C1 exon
GCTGAAGTCACGCAGTTCCTGGAGTCTGAACCCAGGAGACAGTTCGGGACACTGGGGCGTTGGCCCCAAGCTCCTCAGGCTGGAGAAGATCTGGTTCACTTTCTGTTGATCCCGAAGGTGGCACAATCTATTGCTGAGAAGAGAACACTGCGGGGCCTGGAGTGGGGGAATGCACCGTGCCCAGTGTCCTGGGCATCAGCACGCCCAGGTCTTGCAGGCACATCTCCCAGCCCCAACAAGACCAGGACACCCACCTCCCTGACCCAACTCCTGGGCAGGCAGAGAGTGAGGAGTACACAGTAGACCCCGGGCATTGGTGACCACCCAAAACCCAAGGGCTGCGGGCTGTAGCGGCTCTGTTACCTACCACCCTCTGGCCCCTGAGCCCAGAATGCAAGGATGGCCAGCTCATCTCTGCCCAACCTGGTCCCCCCGGGTCCCCACTGCCTGCGCCCCTTCACCCCAGAGTCCCTGGCAGCCATAGAGCAGCGGGCGGTGGAGGAGGAGGCCCGGCTGCAGCGGAACAAGCAGATGGAGATTGAGGAGCCTGAGCGGAAGCCACGCAGTGACCTGGAAGCTGGCAAGAACCTCCCACTCATCTATGGGGACCCCCCACCCGAAGTCATTGGCATCCCCCTGGAGGACCTGGATCCTTACTACAGTGACAAGAAG
Seq A exon
GTCTGGATGTGGGAGGGCTCCCCGATCTGTGCAGCCTGTCCATCTGTCTATCTACCATCCATCTGTCCATCCACCTGTCTGTCCATCCACCTGCCTGTCCGTCCACTGTCTGTCCATCCATCTGTCCATCTGTCTATCTGTCTGTCTATCCATCTGTGTGCCTGTCTATCCATCTGTCCATCTGTCCATCTGTCTATCTACCTGTCCATCTGTCCATACATCTATCCATCCATCCATCCATCCATCCATCCATCCATCCATCTGTCTGTCCATCTGTCCATCTGCCTGCCTGTCTGTCCATCTGTCCATCTGTCTGTCCATCCATCCGTCCATCTGTCTATATGTCCACCTGTCCATTCATCTGTCTCTCTGTCCATCTGTCCATCCACTTGTCCATCTGTCAGTCTGTCTATCCATCTGTCCGTCTGTCTGTCCATCTGTCCGTCTGTCTCACAGTTTCTCTCCCTGCCTCAG
Seq C2 exon
ACCTTCATTGTGCTCAACAAAGGAAAGGCCATCTTCCGATTCTCTGCCACGCCTGCCCTCTACCTGCTGAGCCCCTTCAGCATCGTCAGGAGGGTGGCTATCAAGGTGCTCATTCACGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000012134:ENSRNOT00000016841:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.330 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
GGCTCTGTTACCTACCACCCT
R:
TGGCCTTTCCTTTGTTGAGCA
Band lengths:
351-825
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]