RnoINT0131625 @ rn6
Intron Retention
Gene
ENSRNOG00000012134 | Scn4a
Description
sodium voltage-gated channel alpha subunit 4 [Source:RGD Symbol;Acc:3636]
Coordinates
chr10:94508513-94510250:-
Coord C1 exon
chr10:94510146-94510250
Coord A exon
chr10:94508784-94510145
Coord C2 exon
chr10:94508513-94508783
Length
1362 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCA
5' ss Score
7.88
3' ss Seq
CATGTTCCGTGTCACTGCAGAAC
3' ss Score
9.36
Exon sequences
Seq C1 exon
TTTGGAGGGAAAGACATCTTCATGACAGAGGAACAGAAGAAATACTACAACGCGATGAAGAAGCTTGGCTCCAAGAAGCCCCAGAAGCCAATTCCCCGGCCTCAG
Seq A exon
GTACCAGGTTCTGGGCCCTCCTCCTGTAACCTCTAACAGGCTGCTGCCTAAGAGGACAGCAGGAATCCATGCAGCCTGCATTCTGCCTTTGGGGACTCAACCTCACAAAGGCTCCGCTCCCAAGCACAAGTGTCTCTTGGCTCCTTACAGCTCATCTAGCACCACAAAGCTTTCCAGTATCGACCCACTTTCTCAAGTGGGACCTCTGGCCTGTGAGACAGGAACAGGTTGTGGAGGGCCACACACCCAGCAAGCAATGACTTGGGAAGAATGGATGGAGAGGGAGAGAACTGGGGAACTTCATAGTGATGAAGGGTCCCAGAGTGGAGACTGATGAATATAGAGCGCGCGCACACACACACACACACACACACACACACACACACACACACACACTCACACACACTCGCATACTCACACACACTCTCACACACATATACACACTCATACACAGACTCACACACACTCTCACACACTCACACTCACACACACTCACATACACTCACACTCACATACACTCACATGCACTCACGCACACACACATACACACACTCACATACATACACACACTCACACATACACACACACTCATGCACATACACACTCACATATATACACACACTCACATACACACATACACACACTCATGCACATACACACTCACATACATACACACTCACATACACACATACACACACACTCATGCACATACACACTCACATACATACACAGACTCACACACTTACACTCTCTCACACACACTCACACACTTACACTCTCTCACACACACTCACACACTCACACACTCACACACACTCTCACACACATATACACACTCATACACAGACTCACACACTTACACTCTCACACACACTCACACACTCACACACACTCACATACACTCACACTCACATACACTCACACTCACATACACTCACACTCACATGCACTCACGCACACACACATACACACACTCACATACACACACACTCACATACACACATACACACACTCATGCACATACACACTCACATACATACACACACACTCAGCACACATAACACACACTCATGCACATACACACATTCACACACTCACACTCACATACACACACACTCAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGAGAGAATGATGTTCTAGAGCCTTCCCTCCTGTGGCATTCTTCACCAGTATCCTTTACCCCTTCTCCCCATTCTCCCCTCCTCCCCATGCTATTTTCGTGCCATCCTGTGCCACCCATGTATACCCATCCTGTCTGGGTCCTGATCATCTCCCCAACCCCATGCCCCACCTGTGCATGTTCCGTGTCACTGCAG
Seq C2 exon
AACAAGATCCAGGGCATGGTGTACGACTTCGTGACGAAGCAGGTGTTTGACATCTCCATCATGATCCTCATCTGCCTCAACATGGTTACTATGATGGTGGAGACAGATGACCAGAGCCAGCTCAAGGTGGACATCCTGTACAACATCAACATGGTCTTCATTATCATCTTCACAGGGGAGTGTGTGCTGAAGATGTTTGCCCTACGCCATTACTACTTCACCATTGGCTGGAACATCTTTGACTTTGTGGTTGTCATCTTGTCCATCGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000012134:ENSRNOT00000016841:23
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(20.4=47.3)
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:
GGAACAGAAGAAATACTACAACGCG
R:
ACGATGGACAAGATGACAACCA
Band lengths:
345-1707
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]