RnoINT0131619 @ rn6
Intron Retention
Gene
ENSRNOG00000012134 | Scn4a
Description
sodium voltage-gated channel alpha subunit 4 [Source:RGD Symbol;Acc:3636]
Coordinates
chr10:94513494-94514230:-
Coord C1 exon
chr10:94514057-94514230
Coord A exon
chr10:94513617-94514056
Coord C2 exon
chr10:94513494-94513616
Length
440 bp
Sequences
Splice sites
5' ss Seq
GACGTGAGT
5' ss Score
9.22
3' ss Seq
TGAACGCACACTTCTTCCAGGTC
3' ss Score
7.77
Exon sequences
Seq C1 exon
GCCTTCGAAGACATCTACATTGAACAGCGACGAGTCATCCGCACCATCCTGGAATACGCCGACAAGGTCTTCACCTACATCTTCATCCTGGAGATGTTGCTAAAGTGGGTCGCCTACGGCTTCAAGGTGTATTTCACCAATGCCTGGTGCTGGCTCGACTTCCTCATCGTGGAC
Seq A exon
GTGAGTCCCCCGGGTCCGGCCACGGAGCCGGGACGTCATGGCCTTTAGAGAACCCAGGCTCTGGGGGGTTTGGGGGGGCCTATCTGAATCTATCCATCAGACCATCCAGGTCAGCACTGCTCCCTGTAGACCAGCCTCTTCTTTCCCAAGCATGACAGTTCAGGCCTGGGTCTTATGATCCCTGCCAGTGCAAGATTCTTATTGATAGACACATGGAAGCATGGGAGATGGGTACCGTCCTTCTCATTTATGGTTGTAGGTGACATCATTGAGGTGAGCCCTGGCTCTAAGGGTGCCAGAGGCCACAAGCCTTCTCTTCCCAACAGACAAGATTATCTATCAGGGATGGGGTCTACAGGAGACACAGAAACTGGGACACCCTTCTCATATGTAGAAAAAAGTCAGGGACCCTCCACCTCCTGAACGCACACTTCTTCCAG
Seq C2 exon
GTCTCCATCATCAGCCTGGTGGCAAACTGGCTGGGCTACTCTGAGCTGGGGCCCATCAAATCCCTGCGCACACTCCGGGCCCTGCGACCTCTGAGGGCACTGTCTCGATTTGAGGGTATGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000012134:ENSRNOT00000016841:18
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:
PF0052026=Ion_trans=PU(17.1=67.2)
A:
NA
C2:
PF0052026=Ion_trans=FE(17.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCTTCGAAGACATCTACATTGA
R:
CCTCATACCCTCAAATCGAGACA
Band lengths:
297-737
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]