RnoINT0131624 @ rn6
Intron Retention
Gene
ENSRNOG00000012134 | Scn4a
Description
sodium voltage-gated channel alpha subunit 4 [Source:RGD Symbol;Acc:3636]
Coordinates
chr10:94510146-94511229:-
Coord C1 exon
chr10:94511092-94511229
Coord A exon
chr10:94510251-94511091
Coord C2 exon
chr10:94510146-94510250
Length
841 bp
Sequences
Splice sites
5' ss Seq
AAGATGAGT
5' ss Score
2.29
3' ss Seq
CTGTCTCTGTCCTACTATACTTT
3' ss Score
0.2
Exon sequences
Seq C1 exon
AAAGAGGAGCAGCCAGACTATGAGGTGAACCTCTACATGTACCTCTACTTCGTCATCTTCATCATCTTCGGCTCCTTCTTCACCCTCAACCTCTTCATCGGTGTCATCATCGACAACTTCAACCAACAGAAGAAGAAG
Seq A exon
ATGAGTATCCAGCCCACCCCAGAGGCTCCCCTCCCCCATCCACCTACTCCCTCCTAGGCATGAGCTGCCTGAGCAGCCTCGAGCAGTCACTGACCTAGACGCTGGGGCAGCAAGCATGGATCTAAATCCCACTAGGGACTGAGCAGGGCCTCGAGCCCCGTGAGCCTCGTTTTTCTAATCTATAAAATAAGGTTGATGTAGAGACAGACATGGTGACACACACCTGGAATTTTATTCACTAACAGATCTGAGGGAGTAAGTTCATAAGTTGCAGGCCAGCCTGAGCTACATAGTGTATTTGAGGCCAGCCTTGGCTATAGAGAGAGACCCTATCTCAATAACAATAAATAAAACAGCTATAGACTAAGGACTAACTCATTAGTGAAACATTGGTAGAGCTTAGCCTGAAACTGGGAAATTGGCCTGAAACCCTCTTTGTCTGCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTGTTGCTGGGTTGTTTGGTTTTTTAAGACAGGGTTTCTCTGTGTATCCCTGGCTGTCCTAGAACTCACTCTGTAGACCAGGCTGGCCTCAAACCTACCTCTGTCTCCCAAGTGCTGGGATTAAAGGTATTGCCACCACCACTGCCTGGCTCACACACACCCACTTCTGTAGACCCAGTTTCTCCCTTCCTCACCGCTTTATCTCTTGTCTCTCCAGAGCCTTGGCCTTCCCAGTCAGACACTTCTTAAAGGGGAAAGCCACCCTCAAGGTGGTATTTGAAGTAGGGGTCCGGGAAGCAGGGAAAGGGACCTATCTCAGTCTTACTGTCTCTGTCCTACTATAC
Seq C2 exon
TTTGGAGGGAAAGACATCTTCATGACAGAGGAACAGAAGAAATACTACAACGCGATGAAGAAGCTTGGCTCCAAGAAGCCCCAGAAGCCAATTCCCCGGCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000012134:ENSRNOT00000016841:22
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=PD(15.4=76.1)
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:
AGGAGCAGCCAGACTATGAGG
R:
CTGAGGCCGGGGAATTGG
Band lengths:
239-1080
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]