RnoINT0131618 @ rn6
Intron Retention
Gene
ENSRNOG00000012134 | Scn4a
Description
sodium voltage-gated channel alpha subunit 4 [Source:RGD Symbol;Acc:3636]
Coordinates
chr10:94514057-94515985:-
Coord C1 exon
chr10:94515831-94515985
Coord A exon
chr10:94514231-94515830
Coord C2 exon
chr10:94514057-94514230
Length
1600 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGC
5' ss Score
6.99
3' ss Seq
GTTTGTGCTGGTGTCCCCAGGCC
3' ss Score
9.58
Exon sequences
Seq C1 exon
CCTGTGTGAAGCGCTGCCCCTGCCTCTATGTGGACATCTCCCAGGGCCGTGGGAAAATGTGGTGGACACTGCGCAGGGCCTGTTTCAAGATTGTTGAGCACAACTGGTTTGAGACCTTCATTGTCTTCATGATCTTGCTCAGCAGTGGAGCCCTG
Seq A exon
GTAGGCACCCTCCCCCAGGGGACAGGGCGGGAGCAGGAGTAGGTGCCTTGCTCCCTAAGGCTTCCATACCAAGGATGGAGACAGACCGGACATGTCCAAACCCAGGGGATCTGAAGGGGAGGGGACGCATCTGTGTGTGTGTGTGCGTGTGTGTGTGTCTCTGTCTCTGTGTGTGTGTGTCTGTCTGTCTCTGTCTCTGTCTCTGTGTGTGTCTGTCTGTCTCTGTCTCTGTCTCTGTGTGTGTCTGTCTGCCTGTCTCTCTGTGTGTGTGTGTGTCTGTCTGCCTGTGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGTGTGTGTGTGTCTGTCTGCCTGTCTCTGTCTCTGTGTGTGTGTGTCTGTCTGTCTGTGTGTGTGTGTTTGCGTGTGTGTGCGCGCGCGCGCGTGTGTGTGTGTGTGTGTGTGGTGTGTGTGTGTCTGTCTGCATGTCTCTGTCTCTGTGTGTGTCTGTCTGTCTGTGTGCGTGTGTGTGTGTGTGTGTGTGTGCGTGTGTGTGTGTGTGCGCACGCACGCATGAGAGTGTGTTGTGGATGGTAGGCGTCTTTCTCAATTGTTCTCCATCTTTTGCATTGAGACAGGGTTTCTCACTGAACCTGGAGCTTGCTGTTTGGGTTGTTTGAGGGGATTTCCTGTCTCTGTCTACTGTAAGCCTGGCATTGCAGGCAGGCCGCTGCTGCCACCTGGCTTTGACATAGGTTCTGGGAGCCCAAACTTCCAGCTCTCGCATTTGCAGGACAGATAAGGCACCTCCCCAGCCCAGCATTCATTTTCTTAAAGTAAAAGACGGGGCCCTTTGTTTCGTGGACCCTGTCCCCTCAGCCAACGGGAGGTGGGTGGGAATTTGAAGTTAAGGGTGGACAGGACTGAAGACACATTATATTGTCGACCCCCGGAAGATAGTCGAGAACGAAGACTCCTTCCCTACCAGGAGTCTCGCCCCTCCTGGTGATGGGGATGGAGATGGAAGATACGCAGAGGCCCTACAACCTACGACCCCTGAAAGACCCCTGGGAACCAGCCACAGCAGGCAGGATGGGGAGCAGCGCTTGCTGCCCCATCTGCCGAGCCCCTGGCCATCGTGGTTTGTGCTGGTGTCCCCAG
Seq C2 exon
GCCTTCGAAGACATCTACATTGAACAGCGACGAGTCATCCGCACCATCCTGGAATACGCCGACAAGGTCTTCACCTACATCTTCATCCTGGAGATGTTGCTAAAGTGGGTCGCCTACGGCTTCAAGGTGTATTTCACCAATGCCTGGTGCTGGCTCGACTTCCTCATCGTGGAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000012134:ENSRNOT00000016841:17
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:
PF065128=Na_trans_assoc=PD(19.6=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(17.1=67.2)
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:
CTGTGTGAAGCGCTGCCC
R:
GTCCACGATGAGGAAGTCGAG
Band lengths:
328-1928
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]