RnoINT0131512 @ rn6
Intron Retention
Gene
ENSRNOG00000032884 | Scn11a
Description
sodium voltage-gated channel alpha subunit 11 [Source:RGD Symbol;Acc:3630]
Coordinates
chr8:128465398-128467073:-
Coord C1 exon
chr8:128466804-128467073
Coord A exon
chr8:128465452-128466803
Coord C2 exon
chr8:128465398-128465451
Length
1352 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGT
5' ss Score
10.36
3' ss Seq
GGTTTCTACTTCTGTTTCAGGCA
3' ss Score
8.43
Exon sequences
Seq C1 exon
GTTGTCGTCTACGCCCTGATCAGCGCCATACCTGCCATTCTCAATGTTTTGCTGGTCTGCCTCATTTTCTGGCTCGTATTTTGTATCTTGGGAGTAAATTTATTTTCTGGGAAGTTTGGAAGGTGCATTAACGGGACAGACATAAATATGTATTTGGATTTTACCGAAGTTCCGAACCGAAGCCAATGTAACATTAGTAATTACTCGTGGAAGGTCCCGCAGGTCAACTTTGACAACGTGGGGAATGCCTATCTCGCCCTGCTGCAAGTG
Seq A exon
GTAAGTTCTGTGGGTCTGTGTCTGCATCCAGGAAGGAAGCTTGGAAGAGTGATCAGTCACTAAAAACATAGTCACTCCACCAAGACTGGATCCCAGTCCTGCTCGCAGGGTGGGGCGGGGCAGAGTCTTTTCACCTGGAGTTTCTCACTTTTCTCATTTCTTTGACAAAAACACCTGGCGCAGTAGTTACTTTTCTGTTGCTGTGATAAAATACCAGACAAAAAGAAAGTTTCTTTTAAAAGTCTTTCTTAGATTTTATTATAGCTTATAGCTCTAAAGGGAACACAGTCCATCATAGCGGGAGAGCATGGTGGGAGGATCAGGAAGCTGGCTATCATATCTCCTCTATACACTACATACATCTATAGGCACCTTATAAATCCTCAACTCCCATCCCCAGTGACGCACTTCCTCCAGCAAGGTTCCACTTCCTAAAAGTTCTATAATCCTCCCCAACTGCACTGTCAAGTGGGACCCAGGGAGCTTATGGGGGCGGGAGCTTATGGGGGCGGGAGCTTATGGGGGCGGGAGCTTATGGGGGCGGGAGCTTATAGGGGCTGCATTTCTCATTCAAAGCACAATACCTGACAAAGGCAATTTAAGGAAGGGCTGTTTTTGCACATGCTTTGAGGGACTGGGCCGCCATGGTGGTGAGAATTGTCTAGATGCGGAGGGCGGCAGGAGTGTGAGGAAGCTGGTCCTACTGGCTCTACAGTCAGGAGGGAAGTAGGCAGAAAGAGACAGATGCCGGTGCTTTTTCATTTTTTACTCACCAGCTTGTGGGACGGTGCCGCCCATGTTCAAGATGAGTCTACTGTCAATTAAATATCATCAGAAACACCTTTACCACACTCCCTGATGTGGGTCTCTAAGACTTCCAAAGCCAGTCCGGTTGACAGTGAAGCCCCTTCAGGGTTTTAAATGGCTTGCTTTGTCTTCTATGGTACCTTGCTTGTTGTTCAGATCACCTGCTAGACAGGAGAGCCTTTGGTGCAGGTCAGGGCATTGTCACTATCTTTTTTTTCCAAGCAGCAGCAACAGCAGCCAGCCAGGTGTTGGTCAGGCAGCACAAAAATCGTGTGCTATCTTGGCTCTTCCCAAGTAACCTTTTGTGTAGACGTTGAATTTGTTTTTAAATCATTAGTCTTGGGAGAATAAAGAAGACCGAGATTGGGCACAACACCCCTCCTCATGTCCAGGACTGTTCTTCCCTGCCGACCTCTCTCTGGGGCAGGATAGAGGGTCACCTTACACCCACCCACCAACAGGGTTTGACAAGCTTTTGCGTGGCAAGCCTCTCTTGATGAAAAAAATGTCTACATCTGTGTCTGAGGTTTCTACTTCTGTTTCAG
Seq C2 exon
GCAACCTATAAGGGCTGGCTGGAAATCATGAATGCTGCTGTCGATTCCAGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000032884:ENSRNOT00000034025:22
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=FE(40.8=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(7.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTGTCGTCTACGCCCTGATC
R:
CTCTCTGGAATCGACAGCAGC
Band lengths:
324-1676
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]