RnoINT0131511 @ rn6
Intron Retention
Gene
ENSRNOG00000032884 | Scn11a
Description
sodium voltage-gated channel alpha subunit 11 [Source:RGD Symbol;Acc:3630]
Coordinates
chr8:128466804-128467582:-
Coord C1 exon
chr8:128467481-128467582
Coord A exon
chr8:128467074-128467480
Coord C2 exon
chr8:128466804-128467073
Length
407 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAC
5' ss Score
7.56
3' ss Seq
CTTTGTGTTGTCTCCCCAAGGTT
3' ss Score
9.62
Exon sequences
Seq C1 exon
GTGTCTGTGCTCAGTCTCATGAATCTACCAAGCTTGAAGTCCTTCCGGACTCTGCGGGCCCTGAGACCTCTGCGGGCGCTGTCCCAGTTTGAAGGAATGAAG
Seq A exon
GTACACGCGCAGGTGGATGGGCGGGAACCAGCTATCAGGACTGAAAGAAACTAACTGCCCTCGGTCTTTCGTCAAGACTTTCCTGGGGTCCTACCCAACCAGACCAGGGCCTGGACTGTGAGAAGTGAGAAGACTGGTATGAGTTATCTATCTCAAAACAGCCAAGGGCTCTGTCCTCCCTGAATCCAGGGAAAGACACACCCCATGTACGTCTAGTGTCATTGTCACAGGGCACTTTGGAGGTCATCCTTGGTGGCCATATGACTGGAAAGCTGGGCCAGGAGAGAGAGGTTCAGAATAAAGACAGAAGGACTCTAGGGGCCCTGACCTGCATAGTGGGTCTCCCCTGGAAGACAGAGGTTGGGTGGCCCTGTTTGTAACTCTTTCCTTTGTGTTGTCTCCCCAAG
Seq C2 exon
GTTGTCGTCTACGCCCTGATCAGCGCCATACCTGCCATTCTCAATGTTTTGCTGGTCTGCCTCATTTTCTGGCTCGTATTTTGTATCTTGGGAGTAAATTTATTTTCTGGGAAGTTTGGAAGGTGCATTAACGGGACAGACATAAATATGTATTTGGATTTTACCGAAGTTCCGAACCGAAGCCAATGTAACATTAGTAATTACTCGTGGAAGGTCCCGCAGGTCAACTTTGACAACGTGGGGAATGCCTATCTCGCCCTGCTGCAAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000032884:ENSRNOT00000034025:21
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(15.1=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(40.8=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:
CCAAGCTTGAAGTCCTTCCGG
R:
CTTGCAGCAGGGCGAGATAG
Band lengths:
343-750
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]