RnoINT0131515 @ rn6
Intron Retention
Gene
ENSRNOG00000032884 | Scn11a
Description
sodium voltage-gated channel alpha subunit 11 [Source:RGD Symbol;Acc:3630]
Coordinates
chr8:128455816-128457393:-
Coord C1 exon
chr8:128457289-128457393
Coord A exon
chr8:128456087-128457288
Coord C2 exon
chr8:128455816-128456086
Length
1202 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGA
5' ss Score
7.54
3' ss Seq
CTTTCCTTTTTCCTCTTCAGAAC
3' ss Score
12.65
Exon sequences
Seq C1 exon
TTAGGTGGCCAAGACATTTTTATGACAGAAGAACAGAAGAAATATTACAATGCAATGAAAAAGTTAGGAACCAAGAAACCTCAAAAGCCCATCCCAAGGCCCCTG
Seq A exon
GTGAGAGCAACTGACTCTAAGCACACATGCAGGATGCATGATCTAAACACGCAGGTTTCTAAAAAGCCTGTTAACTTTTAAAGGAAGTATTCTTCTTATTGTTTTAAAAGTATTTGTGTATGTGCATCTTTGTGGGTGTACATGTTCATGGGAGTGTGGTGCTTTCAGTGGCCAGAAGGGGGCATCAGATCCCCCAGAGCAGAAGTTAAAGGCAGTGGTCAGCCATCTGACCCAGATGCTTAGGGAATGAATGCAGGACCTCTGCAAGAGCAGAATGCAGTCGTATCCACTGAGCCATCTCTCCAGACCCCCAGGATCTTTAAAATATATATGTGTTATCTTAGAACTTAAAGAACCAAGATGTACCCAAGTCCTTAGGAAAATTAGACATGCATGTTCACTACTGAGAGTCTGAGAGTTACTTTTCTACTAACACAGAGTCTCATTAGGTAGGTCTGGTGGCCTGGAAATCACTATGTAGACCAGGCTGCCTTGAACCCCTTGCCTCTGTCTCTCACATGCTTGAATTAAGGACATACCTCATTATACCAAACCAAAAAAAAATCTTAAAAAAATCTAAAACTTAAAAAAAAAAGGAGACAGTGTTTAACATCATCCCCAGTCATACTATGAAATAACCAGTTCTCCATCTTTAATAACTGCTGGGCTCGAATGTTGCTTTCCTAGCTTATTCCAACTGGAATTAAACACTGACATTTAAGGATTGTGTGAATGAAGAGTTTTGCTGATTATTCTGAACTGGTAGACAGAGATCTTTGTCTGTTCCACTTTGCCCAAGATGTAGATGCTCTCTGCGTCCATCTTTTGGGTAAATGCAGACACAGACATCAAGGGCCATCTTTCTATCGTTGAAGCATACATGAGCCCTTTTAGCTCAGCCTCACTGACTGCACATCACATCATACATGAGCCATTTTAGCTCAGCCTCACTGACTGCACATCGCATCAAAGTTGTGTCACTACTGGGGATATTTTGATTTATGTTTTTTGTTTTAAAGTAGAAGTGAAAATACAGGCTTGAGCACATAAAACAGTTACCCAAGCCACAATGGGAAGCTATGAGAATGTCTTGTCCTTTGAAGGGGTCTTGTGTATATTTCAAGGAGTTGCCTCCATTGTAAGAGAAAATGAATTTTGTTGTCTTAACGATGTAATTTTCTCCTTTCCTTTTTCCTCTTCAG
Seq C2 exon
AACAAATGTCAAGCCTTTGTGTTCGACCTGGTCACAAGCCAGGTCTTTGACGTCATCATTCTGGGTCTTATTGTCTTAAATATGATTATCATGATGGCTGAATCTGCCGACCAGCCCAAAGATGTGAAGAAAACCTTTGATATCCTCAACATAGCCTTCGTGGTCATCTTTACCATAGAGTGTCTCATCAAAGTCTTTGCTTTGAGGCAACACTACTTCACCAATGGCTGGAACTTATTTGATTGTGTGGTCGTGGTTCTTTCTATCATTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000032884:ENSRNOT00000034025:25
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:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(21.1=47.3)
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:
TGGCCAAGACATTTTTATGACAGA
R:
AACCACGACCACACAATCAAA
Band lengths:
358-1560
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]