RnoINT0131716 @ rn6
Intron Retention
Gene
ENSRNOG00000006639 | Scn9a
Description
sodium voltage-gated channel alpha subunit 9 [Source:RGD Symbol;Acc:69368]
Coordinates
chr3:52633702-52636917:-
Coord C1 exon
chr3:52636546-52636917
Coord A exon
chr3:52633832-52636545
Coord C2 exon
chr3:52633702-52633831
Length
2714 bp
Sequences
Splice sites
5' ss Seq
AGCGTAAGG
5' ss Score
5.87
3' ss Seq
GCCTTTTTATCCCCCTTTAGGGC
3' ss Score
11.59
Exon sequences
Seq C1 exon
TCGCCACTCAGCATTCGTGGGTCCCTGTTTTCTGCCAGGCGCAGCAGCAGGACGAGTCTGTTCAGTTTTAAGGGGCGAGGAAGAGATCTGGGATCTGAGACAGAATTCGCTGATGATGAGCATAGCATTTTTGGAGACAACGAGAGCAGAAGGGGTTCACTATTCGTACCCCATAGACCCCGGGAGCGGCGCAGCAGTAACATCAGTCAGGCCAGTAGGTCCCCGCCAGTGCTACCGGTGAACGGGAAGATGCACAGTGCAGTGGACTGCAATGGCGTCGTGTCGCTTGTTGATGGACCCTCAGCCCTCATGCTCCCCAATGGACAGCTTCTTCCAGAGGTGATAATAGATAAGGCAACTTCCGACGACAGC
Seq A exon
GTAAGGACGTTTTCCATAGCTCAGGCATGGCTGAGCTCTTATTGCGCATCAGTCATTGTCTCTGCTGGGGGGCCTGCTCTGTGGCCTGTGAATGGCTCTGCATTTGGTGATGTCTTCTCTCTGAAAATACAGCTTTAATTCATAGATAAATCCTCAAGTTAGGTGTTATAGTCACCTAATTCAAATCTAGTTTATGGGACTAGAGAGATGGTTTGGTGAATAAAGGGCCCCATGGCACAGCACTCAATTCAGGTAGCTCACAGAAACAGACACTGCAACTCTGGCTCCAAGAGATCTGGCTCCCTCTTCTGGCTTCAGTGGGTACCGCACATACATGTGCATAACACACACACACACACACACACACACACACACACACACACACACACACTCTTAATATTTTGAAAATAAAACTTAAATAAACAAAGATATTTTATGTCTCATGCTGGAAAATATTATTTATGTTATGATTACAGGTTTTCTCTAAAAGCATCACTTTAGGAAACATTTATAAAAGATGTCTATGGCTTATTGAATAGGCTGACCTTATTAGAAGATGGGCTCCACTCTGTAAGAAAAAAAAATTGGATCCCTTGTCATCTACCTCTATTTATTTCAGGTTATTTATTTAATATGTGCTTATTGCATGGGTTGTAGCTAACAACAGGAGGAAGAGTAAACACATTCTGACGCTTTGCTCCACCTGAATGAGATGATTCATTGCTACCACTGCAAACAGGAGAAATAAACCAGAACGTTCACAGGTCCCCATTGTTCATCAGCAGCTCTGACATTTCCACAAGAGCCCTGTGCCCTAAGGGTGTGTTCTGAGCCTCCATCCCCACTGTGTCTCCAAAGGGAATAGAATCTCTGTACTTACTCCTTGAAACAAATGAAATGTATCACTTTCATTTAGAATATATTTTGTCTGAAGTCTCTCCGTACAAAATATCCAAAATATATTCACCGAAACAAATAAATATAAATTTAAAAATATAACGACTCTGACATAACAAATTCCAGTGACACTGAATCACTGAAAGTTTAGACAATGTCACATTAGGCCTGGAAACTAGTCTGGAGTTTTCAGGAAAAATATCTTACCCACTTATTATGCTATTCTGCATTACCAAATATCAGCAAGTGCTGCCATTGACCAAGCAAGTTTCCGTCATGCGTTACGTGTCTATGTGTTTGTAGTAGCAAAGCCATGTATTATTTCTAGTGGGAATAAAGTTCCATCCACGTCATGGCCACACACACACATTTCAGTTTGAAAAAAAAAACTGCATGTGCTGTGGGATAACTTGCACCCTCTCTGCTTGTTCTGCTTGGGAATTGTGCTGTTCTGTTAAGCTGCTTTCCTTCGGAAATAGCATGTTACCTTTCTATGAAATGACACTCAAGCTTTGCCTTTCAATGGTGTTTCTAACCTGTAAAATGTTATTATGCAACTTATGTCATGTTTGAAGCTGAGTTCACTCCTTCGAATTAATATTTTATTTACGAGTTTGCTTTTTAACAGGGGGGAGGGACGACTCTAAACCAGAAAAATAGAAGGCTAAAATTATAAAAGCCCAATAATTACAAATGTGATTATTACAGGCATAGGGCACAGTTTACAGGTTCACCTCTGCTCCAGCATGACAATAAAATCGGTTCGCTGTACACATGCCCATCTGGAAGAAGATTTGTGTAATCAAATTCTTTTTTATTTATTTTGGAGATAAAAGTACATGAGAGCATAGAGCAGAGAAAACACATCACACGCCCATACACATATATACAAATGTGCTGTATGTATATGTGTATACATACATGACTATATACAACTTTACATCCTTATGATTATTTAGTCACAGTCATATGGTAAACTATCTACTATCTATCCCATAGCACATACATGCTAGTATATGACAGCTGTAAAGTTGTATACTTGTTTATGTATATCATGTGTTGGGGAGTGTATACTTTAAAAGACCAGTATAGGCTGGGGATTTAGCTCAGTGGTAGAGCGCTTGCCTAGCAAGCACAAGGCCCTGGGTTCGGTCCCCAGCTCCGAAAAAAAAAATCTTCTTTAAAAGACCAGTAGAGTCTTTTTTACAGATGTTTAAGTTTGCTTGGAAAGCAAGCATTTTCACCTAAAGATGAATATGGCTGGCATGCTTCTATCACTATTCCTGCATGTCTGATTTTTAGAGCTGCACCATGGTTACTTCTTTGAGATGGAGACATCTTCCCCCCAGACTGCCATTGGTCGTAAACACCTTTTTCAAACTGAGTCCCTTAGCACTATGTACACATCATGTCACAAAGTATTCCTTCAGCCGTAAGAAGAAAAAAAATCTTAAAGTGGTGTTCATTGATGTTGGTCACGATAAACAGTCCTGGGAGTCATAATTACAAAAACCAGAGTATTTGACTCTACCCTTTCTTCACACACCTCTACAGCTCTTGCCTGGTTGTATTCCTGTGTGGCTTTTCCTTGGCAAATGTTGGATTAAGTTGTATATGCAGAGAGCTCACAATAGCGCTATAATGATAAAAATGACCACTTTGTTTCCTAACCCAAAACAAGAAGCAGGGTCAACATTTAAATCTAGCAACGTTTAATGATTGATTACACCTACCCAAGCACGACTTTATTTGTACCTATGTTATACTAGAGTTTTGCTCTTAAGATTGGAATTGGTTGCCTTTTTATCCCCCTTTAG
Seq C2 exon
GGCACGACTAATCAGATGCGCAAAAAAAGGCTCTCTAGTTCTTACTTCTTGTCTGAGGACATGCTGAATGACCCGCATCTCAGGCAAAGGGCCATGAGCAGGGCGAGCATACTGACCAACACTGTGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000006639:ENSRNOT00000065126:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.589 A=NA C2=0.114
Domain overlap (PFAM):
C1:
PF0253517=Zip=PD(1.6=2.4),PF119333=DUF3451=FE(53.0=100)
A:
NA
C2:
PF119333=DUF3451=PD(15.5=81.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]