RnoINT0131713 @ rn6
Intron Retention
Gene
ENSRNOG00000006639 | Scn9a
Description
sodium voltage-gated channel alpha subunit 9 [Source:RGD Symbol;Acc:69368]
Coordinates
chr3:52660151-52664209:-
Coord C1 exon
chr3:52663952-52664209
Coord A exon
chr3:52660270-52663951
Coord C2 exon
chr3:52660151-52660269
Length
3682 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
GTCTCTTTTTCCTCCTGCAGACT
3' ss Score
11.84
Exon sequences
Seq C1 exon
ATGGCGATGCTGCCTCCTCCAGGACCTCAGAGTTTCGTTCACTTCACAAAACAGTCCCTTGCCCTCATTGAACAGCGTATTTCTGAAGAAAAAGCCAAGGAACACAAAGACGAAAAGAAAGATGATGAGGAAGAAGGCCCCAAGCCCAGCAGTGACTTGGAAGCTGGGAAACAGCTCCCCTTCATCTATGGAGACATTCCCCCTGGAATGGTGTCAGAGCCCCTGGAGGACCTGGACCCATACTATGCTGACAAAAAA
Seq A exon
GTAAGTTATTGAGACTTCAGTGACAAGAGTTCTTTGATATCATCCCATACCAAAGGTACATGACCATCAATGACCTCATGCCATAAGCATTATAGAAAATACATATTAGGTTGCTGAGAATATGTGCTTTTTCTAGTATTTCGTTAAAATTGATAGTGGTATCGGCACGCTTACTTGAATGGACTAATTATTCAACATATTTTTTTAGGTATTTATGGTGTCACAGCTACTTTGCACTTGTTTAGTATGTGAGGTGTGTGGGTGAAGTTAGATGACTCCTTAGTCGAAGTTATTTCTCTGCTTCCATTATGTGAGGTCTAGGGATCAAACTCGAGTTATTATCAGGTTTGGTAGAAAATGTCTCTACCTGCCCAGAACTCTTGGCAGCTATTCATGGTAATACGTAATCCTTATGTGTGTAGATTTTAAATTTCCTTTAAAGTTTTAAGGCAAATGAATAATGCTGATTTAAATTATTATCCCTTGGTAGCCTGTTTGTTTGCTAATGAGAGATGGAAAGGGCTGGACCCGGATGAGAAGGGAGGTGGGAAGCACGTGGAGGGTGTTGAAAGCAGGGCAACTGTAACCATGATATATTGTGTAAGGGGGAAAATCTCTTTTCAACAAAAGAAAAATATTTTAAAACACAAAAGTTATACTTTTTATTTTTTTAAATTTCAAATGTAACACAACTTGATCTTGCTAAGACTATGTAAAAATGCACTTAGTTTTGACCCCTTTTCTTTGTCTTTTATGACTCAATTCCTCACTAAGTTGTTGTAGAAAGTCGTTTGTTGAGATACTATCTGTCTAAAAAAATAATTTCCCACATGAGTAAAAACATAGAATTATGAACTTATTCCACACCCCCAACTTGGTGAAAATATTTATTATAATAAGCTCATTTATGCTTACATAAAACATAAGGACAACAGGAGAAAAAGAGCTCACACAAGATAACACAAGTATCTTGCTTTCTGTGTCAGAAGACAATGATGTGATTAAGACTTAGTGTTTCTCAGTTCCTCGCCTTGGATTGTTTTAATATTTTACTTGTTTAATTGTTCAACTAAATAAGATCCAGGGAAATGTCATTCACAGTGCACTCACTGAAAAAAAAATCATTTTAAGGACCTTTTAATTTTATTTTTTAATTAACTTTAAAAAATGAATTTGCCCAATGAACTCTAAGGTTTTTTTTCAATAAATGAAGGATTGAGCTATGTACAAGTATATGTTACTCTTTTTAATTTTCAGTGATTGTTGGTGAATACTATTTTTATTTTTATTTTTAGCCATTTCAGCTACACAACTGAAAAACTAGAATTAGAGTGGGTGATTGGAAGAACGTTCTCTGGCTGGGGATGTAGCTGTAGTCAAAGTTGCCTGCACTGCAAGGAGGACATGAGCTTCAACCCAGAGCCCACAATAGAGAGAAAAATGGACCTTATGGATTGGTTTATAATCCTGGACCTGGGAAGCCAGAGGTAGATGGGTTTCTTGAAGTCCACTGACCAGCTAGCCTAGCAGAACCTGAGAGATAAAAGCCTCATAAAAACTAGGTCAGTTACACCTGAGAAATGACGAAGTTGTCTTCTGGCCTTCCATGTACACATACACACTCTTGCACATCAGAACCTATTAGGCAATTGCATGCAAGCACACGTGCGTGTGTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACACACACACACACACACACACACACACACACACACACACACACACACTCACTCACTCCAAGGAAGGAAAAGATACTTTGAACCCTGACATGCCTTAAATTGATGGGAAAATTTTTAATGACACTTCTCAGCATGTTTTAAAACTCTCAAGGTTTTGTGGTTAAAAACTAGAGGGATAGATTGTTTCTACACACTGTTAAAAATCTATATAATAGAAGAAAGAAAGGTTATATTTAAAAACACATGACAAGTGACTATAATCACTGAAGAGAACACATAGGTTTTGGATGCTCCCTCAACCTATCTCACTGTCTCTGGGCTGAATGTGGCTGGAGGAGAGAGAAGAGTGTTTGTCCAACACATTACCACAAACATGTTTACATCATGAAACTTTTTTGGGTCAACTTTATTTTGAGCTTGTTCAGCATGAACTTTGTAGATTGCAATGTGTAGCTTCAATGTCTAAAGAATGGACTTGGCTACAAACTGTATATACTTGTAGGCAGATCAGTTATTTACTTATTGAAAAGAAACAGCCTTGGGGTTCATTGGCCAGTGACTGACAGCTGCTTTCACACATGGTAGTGCTTGCAAAGCTGCGGGGCAGCATTTCCTCAGCCCTGCACTATGCCATAAAGGTATAAAGTGCTCACAGCAATGTGCTGGATTAGAGTGTTGCACACTGAGCTTCATCCTGTCTCTTTTTCCTCCTGCAG
Seq C2 exon
ACTTTTATAGTATTGAACAAAGGGAAAGCAATCTTCCGTTTCAACGCCACCCCTGCTTTGTACATGCTGTCTCCCTTCAGTCCTCTAAGAAGAATATCTATTAAGATCTTAGTGCACTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000006639:ENSRNOT00000065126:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.485 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
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]