RnoINT0131591 @ rn6
Intron Retention
Gene
ENSRNOG00000005007 | Scn3a
Description
sodium voltage-gated channel alpha subunit 3 [Source:RGD Symbol;Acc:3635]
Coordinates
chr3:51606636-51612447:-
Coord C1 exon
chr3:51612134-51612447
Coord A exon
chr3:51606755-51612133
Coord C2 exon
chr3:51606636-51606754
Length
5379 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
TCTTGTATTTTCTTTTTCAGACT
3' ss Score
11.12
Exon sequences
Seq C1 exon
GCAATTCTTATGCAAGAAGCTAAACGTAATTAAATGTGCAGGATGAAAAGATGGCCCAGGCACTGCTGGTACCCCCGGGACCTGAGAGCTTCCGCCTTTTCACTCGAGAATCTCTTGCTGCTATCGAAAAGCGTGCTGCAGAAGAGAAAGCCAAGAAACCCAAGAAAGAGCAAGACATTGACGATGAGAACAAACCAAAGCCAAACAGCGACTTGGAAGCTGGGAAGAACCTTCCATTTATCTATGGAGACATTCCTCCAGAGATGGTGTCGGAGCCCCTGGAGGACCTGGACCCCTACTATGTCAGTAAGAAA
Seq A exon
GTGAGTGCTTACTTTGTGTGGTCAATACATTCTCAATTAGATGTGCACTAGGGGTTTATGTGCACAAGAACATTGCAATTGCTATCTGTTAAATCGTTCACGGCACTCTTTACTGCTATACATCTTGAGGAACAGAAACATTGATAAGAAATAAAATCTCTGCCACAGGGAAATAAGCATAAACAATTTCTACCAATTCACAGTATCGAGGTGAATGGGAAAACTTAAATCTGATGGCAAAGATAAGTGTCTGCTATTGCTAATCCATTTAACAGTTTGATAGACAAATCATAGTTATAAGGTGGATGCTATATTTATTTTTTAGTTCAGACTTGGCTTGATGTTTCTGACAATCATCCGTGTTCTATAAAGCAGAAATCTCCTTATCTATTCCTATAGACAGGTAATTCATGGAGAAGCTTGTTTCCTGAGATATGCATTTTTGATTGTTTTCCTCCAACTTGGCATATGATTAGGAACTTCTATAGGCTTTATTGAGATTGTATAGGAGAAATTCTAGACCATCTGCAAATAGTTAAATCATTACCACAAGGAACGAAATACCGAGATTAGAAGAGAAAACATGGTGATTATAATAATAGCAAGAATCTCCATGTAATTTAAAGGAACAGCTATGACTATGTTTTTCTGATGTTTAAAACGACTACACTGTTCTGCCAGCATTGGTTTCAATAGTTAAACCAGCCTTGTGGGACCCATAGAGAATCTAAATAAAGAATAATATTTTATTCTTTTTACCTAAACGAATACTTTGGTACCTTTTAATCACACTTTATAGCTTACCTTCACAATGAGAAAACAATTTATTGTAAAGACAAATTAACACTATTTCAAGTTGATGATTTTTGGATTGACAAGTAAACAGAACAACTTTGCTTGTCAAAGTAGAACTTTACAAAAGCAATAGTTGAAGACACTGGCTTCTGTAAGTAATGTACGATATGGACTTTTAAGTCCCGGGGATAGGAGATGGCTCAGTTGTTCAGAGCACTCCCTGTTCCTACAGAGGACTGAGGTTTGGTTCACAGCACCCATGTCAGGTGACTCAAGGCTGTAACGACAAATCCAGCAGATCTGACCCTCTCTCTGTGAGTACTCTCCACACTCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTACCAAAGACATACACCTAGATAAAAATAAAACAAAGACTAACAAACATTGTAAGTCTTTTTTTACTAAGTTTAAGAAAGGAAGGCATTCACTATGCATTCATATGCTTCTCAAATAAACTGTGATATACTACAGAGATGATCAAGAACTATTTGAAATTTAGGAACTCCAATGTTGTAAAGGATGTTTAGCAATAAGATACTTCTCCCAGAGACTAGAAAACTAGACCTCATTTGAGGGGAAAAAAAAAAGTCTTAACATACACATTTGCAGCCAAGTGTGTTGTGTCCTATTTGTAAGTCCAGTACTTGGAAGACAGAGCCTAAAGTATATGTTTTACAAATTATTTTCAAGACACAGGAGTTTGTTTTACCTTGATATAAAATTGGTATTATTCCTTTAAAAACAAACAAACAAACAAACAAAAATCAAAGGAGTCAATCGGTTTGATAGACTTACCAGGGTAGAAAGGAAAAAATGGAGATATTACCCAATGGAAGGAGAGCTATAATTTCTTTCATTAGAAGCATTTCACTTCCAGTGACAATATCATCTCTGTATGACAGGGCTACCCTGGGCTACACCTACCATTTGATTAAGTAAGCGGTTTGGATCCCATGTTCAACAAGGACTCTCCTGTCTGATTTGTTTTCCCATAGATTTCCTGAGGGAAAAGCACCACTATAATTCTTTCTCTCCGTGAGAATATAACATACCCATTTTCATGTCAATTGATTGGCATCTGATTTTACAGGCCAGGTTTTCAAGTTTGGCTAACGTTCTAGTTTGCTACTGGAAAACAAAAATTGTTCTCCGTGCACGGGAAAGGACAGGCATTGCTCACTGCACACTGGAAACCCGACTTGGATCATAATTCATTGACAGTGACTCTGAACTATCAAGGGAGAAGCCCTGCCTTCGTTTATGAAGTACCTCTGAGCGTGAGGATGCAGGTGCTGCTTGCAGAAACATGATTGGTGACTCACAAACGCTAAAGGGAGAAGACAGTGTGTGAACTCATAGAATCCCACCCTAGTAGAAAGCCATGCTACTACATGACAACTTGTGTGGAAGACAGCATAGAGCTTGAGGGCTTCGTGTAATGATTTGCTGTCACTGATTAGCGATGTGTCTCAGTGCCTAATATAACTAGATGAGTAAGACCACAGTATATTTTAATAGCATTTAAGTTGGCCAGGTTAACAGCTTAAAAATAGTGGTATGATAATAATAGCTAACATTTGCCGGGCTCACCCTATGCGAGGAACCACTTGAACACTCCAGTTCATCTCATACCAACGAGCCAGTGAAGCAGTTGCTACTGTTAGTCTCAGTTTCCAGAAGGGAAAGGAAAGCCAAGGCCAATACTTTCACTTACCAAAGTCATGCTCCATCAGTGATAGATCACGGATTGGACCCGCATCTGGACCACTGGTAACTGCAGTAACAACAAATGTAAAATAAGATGGTCAAGCGTTGGTTGCGCCATTTTTTAAACACGTTTTGCTGATTCTTTGTGAATTCTGCGTGATGCAACCCAGTCCCGAGCATCTCCCTGTCCCTTAGTACATACCTTTTGCCCTTGTAGCACTCCCCACCCTGTATATAAAAACCAAACCAACCAACCAAGCAAAAAATACCTGGCCATGGAAACTGCAGTGTGTCCTGGTGATCACACGGATACTTTTTCCTCCCAAACAGCCCTAGTTGTAAATGTTCATTGCTGTGAGTCATTGCTCTGGTTCAAGGCCTCTGCTCATTGTCAATGCTGGATCCTCATAGGGACTCCTTTCAGATATCCTGTTGTTGCCCTGGGCTGTACCATCTTTTAAAACTCCGTGCTTGATATATTCCATTGAGGTATAAATCTGCTGCTGCTTCCAAAAAACTAAGAATTTCAGTGAACGTATTAGTATTTATCCAGGGGGAAAAGGAGTTAGCACTCCAGATGATAACTGTTGGGACAAACTTCAGTCACAGGGCTTACAGCAATACTGGGGATGAGTACCGAAATCTTTCCGCGGTGAGGCACCGCGGAAAACCAGACTTTAAAGTCGGTGTTCCTTCCAGACATGTCTTATACTCTCATAAGTTTTTGGAGTAGGTACATCAGAGTCCCAGACTTCAAACATCTCTTTGTAATTTCTTTCACTTTCCAGATCATTAGAATTTTACTCCTTGCTTCTCAGCCCCTGAGGTATGCATCGTTACACATTCAGAGTAGGAGCGCCACACTCACCAGTCCAGGAGCCACTCGCACCCACAGGCTAACCTTGCAGGAGAAGCAGAGGGCTTCGTGTTTGAAAGGACAGTTCATTCTTGCGTAGTCTATTTTGGGAGATATTTCGAAATACGCCCCCCCCCCTTTCTAATGTTGCAAGTAGAAATTGCTCTTTCAGGGAAATTGTTTCAAAGAGCATGAGTTAATGCACTTTGAATCATTGGGAACGTTTACACACTATTGCTGCCTCTGATGCCTAAATGGAACTTGATTGCCGCACTGTGAATTCGTGACAGCCCACTAATGCTTCCGTAGTTCAGGGGCAGTCTTCGTGAGGCTCATTGTCACTTGCCCGTAACCCTGATGCTAGCAAGGGACAGGTTACTTGCCCTCTTACTAGAATTTATAGAGCTCAGCTCATTGAAAATGGTTAGTTAAGTAACCGTTGGCTCAGTGGTCTGCAACCCAGAAGGGCGGTGAAAGGGTTGCTTGTTGGCCCTGCCCTTTCTGCTCACAGTGTAAACATTCCTGCCTGCCTCTTCAAACAGACCTGTCGAGAGCTGCTGTGAATGTATGGGATATAGCCTTTAGTAAAAGGGTGCAAACATATTATTAAGTAAATCAGTACATACGGCAGATGTCATGAAGGTGAACAGTGCCTTAAAGGCATATTTAATTAGAATAAGTGTTTATTGGCAAAGCACGCTATTAAAACTGTGGGGGAAAGCAGGTTCTTTGTCCTCAGTCATTTATAAAAGCAACTAACCAGGTTCTCCCACAAATGAATCCTACGTGGGAATTGCTACTTGGTGGTGATTACCAGCAAACACGTGAGAGAGCCAGTGCAAAGCAATATGCTAAGAGTTAGTGGCAGGAGAAACAGCTAAGGAATGATCAGAAGGCAGTGTGATTTATATGGGAAAATGGAAAGGAGGGGGTGGTGATTTGGGTTCTGAGAATGGAAAAAGAGATTGGATAGTAAGGCTGCCTGCATATTATAATTTACCTAAGCAGAAAGTTGAAAACAAGTAATATCTGCCTATACCCCAAAAACTTAAATATTGACAATTCTGAAAAACTTCTAGAACTTCCTAGCACGAGGGTCATGATAGGCACGATAAACTTGAATAGTGAGACCTTTCTACAGGTATAGATAGCTGTCTTCACTGAGTCTATGGCCACGCCCATCACAGCTGGAGGGAGAGATTGACAGGTTCTGTGTGGGACTGACAAGTGGCTTAAATGGCTGGAACAGAGATGACTGTAGTAGTAAAAAATAAAGGATGACCCATCCTGGGAGTCTTGAAAGGTAGCCCTGGGTCTGCATAGCTTAAATGCTATGAGGATGTGTGCTTCAGATCCTAGACTTTTAACCATGGCTTGGCCTTTGAAGTCATGTATTTAAAATTAATTTTCAATGCAGCTGTCTTTCCTCAAGATCCAAGTGGATCCTTGTCAGCACGCAAAAATCAGGTTCTGTAACTTATTTAAATGTCGTAGATCAAGGCAGCTGCTACAGAAATGATGGGAGGCCACCACAAAAATAGGGTTAGAAGGTTTGGAGTTATTAATTTCAATGAATTCAATAATTAACTAATGATACTCATAAAAGATTATTTTGACACTTATATATACCAAATGATCTGAAAAGTCACCAAAGCTGGAGGCATATGGCAAGCCTCAAGTAGAAATGAACCTTGTAAAGTTCTTTAATTTGATTTCTAGTCATGTGTAAGGCTATCAGTTTGGATCGACAAGTTTGGAGGCTTAGAGACAGGTAAGATAGTAGTCCACTGGGCCTTTGTGTGACTATTTCTGTAGGGGAGAAACACTTATGCTGGGTCTAGTAAACAAGATACTGGTTATGTTCCAACTGGTCTAAATGAACACGTTTGTACAAAAAAAAATCAGGTAAAAAGTTCTTGAGTTGTGTTGTAAATGCCTCAAATAAACCTGCATGTCTAATCTCTCTTGTATTTTCTTTTTCAG
Seq C2 exon
ACTTTTGTAGTGTTGAATAAAGGGAAGGCGATTTTTCGATTCAGCGCCACCTCCGCCCTGTATATTTTAACTCCGCTAAACCCTGTTAGGAAAATTGCCATTAAGATTTTGGTACACTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005007:ENSRNOT00000006646:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.330 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]