RnoINT0131720 @ rn6
Intron Retention
Gene
ENSRNOG00000006639 | Scn9a
Description
sodium voltage-gated channel alpha subunit 9 [Source:RGD Symbol;Acc:69368]
Coordinates
chr3:52625235-52629970:-
Coord C1 exon
chr3:52629614-52629970
Coord A exon
chr3:52625712-52629613
Coord C2 exon
chr3:52625235-52625711
Length
3902 bp
Sequences
Splice sites
5' ss Seq
GTGGTATGT
5' ss Score
7.64
3' ss Seq
TCCCACCCACCCTGATGTAGGTC
3' ss Score
7.43
Exon sequences
Seq C1 exon
CTCCGAGTCTTCAAGTTGGCAAAGTCCTGGCCCACACTGAACATGCTCATTAAGATCATCGGCAACTCGGTGGGCGCACTGGGCAACCTGACCCTGGTGCTGGCCATCATCGTCTTCATTTTTGCCGTGGTCGGCATGCAGCTGTTTGGAAAGAGCTACAAGGAGTGTGTCTGCAAGATCAATGTGGACTGCAAGCTGCCGCGCTGGCACATGAACGACTTCTTCCACTCCTTCCTGATCGTGTTCCGAGTGCTGTGTGGGGAGTGGATAGAGACCATGTGGGACTGCATGGAGGTCGCGGGCCAGACCATGTGCCTTATTGTTTACATGATGGTCATGGTGATTGGGAACCTTGTG
Seq A exon
GTATGTAAGAGCTATTCATATACTTAAATTTTCTATTACAATTATTCCTGATGTTATTGTTGCAATTTTAAAATTAACTTTATTTTAGAAACAAAATAATATTTTTAATCTCCTTGGCCAGGAAAACCTGTATTTATATTTTTCAAAATTACCTCCTAGGGTTTGTCAGATGAATTAAATCTGTGGCTTTCAAACCTCTTAAAACATGACCTGTCATCAGATACGAAACTATGGTGGTAAATACTGCATGATTAAATTAATGATCAAGACTAATGGAGCAAGGCAAATGAGAACACTTGTTATCGCTCCTCACATTCATAAAACTAGCAAGTGGGCTAAACTTAGTTTAGTTCTTCCTTCTATGTGACCTTTTGAGTTACAAAGGATTCCCATGGTCCATAGCGGCTAAAAAGAATAAATGGAGAATATTTTGTAGCATATGTACATCATAGGAAGAAGTTCAAATTTTAGTGTCCATATAAAGTTTTAAAGAAAATTGGATATATTCATTCTTTTACATTTTACATATGTGTGCATTAATGCCCAGTGTTCAAAGAGAGGGACTGCTGAATGCCCCATGTCCTACAACATACCAATTATTTATTATATGGCCCTTTACAGAAAAATTTACCACCCACTAGTTTATAGCATTTCTTTCAAATAGCAATCTCCTTGTATTTCCAATTAGTGTTTTCTTGGCTTCTGATGGCTTGTTTCTTCCATACACTGGTGAGTCAAATTTCCCAAGTTTACAGAAAAAAGAAAATTAGATAAAATATTCTTCTATGAGCCATTCAACTTGCTTTACGAGTCCACTATCTTGTCTTGTCCTAGTAGTGGTCCACTGGACATCAAATCACTTGCCAACCATATGGTAAGTACATTCTCTCCCACTGGCTTCAGAACAAAGTTACTAAATATTTGTCCCTGTAGCTTCCATTAAAGCATCAGAACAATAAATCTACATTCACCAGATGACACACTAATTTAAAGCATGGGTCCGTAGAGTACATTATACAATAATAATTCTACATCCTTGTGGCATAAACAAAACATGAATTGCCAATCTGCAATTCTTTATCCCCCTCCTGTAGTGATGATACATTTTCTAATGTGACATAGGTTAACAAATCCTTCCAATATGCAAAAATACACATGGTTTTCTTTTGGCCTCAAACTCATGATCCTCCTGTCTCAGCCTCCTGGGAGATGGGATTACAATAATGCAATGCTGTGTTTACCTAAATACTTAAGTTTTGCACATTGCTAGCAGACCTTTATCTTCTCTATTTTATGTTAAACCTTTGTAAGTTAAAGCCTACAAAATGAAGTGATGTGGCCTTTGTCTTCTATAAGCTAGTGATGTGTCAGTAGCAAGAAAAATTATGTGGAAAAATTACCAGGCAAGCAAGTGATGGATATAGTTAGATATATAGTGAAGGATATATCAAAGAAAATGTTCTTCTCATAGTAAAAATGAAGTTCTAGACAGATACTCTTGGAAAGTTTTGAAGCAAGCCTTTGAAGAAACACAATGCAATATTTAGGTATGAGAACAAATCTAAAAGGAATATTTTTCTTTGAGAAGAAAAGTAGATTGGTTGTAAAGCATAAGTGAACGTTAATTCTACATGGAACTAGCTATAAATAACTCACATTTCAGTCACAAAGTATTGATCCAATATAGTAAACAAGAACAGAAGTTTGGCTCTTTTTCCTGGTGCCTTCTTTCCAGACACCAGCTGTCAGAAACTCATTAAAGTGGGCAAAGAATGCAGTCTTCATGCTTTCTATAAGAAGTGTATGGACACAAAGTATCTGCTGGTACTCCTGGTGAAGAGTGAACGTGTTATGTGATCCGACTCAGTGTTGGGAAGGACAAACAAGGCTTTTCCAAGATGTCAGGTGGCTTGACCTGCTGTTGAGGAAGGAACATTCTATCTTACAGACCCAGGAGAACTGGAAAGAGAAAGTACAAGCCTGTTCTTAGATACATTATAAGTGACAGTCTGAGTGTTCTCAGTTTTATTATTGTTGAAAAAGAAGAGGCAGAAGGAGGAGGAAGACGAGGAGGAGGAGCGGGAGGAGGAGCAGGAGGAGGAAGAGCAACATAATCCGAGACTGACAGATACCATGATTTGATCCCAAAAAAGCTAGCAGAATTGAGAAGATTTTTAATCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTGTCTCTCTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCAAAAATAATGTCCATCAACATATTGTCAGCACAAACCCCTGAACAAAGAGGGTGAGAGTCCTGTAACAAGAACACCCAAGATTCAATGTTTTGTTACTGCATATGACCCGGAACACAAGCACCGATACATTGCTCTGAAAAATTACACTAAGAAAAACAAGGAAGAGGCTGTGTACTATGCTAAAACTTTTGGCCAAAACAATGAAGGAAGCCAAAGCAAAATGTCAGAAACAGATTACCAAGAGACATAGGCTGTCCTGTCCTCTTTGAGAGCTTCTACTTCTGAGTCCAGTCAAAAGCAAGTCTGTCAGATTAGCTCTTTAAGTAGCAAGGAACTACAATCAATATAAGTTTAACACGGGAGAAGTATAAAAATGTTTCTGAGATGGACCTACGCATTAAAGGATTACAGTTTACTGATCTAATGTTTTCAAATTTTCTCATGGGGCTAGAGATATGGAAAGTGGATAAGAGAGCGGCCAGTGTAAGGAAAGAACCCTATTTCAGTTCCCAGAGCCATTTTAAAAGCAGAGACATACGTGCCTGCAAGCCTGGCATTATAGAGGTAGAGATAGGAGGGTCTTTTTGGCTTGCTGGCTGTCAATCTGTCACCAATTCAGATTTGGTGAGAGACGCTGACCAATAGATCAAATATGAAAGTGCTAGAGGAGGACAGCATACCATCTCTGCTCTCAGCATTTGTACATAGACACAAACACAGGCACGCATGCGAGCGCGCGCGCGCACACACACACACACACACACACACACACACACACACGCTCGAGAAACTCACATTTACTCCTTATGTCAGTTTATTTCCAGTTATTGAAATCAGTAAAACCACAAGGTTTAGAAGATTTTAGTCCATTCTACTTTGTGGTAAGATAATGATGAAAACTGTTCTCTTCAAATTGGACTTTATAAATCAATTGTTTTCATAAGTACTTACTTTCCTTTCTAATGTGTTAGAAGAAGTTATATGAAATTGACTTTGTTTTCACTTTTGATATCCATATATATATATATATATATATATATATATATATATATATATATATGACCTTGCTTCAAGGATACAAATTTCCCTGACATCCTTGACCACTTCTTCCGGGATTTAATGATACACAATAAAGGCAGCTAATCCATTTTATTGTCTTGCATGACTTGTGTTCAATGTGCTTCAACCTTGACTGGAATGGTCAGCACAATGACAACAGTATAATTTTCTTGTACTCTTTGTTTTCCATGAAAGTAAGGCAGCAAGTATGGTTGAGTTAAAAATAACCTTTTAAGAGCCCTTAAAGGGAATTTGACTGGCTCACTTTAGAGAGCAACAATAGAGTGACCAATGGCGTGATGACAGTGGTGTGGGACGATTCTCTGATCCGCAGGGCAACTCCTCATGAGTATTGCTTGCCCTCTGCTGCCCAAGTCTTCATGTCTATATGTGGAAAGAGTATTGAGACCACTCTGATCTGTTTTTACCAGTTCTCGAAAAAGTGCTTTTTGTCTTTTTGTCATGGTGGGTTTGCATCTTGACTTATAATTCTAAAAAGTACGTTTCTTTGTATTTTCCATGTCCCCGTTCTTCCCCCTCCCACCCACCCTGATGTAG
Seq C2 exon
GTCCTGAACCTGTTTCTGGCTCTTTTGCTGAGTTCATTTAGTTCTGACAATCTTACAGCAATTGAGGAAGACACCGATGCAAACAACCTCCAGATCGCAGTGGCCAGAATTAAGAGGGGAATCAATTATGTGAAACAGACCCTGCGTGAATTCATTCTAAAATCATTTTCCAAAAAGCCAAAGGGCTCCAAGGACACAAAACGAACAGCAGATCCCAACAACAAGAAAGAAAACTATATTTCAAACCGTACCCTTGCGGAGATGAGCAAGGATCACAATTTCCTCAAAGAAAAGGATAGGATCAGTGGTTATGGCAGCAGTCTAGACAAAAGCTTTATGGATGAAAATGATTACCAGTCCTTTATCCATAACCCCAGCCTCACAGTGACAGTGCCAATTGCACCTGGGGAGTCTGATTTGGAGATTATGAACACAGAAGAGCTTAGCAGTGACTCAGACAGTGACTACAGCAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000006639:ENSRNOT00000065126:16
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=0.319
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(62.1=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(4.2=5.0),PF065128=Na_trans_assoc=PU(61.4=84.9)
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]