RnoINT0131730 @ rn6
Intron Retention
Gene
ENSRNOG00000006639 | Scn9a
Description
sodium voltage-gated channel alpha subunit 9 [Source:RGD Symbol;Acc:69368]
Coordinates
chr3:52583951-52591224:-
Coord C1 exon
chr3:52590954-52591224
Coord A exon
chr3:52588484-52590953
Coord C2 exon
chr3:52583951-52588483
Length
2470 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGG
5' ss Score
9.31
3' ss Seq
TGTTTATTATTCCAATACAGGAA
3' ss Score
7.75
Exon sequences
Seq C1 exon
AACAAATTCCAAGGATGTATATTTGACTTAGTGACAAACCAAGCTTTTGATATCACCATCATGGTTCTTATATGCCTCAACATGGTAACCATGATGGTAGAAAAAGAGGGGCAAACTGAGTACATGGATTATGTTTTACACTGGATCAACATGGTCTTCATTATCCTGTTCACTGGGGAGTGTGTGCTGAAGCTAATCTCCCTCAGACATTACTACTTCACTGTGGGTTGGAACATTTTTGATTTTGTGGTAGTGATCCTCTCCATTGTAG
Seq A exon
GTAAGGCCGTTTACTAATCAAATCTTAATTGTGGATAAAGTCCACATTTGTTCTAAGAAGTAGTCTACATGTGTGAGATCCGTTTTACCATTGAGTGAATTATTAGCATGATAGAAGGAAGGAGATTTAGAAAGAAAGCAAAGTTCTGGTCAGAATTTCCAAGTTCAAACCCCAGCCCAGAAAGCCAAAGGTATGGGTCTGTCAGAAAGAAATTCCCATTGAGATTAGTTTCCAAAACTGCCCCATGGAACCTGCTCATAGACATCTATTCATAGATGTGTCTTGGAAGCCAATGAAGAATGCGCAATTATTTTTATTAGCAGGGCCAAGCTAGTCGATATGGATACTGGCTTACTTTTGAAATTCATCCTGATTTAAAATGTACAAAAAAATTGACATTTCATCTCTTATAATTAATACTGGAGCAGTCTATAAAATTCAGTTATTTCTCATCTAGCAGCTGTGTCCGTGTAGCACAGATATGATTTACAAGTCTTCTTTCACTGTCATATCTTTCCTGTTCTCTTTTTGTCCAACATGCCTAATATCTTAAGGTTACATTTAACTTTTAGCATTGAACTTTCTAGATGGAAGAAACTGCAGGATAAAATGCACAGCTAACCAAACAGGGCCAAAAAATCCAAAGTTTATATAATCCAGAACCACAATAAAAAAAATACCAAATGACTTAAAACCAATGTTCGAGCAATATTGCTACCAGATTGATATATCCAAGCAAATTAAATTTCAGGTAGTAATTAATGCCAGAGTGACAAGATAAAGTGTAAGGATGGAAACGTTCATGTTCAGTCAGGACAATAAAATAATGTAGTCTTAGCAATGTTAGCCAGAGCATTTAAACAAGAGAACAAGGAGGTTATGCATTAAAACCAGGAGTAATTCTTTGTTATCCTTGTTAAATCATGGCACTCTTCTAAAGGGAAGAGTTGACTGTGGCCCTGTACACTTCTCTGCCATTCCAGCATTAAGGAGGCTTTGCCTGGAGGATATGGAGTCCCAGACTTTCCTAGGATACCTAGTGAGACAATCTCAAACTTTAAAATAATAATAATTAATAATAATAATAATAATAATAAATCCATTGGAGTTAACTTTCTGAAATGTTGACCAAAAAAGTAGAAAACATATCTGAAGAAAAGTTTAATTCAAACTCACAATAAAAATAGGATTACAAATCTAGTAGTAAATGTACCATATAATGTATCAGATATCTATGGGAAAAAAAAGACAAAAAAGCTGCAATAATTGAAGGCTTATCTTACGCGTGCTTCCAAAGGCTTTCATTGCAATGATGACTTTCTGAAGGTTTGTTAACGTTTACTCATATGAGTGTGTACCTGTGTGAATGCATGTTGTATGTCTGAGCTCCTCCAGACGGCAGAAAGAAGGTGCTAGAGCCCCTGAAGATGAAGTTACAGGCTGTTGTGAATCATCAGATACAGAACTCAGGTCCTCTGCAAAAGCAGCAAGAAACCTTAGCCTCTGAGAGACCTCTCCAGCCTCAGTAGCCACCTTTCATGGAAATTAATTTATGATTTCAATAAAACTATCAGGGAAACTTTTTATATGGCGGTGGTTACTGACAGAAAATACAGCAGTGAGGGCAGCTGCAACGGTGTGTGAATTTTTAAAGAATTCCAAGGAACTGAACACTGGACTGTAATGCACAATTAGGAATTTATGCAGTTCTATAGGCATAGAAATCACAATATTTAAAACATGGGCAGGTGGAGTGAGATCTATCATTAATCCCAGCACAGGGGATAAAAAGGCAGGCAGATCCCTGTGAGTTCCAAGCTAACCTGGTTTACATAGCAAATCCCATTCTCCTTCCAAGGGCAAAGGCTACAAACTAATACTCTACCTCAAAGAAGGAAAGAAGGGAAGGAAAGAAGGAAGGAAAGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAAGAAGGAAGGAAGGAAGGGCGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGAAGGAAGGAAAAAGAAAAATGTTTTAAGATCGAAATTTTTATAAATGATTTTACTTACACACTCTCTCTCTCTCTCTCTCACACACACACACACACACACACACACACACACACACGTGTTTTATTAGTAGGATTTAGTTTGCACATAGGTCTAGCACTGAACTCCATTCTGAACCCTGGAATTAAATTTTTGAGCATGCACATGTGAAATCTTTTCTATTCATGACACAAACTTTAGTCTCAAGAGAATGAAAAAACAAAATCTTACCAGCCAAAATAGAGAGGAGTGTGTCCATGAATTTAGTTTAGATGAAAAACATTCACAAGCAGTTAATAAAATATCAAATCAAGATAGAACAGCAATTCTGCATTTATCATATGTCGAATGAAGCTATTTAGACTCATGATATTGTGCTTAATGGATCTTTGAACATTTCTGTTTATTATTCCAATACAG
Seq C2 exon
GAATGTTTCTCGCTGAGATGATAGAGAAGTATTTCGTGTCCCCTACCCTGTTCCGAGTCATCCGCCTGGCCAGGATTGGACGAATCCTACGCCTGATCAAAGGCGCCAAGGGGATCCGCACTCTGCTCTTTGCTCTGATGATGTCCCTTCCTGCGCTGTTCAACATCGGCCTCCTGCTTTTCCTGGTCATGTTCATCTACGCCATCTTTGGGATGTCCAACTTTGCCTACGTTAAAAAGGAGGCTGGAATTAATGACATGTTCAACTTTGAGACTTTTGGCAACAGCATGATCTGCTTGTTCCAAATCACCACCTCTGCGGGCTGGGACGGACTGCTGGCCCCCATCCTCAACAGCGCACCTCCTGATTGTGACCCTAAAAAAGTTCACCCAGGAAGTTCAGTGGAAGGGGACTGTGGGAACCCATCCGTGGGGATTTTCTACTTTGTCAGCTACATCATCATATCCTTCCTGGTGGTGGTGAACATGTACATCGCTGTCATCCTGGAGAACTTCAGTGTTGCCACCGAAGAGAGCACTGAGCCTCTGAGTGAGGACGACTTTGAGATGTTCTACGAGGTCTGGGAGAAGTTCGACCCTGACGCCACTCAGTTCATAGAGTTCTGCAAGCTTTCTGACTTTGCAGCTGCCCTGGATCCTCCCCTCCTCATCGCAAAGCCAAACAAAGTCCAGCTCATTGCCATGGACCTGCCCATGGTGAGTGGAGACCGCATCCACTGCCTGGACATCTTGTTTGCTTTTACAAAGCGGGTCCTGGGTGAGGGTGGAGAGATGGATTCTCTTCGTTCACAGATGGAAGAAAGGTTCATGTCAGCCAATCCTTCTAAAGTGTCCTATGAACCCATCACGACCACACTGAAGAGAAAACAAGAGGAGGTGTCCGCGACTATCATTCAGCGTGCTTACAGACGGTATCGCCTCAGACAACACGTCAAGAATATATCGAGTATATACATAAAAGATGGAGACAGGGATGATGATTTGCCCAATAAAGAAGATACAGTTTTTGATAACGTGAACGAGAACTCAAGTCCGGAAAAGACAGATGTAACTGCCTCAACCATCTCGCCACCTTCCTATGACAGTGTCACAAAGCCAGATCAAGAGAAATATGAAACAGACAAAACAGAGAAGGAAGACAAAGAGAAAGATGAAAGCAGGAAATAGAGCTTTGGTTTTGATACACTGTTGACAGCCTGTGAAGGTTGACTCACTCGTGTTAGTAAGACTCTTTTACGGAGGTCTATGCCAAACTCTTTTTATCAAAAAATTCTCAAAGGCAGCACAGCCATTAGCTCTGATCCAACGAGGCAGAGGGCAGCATTTACACATGGCTATGTTTTGCTTTGGTAAATGATTCTTTTAAGATTTGAGAGTGTAACTCTGAAGGGAAGAGCCATCACTGCATTCAAGGGTGACTTAGACATTCTAAAAATCAGAAAACCAAGTCAAACATTTTCTCATTTGCCTCCATGTCTTTTCTCTAGGTTCTAAATAAATGTGCACCCATGTGAATCTAGAAATCCAGGCATACATGCACACATGCACACAGTCACAAATACAAACAGGATTGGCTACGATTTCAAATTCTATGTAAATGTTTCACTTTGGTTTGCAATGAAATTTCCTTGTAAAGGAAATGGGATTAGTGACGAAGGTTTTGTCAAAACATCTTATTATTAGGGAATCAGAATCTTTAATCTAAAAAGAATTCAGTTTATATTTTTGAGGTGCTGAAACTTATCCTACATTGCGTCAAAAGCAACTTATAGGAATCTATAAGATGTCATGGAATTGAAAAACGTATGTGGGCTACTTATTTAAGAAATCACTTTCATTTGTATATTAGCATCATTCACCTTGATTTATGGACATCTTGGACATTTTGTGGTCACATGATGCTCCCACAAAATTGTTTAGCTGAAACTTCAGGCACACATCACAGAGAACAGCTACCCAGTCTTACGCTCCACCCTGTTCATACAATAACCACAGACCTTTAAACATTATTTGGAATATAAATATTAGGTTTCTCAATATAAACATGTGAATATTAACAGAAAAGTTAATTTACAGCGTTTTACTTACTAATGTCTATCCAATCTAGTTTGCACAATGAGACAGCTCTCACCTCTTACAGCCAGTTGCCACATTTCTCTTCTTACGAAGCTTCGGTTTGTCAGACTTTATCTCTAAGCAAATTCTATGTTTCCTTTTTAATGAAACGTATCCTGAAAAGCGATTAGCTACTTGATACTTTAGTGCTTGTTTGAGCAGATGACTGGAGCATGGTATGTACCCCATCTTTTAAAATACAATCCTTAATGTGTTTGGCAGCTTCCCAAGTTACAGGGAACGCCGGGCTTTTAATATCTCTCCGTTCACCAGGTGTTTTGTATGAATGAAATGACATTCAAAGAGTGAGTCTCATTGGCTTGCTTTATTACCAACGACTTTCCTAAATGAGGAACTAATCCTCTGAAGCACTATTATATCCCCTTGTAAATAACATAGATGTCACTTCGTTCTTAATATTCTAATCCATGGTGTGACATATATTTTGCATTGATCAGTAAAGTAGTCTGGGATAACCATTTTAAGAGCATATACATTTTGAGGTAGTTGAAGTTAATCTACCAAGGATTAGAAACCTACTCCAAGTTTTTAAAGTACTTGATAAAAATGAATGACCCTGACAAATTCTCTCATAATTTTATTCCAGCAATGTGAAATCTTTCCTCCAACACTTTATCCTTGCAGAGAAGAAAGAAAAAACAAAGATAAGCCCATGGGCCATGTAAACAAAGGGGCTTTATCTAGAAGATTCTGAGAGAACCTTTGAAGTAAATATGTAAAACATACTTCCTCAGTTTGCCTTTGAAATTAAAAAGTAACACAAAAATATGGATTTAATAAGTCATCAAAACACATTCTTTATTTCTGGCCCAGTTTAAAGGAAAGGATTAAAAATCCCTATAGAGGGGAAGGGACAGAGAGAGAAAGAGGGAGAGAAGAAACAAAGTACTAGGGACAAAAAGATTAGACAGAATACGTCCAGGTTTTCACACTATGGGCTTTGTCCGGGATGCTGTATAAAAGTCTCTTTCCAAATGTTTGTCATAAGGGGATCGAAGAAATTAAGTGCAAGACTAAAGGTTGTTTACAGATATCATTAATCATTAACAGTTTGGGAAGCTGCTTTTACATTTCTATGGAAGATGCCAAGGAATGCTAAGCCAGACAATACAGATGCATTGTGCATCTGTCAAGCGGCTAAAATATGTTTGGGCAACTTAATTAGGGAAACACACAAAGCCTTACATTTCTGACAATTTTAATACATTTAATTAAGAAATCAGTACTTTTATTATTTCACATTCCTAAAATATAACTATATCGTCCATTTTTATTGATATTATATGTGTGGATGTTTGTTGTAGATTATCTGTAATTTACTATTAATGTTTTTACACTGATTTTTGTGAAAATTTAAAATATGTTGGCAACTGGTTCCTCAACACAATTTTTTTAGCATTACAAAAAATAAACAGGTATAAAATTTCTCTTTTTTCTACATCATGTTGAACATATTTCATTCTGATTTACACAATTTTAAATGTAATATTATTTTATATGCATATGTTTATCTCCAAAATCACTACTTATGACATCATATCAATTAAAAATGGTATTTGACACTAGGACTGTATTTAGTAAAAGTTAAAAGCTTTCACCCTTTTTCATGTTGATTAGGGTTTGCACTAACTATAAAATGTCACCCACGGAAGCTACTAGTCACTGAAATTATTTTACCTATTGGTGGAGAATGGTGACTGGCCAGAAAATATGAGTTAGCATTAAGTAGAAGACAGCATACGTGACCACAAATCCATGCAGGTAGTTTGCGTGAAAACGGGAGAATCTCATTTTTCTGTTTTGTCTCTTCTCACTGTGCAAAAAGGACAAGAAATCTTTGGGCTATTTCTAAATTCGAATTGTCACAATTTGCAATCATAAATGTTTAGCACGACTTTGTAGAATTTTGATAGTTTTATAAAAGAGTGAAAAACAAATGCATATGTAAATAAAGCAGCCCATACTAACGGATTCATCAAATGTTAATATGTAAATAAAGCAGCCCATACTAGCAGATTCATCAAATGTTAATATGTAAATACAGCAGCCCATATGAGCAGATTCGTCATATGCTAAGGGAATTAATTAAAAGGAAGCAACTAAATAAGGATGGTCAGTGATTGATCTGGGTTTAGAACTTGTGTTTGGAGCCACCAATTTTTAAGTATGTATTCTCACTTTATTAGTTTTCTAAAGAAAGCAATCAAGAATTGCTCCCAGAAAATGAGTAAGTAGCCATGAATATATGAATGCTGTTTACAAAACCCATAGACCCATGAATGCTCAAAACGTCTGAGTTTGTAAAAAAAAATACATTGTAGTTATACTTGACAATTTAAAATGTTAATAGAATCTAAAATAAAAGTCGCTTAAAATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000006639:ENSRNOT00000065126:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.223
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.4=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.1=42.2),PF0061222=IQ=WD(100=5.3)
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]