RnoINT0131529 @ rn6
Intron Retention
Gene
ENSRNOG00000053122 | Scn1a
Description
sodium voltage-gated channel alpha subunit 1 [Source:RGD Symbol;Acc:69364]
Coordinates
chr3:52421613-52430353:-
Coord C1 exon
chr3:52429871-52430353
Coord A exon
chr3:52421734-52429870
Coord C2 exon
chr3:52421613-52421733
Length
8137 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGA
5' ss Score
10.06
3' ss Seq
TATGACCATCTTATGCCCAGAAA
3' ss Score
4.22
Exon sequences
Seq C1 exon
GTCCTGAACCTCTTTCTGGCCTTGCTTCTGAGCTCATTTAGTGCAGACAACCTTGCAGCCACTGACGATGACAACGAAATGAACAACCTTCAAATTGCTGTGGACAGGATGCACAAAGGAGTAGCTTATGTAAAAAGAAAAATATATGAGTTTATTCAACAGTCCTTTGTTAGGAAACAGAAGATCCTAGATGAAATTAAGCCACTTGATGATCTAAACAACAGAAAAGACAATTGTACATCTAACCACACGACAGAGATTGGGAAAGATCTGGACTGTCTGAAAGATGTGAATGGAACCACGAGTGGCATAGGGACCGGCAGCAGTGTGGAAAAGTACATCATTGATGAGAGTGACTACATGTCATTCATAAACAACCCCAGCCTCACCGTGACTGTGCCCATTGCTGTGGGAGAGTCTGACTTTGAAAACTTAAACACAGAGGACTTTAGCAGTGAATCAGATCTAGAAGAAAGCAAAGAG
Seq A exon
GTAAGATGCTATAAATTGGGGAGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAGATGTATAAATATATGTATGGATTATAGTGTCTATATTAATGATTTGCAGAATCTTTCTGATATAACCTCAAAGACTATTTTATTAAGATACCAAAGATCTGATCTCAGGGAGATGAATGCCAAAGCAAAGTGTAATATACTGTCGTGTGAGTTTTCTCTTTCTTCTTAAAGACTATCAGTTACATCGATAACAAATGGTAAATGAAAAACTAGCACAATTAGTTACTTAATCTCTGTAATGAACAGAGAAGAACCAGATTATTGTAACACTTCCACTAAAACAATTAAAACAGTTTCAGCTGCCCAAGAGCATGTAAGCTGTGAGGTATGAAAACTTACCTTGAACCTGGAGTCTTTGTCTACAAGGTTTTTATATTTTTGTGTGTGTCACCTCAGCTCAAATACTTTGAGATAAACTTCAGAAAGAAGTGTTCCACACCAATCCTAACATTAAAATTATATAATGTTATAGTTCTATATGAGCTAAAATCACACTATTCTAGGAACTGGATGGATTATACAAACAAAATTTATTTATTCACTATTCTGGAAAGCAGGCAATTCAAGACGATGGTACTGCATGGTCAGTGTCTGGTGAGAACGATCTGCTAAGGTTGTAGATGGCTGCCTTCTCATTGTGTCTTTACAAGACCTGACTGTGATATGTGCACAGAACAGAAATAAATCTGTTGTCTCTTCCTCAACTTGTAAGGGCATCACTCTATTGGATTAGACCCTTGGCATAATGATTTATTTGATATGTAGGGTTCATTATCAAACTTCACTTTCAGATACATAGAGACTCTCAGCTTCAGCATTTGAATTTAGAACAGAAGAATGGGTGGGAGAATGCAATCCAGTCCATGAGATCCTACTTGAAAATACTAAGCTAAAACATTCATGGATATTAGGATGTCTCTAACTTCGGCTAACCTGGGCTAACTTACCATTACTACTTCTCAACAACCAATACATTCCTGTGAGTGTATTGCTCGCTGTGGTGCTCAATAGTCTGTGTGTCCCAAATGTTTTTTATCGAACTACATTTTCATCATATGGTGGGCTTTCTGAGATATAACGCTGTTACGCATTGAGGAAAGGAGCAGTTTTGTAAGACAATTCTGAAGAAGTCAAAAACTAAGAATATGTGATCAATTCTTTCATGCAAGTCTTAAAGATAACAAAGCATATTTAGAGCTTACATAATCTAAATACTTTAAAGCTATCAGTTAAAGATACTCTATTCCTAATAAAAATTGACTGGTATATCTGTGGGAAACATTGGCGTGTTTTGGTTAGTAGTTGCCTAGAACACATACATAGACATATGATATAATTTTAGGTTATTGAATATGTCCATTTAATGATGATTCAAGCTTTTATAACAACTTTTGTGTCATATGGGTAATTCCCACTTTTAGAAGTAGGAGCTGATATTAAAGCTTGCAATGGTTGTATCGGGATATTTTGGGGGTTTGTCATGAAAGAACAGAAAGGGGAATAGCACAGAGGCACCACGGTGGGAAAATACTAACTGCAGTGTCCATAGAGATGGATTTTGTGTGGGAATGAAGATGTGGGTTTTTTTAAACTTGATGAGTTTCTTAAGGTCTACTATGTGAACATTATCTTATTTAAATTGTTTATTTGTTACCCTGTGTTTCCTAAGCATAAATGATAGATGTTGACTGAGAAAGAAATGTTTGCCAAGCATTGTGCTTCATGACTAAAAGCCCATCATTAGGTAGGTAAAGTCAGAAAGGCCAAGAATTCAACATCTCAGCTATATAGTAAGCTCTAGGGAAGCTTGGAACATGTAAGACCATACCTAAAAGTAAAAATAGCAACAAAATATCTTGTTTAAGCACTTCATTCTAAATTTCTAATAAAAATAAATTAACAAAACTCTAATTTGGACCTCCTCATCTTATGTCATGAATCTATATGTATACATTTAATATTTGATGAATATAACAATGACTACTTATTATGTACTGAATGCATATTACTGATAAACTATTTTACTGTAAAATCATCCATAAAAAGTATTTTTCCACTGAAAATTCACATGACTCATATTTGCACATCTTATGTTTGTATTCATCAGATATAGAAAGAACACTGACATCTTCATCAATGATTGTCTACAGAATCCCTAGAGGCAACTCCCTTTCTCTGTGCTTTTGTAGCTTAGAAAATGCTGAGTTAAAAGTTGTAGATATTAGAATAGTATAAAACATTAAAGATGTAATGTTTCTAAATTACAAGCCATTACTCAGAGTTTAAAAGGCAATTTGTCACATCATTTTTTTTATTTTAGTATAGTAGACTAGATTATGTCAATGTCCTTTGTCTATTGTGGTAGTACCCAAACAGTGTATACTGAGAATACCACTTGGTTTTATGTCAGGAAGTTAGGGTAGTGAAGAGTGACATAGGGAAGCAGACATGATGGGGCACTAAGGGCTGCTGTTTAATGTTGGGGAGTGTGATGGCTAGTCTGGGAAGAATCAGCTATAAAACTGTGAGGCACACCTCAAGGTATTTCTATTAGGGAGTTTATATAAAGGGTTAACTAAGGAGAAGACTATCTTTGAATGGAAGTAACACCCTGCCAGGGGCTAGGGGCACAGAGTGAAGGAAAGGAGAAGGGGGGGAGGAGAAGAAGATGACAAGAAGCAGGAGGGAAAGGAGGAGAGGAGGAGGAGGAGAACAACAACAAGTACAAGAAGAAGGAGGAGGAGGGGGAGGGGAGAGGGAGAGGGAGAAGGAGAAGAAGAAGAAGAAGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAAGAGGAGGAGGAGGAACAAGAACAAGAAGAACAAGAACAAGAAAAACAAGAACAAGAAGAAGAACAAGACAACAAGAACAAGAACAACAAGAAGAACAAGAACAAGAAGAACAAGAACAAGAAGAAGAACAAGAACAAGGAAAAACAAGAACAAGAAGAACAAGAACAAGAAGAAGAACAAGAACAAGGAAAAACAAGAACAAGAAGAACAAGAACAAGAAGAACAAGAACAAGAAGAAGAACAAGAACAAGAAGAACAAGAACAAGAAGAATGAGAACAAGAACAAGAACAGCAAGAACAAGAACAACAAGGAGAAGACAACTATGATGACAACAACCACCACCATCACCACAACCACGACTGTGATGACGACGAAGACCAGTAGAGGCCAGGTTCCCTCTCTGTTTCCTTGCTCACTGTGAAATGCACTGCTCTCAACCAGCATGCCCCGCCCCCATCATGCACTGCCTGCTCAGAAACTATGAGACAAAAGAAAACATTCCTCCATTTAAACTGTTTTGCCAAGTATTTTAGTCCTCCAAGACAATAATGACTGATCAACAGAGCATGAGGGATCCCATTAACATGTGTTTGCATACATGTATCAACTCAGTGAAAGGCTAAGATTGAAAACAAGTCATGCTTTGTTTGTAGATAACTATGGACTCCTTTTATAGATAAGTTCTTTCCGTGCTAATCTATATTGCATCTCTATGTGCATACAGCACTGAACTATGTACTCTTTCCATTTATTTTATGACTAATTAAAATTAAACTTTCATTAATATCCATTAATAATATCCCTGTAATAAACCAGGTCACAAAATAAAGACATTTCCCTTTCAAAGTTAAAGCTAAACAGAATGAACCACCCATTTGGTTCCTTCCAAGAAACACCAAGCTGTTGCTGGCTCTTTTGCTCTATTATGCGTTGATTCACCCTCAAGGTCGAAATCATTTCTTCTACCAGAGAACAATTTTAAAAGCAAGAAAAGAGGCATAAATCCACCGTGAAGGGAAAGTGCTCTTACCGTCAGGGTCACTGTTACTAAGTGATTTTGGAATGCCCTAGTGGACAAGGCAAAATGGGTATTTGAAATGCAGTGCGGTTTCTGCATTTCTTCTTCTCACCTACTAAATAACCCTGTCAAGTACCTAAAGATTGCACAGACCAGAGGGTTCATATGTAAAAAATACCCAGCTTCTAAATAACTAGCCAACTGAGGAATTAATGAATTAAAGATTGATTAATAGAACAATAAATGCTGAAATGTATTTGAAATATTTTATTAATTTCAAAACAAGGAGAAACATACTTTAAAAACAAAAGTTAATGGCAGTTTAAGAATATAAAAGAAGTAATATATTTCATTAAGTTTTAAATTAATAAAATACTTGTTTGACAACACTGGGCTTCGTTGTCACCTAGGATCTTTAGAATGTTGTATGAAACGTGTCTGTGTGCAAAGCTGAGGAGAACCCCTCCCTCACAGCTCTACAGCTCCCTCCAACTTGAGCGGCAGTGCTAGCTCAACCAAAGAACTGCACTTACTTTTTGTCTTGTTTTAACAATGAGAAAAATAATAAACTTGCATTTTCTTTTATAGTTCTGAAACATTGTTTTATCCTGTGATTAAAATGTGAGTAACAACTTAAATGATGACATTGAGACTCTTTTTTTTATTTCATATACTAAGATTTACAAATACACCACACACACACACACACACACACACACACGAGTATTTGCTTTTATGTCTATCTGTGCACTGCTTAGATACCTGCTGCCTACGAGATCAGATGAGCGTGTCAGAACCTCTGGAACTGGAGTTATAGGTTAACAGCTGCCATGTGGATACTGGGAATTGAACCAGGGCCCTCTAAAAAACAGACAGTGCTCTTAGGTGTTGAGCCATCTCTCCAGACCCAATATTAAGACTCTTAATGACACAATGATGAGAGTGGGAGTATGAGATGCTTTTTCAAATATACATGTATGTGTGTGTTATATAAATATATACACATATATATATCCTATTATAAGTATGAGTAGTTCTTTTAAAGATTTATTTATGTTATACATGTGAGTACACTCTTGCTGTCCTCAGACACACCAGAAGAGGACATCAGATCCCATTACAAATGGTTGTGAGGAACCATGTGGTTGCTAGAAATTGAGGTCAGAAAATCTGGAAGAGAGGTCAGTGACCTAAACCACTGAGCCATCTCTCTAGCCCAGTACTAGTATTTTTATTGTCAGTATATTCACAAGTATCCATAAGGTGTTTATGAAAATGAACTTTATACTGGAACTCAAAGTGACGCTTAGTAAATTAAGATAGCAGATACTGTAGAGGATTATCTGACTTCAGGTCATTTCAAGCAAAGTTAAAATATAAATCAGAAGACAGAATTCCATCTAAAAACTAAAGGAAAATAGGCCTTTATGTAGCCAAAATTTTGGTAAACATGGTTGAGTTTTTACACACCAATGTTTATCTTGTTTTCATTTTTTGTCTTACTGTCCTGTTATATCCTCATTGGAAAGAATTGTTTCAATAACCCAAGAGAATCCAGTACAAATAGAAGTAATGTAATCCTCAGACTATCTTTATGAATTAGGATACCAATATAAAAATAACAAAAAAACTGTCAGTCTGCATATATTCATTTAAAAGACTTTGGAAGAGTGGAACCCTTATGTAAGTAGCCTAAAAAGTCAAAATGTGAAACATGAATAATAAATATAATCTAAAAATGAATTTTCCTGGTTTATATCTGTTTGCCTTCTACATAAAGTACTTTTGAAGATGTGTCTAAAAAATAACATAGTGCCTTTTGGGTTCTTGCGATTTTCATTCCAAGCATTTCTCAGACAAGCCTTTTAATTAGGCCAAAAACAAATAGTACTTAGTTTCATCAAACAAGTAATCTTTTAAAGGCAGAATAAGAAGACATTACTTTACGTGCATCAATGAAAACAGTGGTCATTGTGAAAAAGATGCTATGGTTGGCAAGATGTGGAACCAGCTCTAGGCAGTGTCTTACTAGTGAATGCCAGTGCTACAGCCTGGCTGCTTAACAGCTTTTTGTTTTACTTGACATTGAAAAATGATACCACTGACGATGATGAGGTTTTATTTGAATGATACCTGATATTGTGATTCTTGATAAAGGCTAAAATATCTTTAGAGGTCTAACAGACCACTGTTAGATGCTCAGCAAGTTAAAAATTCTATTTAAAATAAATTTTATCTGAATCCCTGCCCACACATAAGTTTATTCAGAGGGAAAGAGGAGATAGAATTTCTAGTAATTAGTGAATGTTGGTGAAGACTCTCAACTTCTCAAGTCAATTCACCTATTACATGAAGAGAAGGCATCTTACACAAAATGTTTTCTTTTATACTGAAGAATGTTGGATAATAATAAAATGCTGCTCACAAGTTTTTTTTATAAAATAAGGAATAATTCTTGCAACAATAATAACGCCAACTAAAGCTATTGAATATGACTACTGCAGTGGCAAATCTCAGCATAGAACTGCCCTGTTACAGCCAAGTATAAATTCCAGTTATGTTGAGGATAAGACATAGGACTCCTCAGAATGGGAATTAGCCCACGGTCTAATGAATCTCTTCATTTATTATATGAGCAAGTGTATGTCTTGTCTATGGATATGTTTTTAAGTCAGGATAAATGGTCGAGTCATGGATAAGGTCATTCAAAGCAAATGCAGCTTTAAATGCAGATTTAAAATCTACCTGTTGTATCCTGTGCCGAAGAGCAAATGCTGAATGTGTAAACAGGCTACCACCATACATGTTGAAAAGTTACAATTAGTTTGCAGTGAAGAATCTATGCATAACGACAGGGCTAATCTTTAAAATGGACACCCAGAACTGTGATTAGTCTTTCATGTCAATGCAGATCTCCATGACTTCTAGCTTTCTATTTCACAAGAAACCTAAAAGGAAGGGTGGCAGTCAGCTGGATAGGGACGCAGGTGTAGAAGCCATCTTCCTTTGATGGAACAAAGAGAATTCTGTTTCATATATATGAAATTATTATTAATAGTTTTAACATGGTGCTTAAAGTTTATTATTTAAAAATATGTGTTGATTGGGTACTTGGTGTGATCTCCTTTAGGTTAAACATAAATCCATAGTTTGGAAGACATCATATTCTATTTCAAGTATCTAATAGGGCTATGGATGTTATAGTTGCCAATAAACACTAAGTTTCTAATGGCGCTCAATGTATCTTCCTTGACTAAATTACCAAATGTACTAATTACTTTTACCCAGATGAAGGTCACAGGATAAGTTGATGTTTTCTGCCATTTTGCCATCCTTGACTCCTGAGAGGCCAAAACGAGAACCATGTGTCTGGTTATTACTGCCAAACTCTGAGAAATGCTGCTTCTACTTAACTAGCTTTACATGGGATATTAGTATAAACATTACTCATTGAAGGGAAAACTCATGTTTCCATGCATCTATTGGTCTGTTCCTGCAACACTTTTGATTCTAAGATATTTTTCTAATAATGAACCCATTAAATTAGGAGTCTAAGGTTATTTGTTCATTGACGTATTTTTTTTACTTATTTTAAGACATCTTTTCTCCAAAGGTCATATGAAATTTATATTTCATATGTGAATACTTTGATACTAAATAAATAAATCTGGTCCTCTGATCTACCTGTTAGTAAGTATAAGTTAAAGCATTGGGCTGCAGTTGCTCAGAATTGAGACACTATTAAAGAAGCATGTGTAAATGTTTAAACACGGAATAGCTTCATGATTTTATTTTCTTCTGAGGTAGGGATTCTCTGAATTCCATTTCCCTTCACTCTCACCCAACTCCTACAAGTCATGACACCTTCCCCGTCTCCAAATCCACGGGATAGACATTTCCTCACTACATGCTGCTGACGGTCATTTGTAACATCCCAGCACAACTCAACAATCTGCACACAGAAATTCCTGGGAAAGGAATCAACAGTGAGGTTTTCCTACTCCCTCTTCTGAATGTTCTTTTTACTCTAAATTTACATAGCACCTTACCTTGAGGAAAAACAAAAATACATTCATAGTCATAATCTCTTCTTGGTATGCCACTCACTGGGGAATTAACTGAAAAGAATGTGCTTTTTATGACCATCTTATGCCCAG
Seq C2 exon
AAACTCAACGAAAGCAGTAGTTCCTCAGAAGGAAGCACAGTAGACATCGGGGCACCTGCGGAGGAACAGCCTGTCATGGAACCAGAAGAAACCCTTGAGCCCGAAGCTTGCTTCACTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000053122:ENSRNOT00000083552:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.161 A=NA C2=0.780
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=5.0),PF065128=Na_trans_assoc=PU(61.4=85.1)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(17.9=100)
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]