MmuINT0139769 @ mm10
Intron Retention
Gene
ENSMUSG00000034810 | Scn7a
Description
sodium channel, voltage-gated, type VII, alpha [Source:MGI Symbol;Acc:MGI:102965]
Coordinates
chr2:66673425-66680345:-
Coord C1 exon
chr2:66680075-66680345
Coord A exon
chr2:66676562-66680074
Coord C2 exon
chr2:66673425-66676561
Length
3513 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
GTATCTTTTCTCCGGTGAAGGGC
3' ss Score
5.34
Exon sequences
Seq C1 exon
AACAAATTCCAAGGCTTCCTTTTTGACCTAGTAACACACCGTGTCTTTAATGTTATCATCATACTTCTTATCTGTTTCCAAGCAACAACCATTATGATACAAAAGGATGAGCAGAGTCCACAAATGGAAACTGCCATCTTCTGGATGAACTCCATTTTTGTCATGCTGTTCACTCTGGAATGCATACTGAAGCTCACTGCCTTCCGTTGCCACTACTTCACCAGTGCATGGAATGTTCATGACTTTATGGTGGTCATTTTCTCCATTACAG
Seq A exon
GTAAGGTTGGCTCTTGTCATTTTTCTTTAGAATATTACTTCAGTCTATCACAATATGTATTGAGATGGTGACCTTGAAGAAGCAATGGTGAGACCATTTTCTTTCCCAAAAGATAGATCACTGTCATATGTGTGTGACTGTGTGTGTGTCTGTGTGTGTGTACAATTACTATGTTTTAGACAATACAGCATATTACATATTATATGTGTTTGGAAACATAAGTGTTATCACAAACTCGTTACGTGCTTGTTTATCCCTAATCTATAACATTGTCGGCTACCATGAGAAGGAGCACCACGTATTAAAATACATGGCTTCTAAAGCTCACTAAGATTCCCTACTTTTAAGTATTTTCAAATGTTCTCAACCTTCTCCGCATTAAAATTTTAGTACTTAAATGACTTTGTTCCTAGTCTGTGAATTTGTCTGTGGTTTTCTCTTACTTGAGTAACTTTACATTTGTTGACAAATACATTTCATTGTCCTCTTGCTAAATAGATAGAACTCTGCATGTTAAGGTTAGGAAGATTTTCTGCATACATATCATTTACAGACTATCAGGGCATACATATGCAGAGCAGAACAATCACACATGTGCTGAAGCACAGAGTACCATAGCACAAGGCAAATGAAAGAGCACCTTATCAGTAACTGGGGGTCCCCAATGGAGGAGTTAGAGAAAGGACTGAAGGAGCTGAAGGGGTTTGCAAGCCCATAGGAAGAACAACAATATCAACCAACCCAGAACTCCCAGGGGCTAAACCACCAACCCCATGGCTCCAGCTGCATATGTAGCAGAGGATTGCATTATCTGGCATCAGTGGAAGGGGAGTCCCTTGGTCCTGTGGAGGCTCAATGATCCAAAGTGCGGTAATGCTAGAGTGGTGAGGCAGGAGTGGGTGGGTGGGTGAGCACCCTCAAAGAAGCAGAGGGAGTAGGGATGGGATGGGGGTTTGTGGAGGGGAAACTGGAAAAGGGGATAACATTTGAAATGTAAATAAAGAAAATATCCAATAAAAGAAAAGAAAAAAAAGAAGTGAATTTAAACAGAGACCTACTGTGTAAGGGCATATCCGGGCACTAAACTTAGGGCAAAATTATAGCAGGAATAGAGAAATGTCTTTAGTGTTTGCTTCTGGGTAAACAGGGTGTGATCTCCATGTGAGTAAGGAGTATTTAAGAATCAAAGATTTAATGCCTGCACTTAAGGCACAGGGATCGTTGCAGAAAAGGGGTAGATAGGAAGAATGTAAGAGCCAGAGAACCAGGGAATCTGCTGTGAGATTGTGTCTCCTAAGAATGTCAGAAACTCCATCCATGGAATCTCACCAATGTGGCTGTATAAACACTAGATGAATAAGGATGATAAATATGCTACAAGGGAAAGCCCAGGATATCTCTACCATACACAAACAACTATAGGAAACAAGTAATGTTATCAGTATTTCCAGGGAAGAGCACACCAATTGGTTATCCCATGCCAAATGGTCAACCCTGAAAATGCATATATATATATATATATATATATATATATATATATATATATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTATATGTATGTGTATATATATACATATATATATATATATATATATATATAAAACACTACACAGAATTGGCAGGTTGTATTTGCATATTAAGGAACAATTATGTATGATGTGTTTATGCATATATATATATATTCATCTGCAGAATCAGAGAGAGAGAGAGACATAGACATATATAAATATATGTGTGTAAACAATTAATGTAAAAAGGAGCCTTAAATTTAAAATAGAGGAAGGAAAGGTATATGGAAATGTTTATATGAAGGGAAGGGAATCTGATGGGATTATATTATAATCTCAAAAAGTAAAAAAAATTAAAAGGTTAATGATATCAATCAGAAATTTCATAACAGAAAATAAATATATACATTACCTGTCTAAAATGAGTTCAGAAATTTCACTTTCAGTAAAATAGTGAATTCATGTCACTGATTACTGAAAGAAAAATATGAGTTTGATAGGAAAGCATATAGAGATGGAAAGAGGCAACAGGAAAGAAACAGTGAATTATATACCTACAGTGACTGAGGTAGGAGTTACAGAGTGAGCAGGAATAACAAAAGCAGCCACAGAGAAGGTGATTAACCCTGAACTTCCAGCCTTCTGAGGCAGTCATCTGGCCAAGGCACTGATGCAGTCAACTGAACTAAAATAATGAGTATTATTAAAATGAGATGGTTAAAGACTGACGTGAGCCCTTGGATGGTTCATTGAGGGGGAGGCTGAGGTGCACAAGGAGACCATGAACCACTTACTGAGTCTTCAGCTGAGTGTAAGAGATGAGAACAGCATGAGTCACAGATCAAGGGGACGATGAGAAAGAACTGAGTTGGACAGATAATCCACAAAGGGTCAGGAATGTATCATAGCTTTTAATTTAAAAAAAAAATGATTGGACAAAATGTGCCTGGGAGTTTCACTGGAAAGTTACAAAGATACTTATGCTGCCATTTTGCCTTAGAAATATAGAGTAGATGAGAATATGCATTCTGCACATTAAAGTGTTACACGAAAAATAATGTCATCTGCAGAGTCAGAGTTTAGATAAGGGGTTTAATTTCCTGGCAGTGAGCATGAGGATGAATTTGTGCTCACGAAAGTGAGGATGCCTCTTTATTAATGGAACACCTTGGAAGATGGGAGAGAGATGGGAGTTTGTCTAGTGTACAAGAGTCACTAGTATCCATTAGAAGGAATATACATGTGACAGAACCCCACCAAAATGCCATCTTGGAGGGTGGGAATGTTAACAGAAGTATGAGACCTGATATTTCCTCTCAGCAAATACAAAAAAAAAAAGCCTCAGGACCCTGTCCTTTGCCACCAAAACTAACATGAAGCTATAAGGACATGCTCACACCGTCTGCTCATATTTAAAGGTCTTCGGACTCAGATACTATTTATAAAAGAAATAAATTAGATTACAATCTATGAACCACTGAATGCTATACATTTTTATAGTCTTGGTTATCAATAATATCTCCCTGCCTTGCATTCTATTCATCTTTAATAACTATCATAAGTTAATGCATTATAAAGTCATTGAGAGAAATTATATTATCCGTCTTTCTATATTTACATGATACATTGTGAAGGTGTTAGGCAAAATTCCTTAATCCAACAATGTTAGAAAATTTTTGACTATTGAACTACAGTGTGGATCTGGTCATCTGTGATTTCAAACCTAACTTAAAATAATAGCACAGACGAATTCTATTCTAAATTTTGGTACAGATCCTGACCATTGGTACAATTAGTAGTCAACTAACTCAATGTTCAATGTGCTTTTCCAGGATATAGGTTAAGTGATGGAGTAATGGCAGACTCATGAACTACAAAACTAGATCAGTTGCAAAATTAATTGTATTTTCTACATCGAGTTGTGTTTGAGTAACTTGGTTACTTCCCTGTATCTTTTCTCCGGTGAAG
Seq C2 exon
GGCTGCTGCTACCCTTGACAATAGGACAATACTTTGTGCCTCCTTCCCTGGTGCAGCTGATTCTTCTCTCTCGAGTCATCCACATCCTGCGTCCTGGGAAAGGACCGAAGGTGTTCCATGACCTGATGCTTCCCTTGATTCTGGCGCTCCCAGCATTGCTGAACATTAGTCTTCTCATCTTCCTGGTCATGTTCATCTACGCCATCTTTGGAATGTACAACTTTGCCTATGTAAAGAAAGAAGCCGGAATTAATGATGTGTCCAACTTTGAGACCTTTGGAAGCAGTATGCTCTGTCTCTTCCAAGTTACAACGTTTTCTGGTTGGGACGGGATGCTGGATGCAATTTTCAACAGTCAGTGGTCTGACTGCGATCCTGATAAAATTAATCCAGGGACTCAGGTCAAGGGAGATTGTGGGAGCCCTTCTGTTGGGATTTCTTATTTTGTCAGTTACATCCTCATATCATGGTTGATCATTGTTAACATGTACATTGTGTTGATCATGGAGTTCTTAAGTATTCCTTCTCAGAAAAAAAGCAGGACCTTGAGTGAAGATGACTTTAGGAGATTCTTCCGGGTGTGGAACAGGTTTGACCCTGATAGGACCCAGTACATAGACTCTAGCAAGCTTTCTGATTTTGCAGCTGCTCTGGATCCTCCTCTTTTCATGGCAAAACCAAACAAGGGCCAGCTTGTGGCCATGGATCTCCCCATGGCTGCGGGAGACAGAATCCACTGCCTCGACATTTTACTTGCCTTTACGAAAAGAGTGATGGGAAAGGATGAGAGGGTGGAGAAAATCCTTTCAGAGATAGAATCCGGGTTCATGTTAGCGAACCCTTTCAAAATCACTTATGAGCCGATTACAACTACTTTGAAACGCAAACAAGAGGCAGTTTCAGCAACCATCATCCAGCGTGCATATAAAAGCTACCGCTTAAGGCAAAATGACAAGAATGTATCAGATACTCCTGCTATAGATGACCGCAGAGATGATCTTACTTCTAAAGGTGCTCACTCTGGCAAAATCGAGGAGAAGGCATCTATTCAGACCCAGATTTAATGACACTTCCCACTTCTACTTTCTTTACATATGTCCCCAAGCACTAAATGTTAACTGATCTTAAGCTGGAGATCAGAAACTAGAGATAATGATAACATCTGTGTGCCCAGACATCTCCATGACAAGCTCAGCTTTAGGGTCAGTCTTCTGATGCATCAGAAAAGACAGCAGCTCAGCGTTGCTGCGGGTAGCTGAACTAGGTTACTGTTGTCTTTTTGGCTATTTAAAATGTTTCTACTTGGCTTGTCTAGTGTGGCCTCTAGTGGAAGATGTGTAGGAGGAAAGGAGAAGAAAGGGAAATAAAGGTCAGCAGCTATACAGTTTTCCTTGTATATTTTATATATAATTTTAGAGGCAACATGTTGCCACCCTTGAGGCTTAGTGGTTAATATGAGATAATTCCTTAAAGTGCAATTGTGCTTCAGAAATAAAAAAGCCCCGCATTAAATCACAAACATGCATAAACAAATGCTGGGAATGGATGGGAGAGGAATAATGCAGGTCTTCAGAAAGTGCCTTTCAGTTCAGTCTTGGGCTAATTTACAAGATCTATTTCTTAAAACTTTTAACTGAAACCTCCCCTTCCATTTTTTGCTTTCTTCCTGTTGCCTTTTTTTATTTTGTTTCCTTTTTTTTTTTTTGTTTGCTTGCTTGCTTGGCTTTGTTGCTGTTCTTTAGTTTTGGATAGTAGATGACATTGTTTCATTGCTCCTGGTTCCTCCTGGCTTGGCAAGCTCTCTGTGAGCTCCCCAGCAGCTGAGATTTCCAGAGCAGGAAGCATAGAAGAAACCACCCTTAATAATGAGTACATTTTCTGTATTTGATTCACATTTATATCTTTTTTAAAGTGCACATTTACTAAAAGGATACAATAAAGAAAAACGTTAATGGACTAAAGCTTTACCTTATTCTAAAAACTGGTGTATTTTTTACCACTTATCCATAGCAGGTGCATGCTATCATTAAATTAGAAGAGTCAAGGGCAACCAGCATGTTTAGGGATTTTCTGTGCCCTGACCCTTAATTTGGAAACTGGCCACTTGAAAGGTCTTTCCATTGCACTTTGTATTTCTTAAAATGTAAAGAAGAAAGTTATCCTTCAAACAATAGGGCTTGTCAATTAACAGATGAAAGTTAAGTTGGTATTTTATAACACCATTATATACACATTAGTTTTAGTGTTCACTTATCTTTTCCTTTCTTTGTTTTCTATCTTGTTATACATCTAAATACTCATGCAAATGTTTTCTAGTTGAGAATCTATGAAATAACAGACATTAGTTTTAACTACTGACATTATTTTTGTTAATATAAATAGTTTTAATTTCTTCACAAAAATTGTTGACTTCCATTCATGTAGTTTGAGAAATGATATTTTCTTCATTTGAATAAAAAACTGATTTCACTGTGCCTATGAAGTCCTCCAGAATTAAAAAAGAAAAAAATATATATTCTACTGACTTAGATAAGAAGCGTTAAATAGGTTTTATGAAACTCAATGCCATTATATCCTAGAGATTGTATTTTGTAATGAACGCATGGACTTGAGCCTTAATTCCTGTAATCTACTTCCAATCTTCAAAACTCTGTGACCTTACCAACTTGCCTTGGATGATCACCCAAGTAAATGTAATTTCAGAATCTGGTGGTTTTTCTGGATGTTGCTTGTTTGTTTGTTAGTTTGGTTTGTTTGGTTGGTTGGTTGGTTGGTTTTTATTAAAGTATTTCCCTTTCACTCTTCACTCTCTGTCATGTGATGGAGCCTAGAGAAGCATGGGAGGTCTAACTGGTGACATGATGACAGCTTCTGTGTAACCGCAATGTCTCAGTTTTCCAACTTCTGGGAATGTCTTAGTGAGGAAAGTGCTACAGATAGTAAGACTGAATCATAACTTGCTTCCATAAATCCCATTAAAACAACACACTGAGTTTGTAAAGTATTTTGCTGTTACCTATAAAGAATGACAAGCAATAGCCATCCAAAAAGTAGAATGTTTCATTTCTGAATGACTGTTACAGAATATCCTTCTTCTGAGATCCCATAGAAAATAATAAATATAACCTGCTAAGCAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034810:ENSMUST00000042792:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.090
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.4=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.1=47.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
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]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types