MmuINT0139769 @ mm9
Intron Retention
Gene
ENSMUSG00000034810 | Scn7a
Description
sodium channel, voltage-gated, type VII, alpha [Source:MGI Symbol;Acc:MGI:102965]
Coordinates
chr2:66511483-66518402:-
Coord C1 exon
chr2:66518132-66518402
Coord A exon
chr2:66514619-66518131
Coord C2 exon
chr2:66511483-66514618
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
GGCTGCTGCTACCCTTGACAATAGGACAATACTTTGTGCCTCCTTCCCTGGTGCAGCTGATTCTTCTCTCTCGAGTCATCCACATCCTGCGTCCTGGGAAAGGACCGAAGGTGTTCCATGACCTGATGCTTCCCTTGATTCTGGCGCTCCCAGCATTGCTGAACATTAGTCTTCTCATCTTCCTGGTCATGTTCATCTACGCCATCTTTGGAATGTACAACTTTGCCTATGTAAAGAAAGAAGCCGGAATTAATGATGTGTCCAACTTTGAGACCTTTGGAAGCAGTATGCTCTGTCTCTTCCAAGTTACAACGTTTTCTGGTTGGGACGGGATGCTGGATGCAATTTTCAACAGTCAGTGGTCTGACTGCGATCCTGATAAAATTAATCCAGGGACTCAGGTCAAGGGAGATTGTGGGAGCCCTTCTGTTGGGATTTCTTATTTTGTCAGTTACATCCTCATATCATGGTTGATCATTGTTAACATGTACATTGTGTTGATCATGGAGTTCTTAAGTATTCCTTCTCAGAAAAAAAGCAGGACCTTGAGTGAAGATGACTTTAGGAGATTCTTCCGGGTGTGGAACAGGTTTGACCCTGATAGGACCCAGTACATAGACTCTAGCAAGCTTTCTGATTTTGCAGCTGCTCTGGATCCTCCTCTTTTCATGGCAAAACCAAACAAGGGCCAGCTTGTGGCCATGGATCTCCCCATGGCTGCGGGAGACAGAATCCACTGCCTCGACATTTTACTTGCCTTTACGAAAAGAGTGATGGGAAAGGATGAGAGGGTGGAGAAAATCCTTTCAGAGATAGAATCCGGGTTCATGTTAGCGAACCCTTTCAAAATCACTTATGAGCCGATTACAACTACTTTGAAACGCAAACAAGAGGCAGTTTCAGCAACCATCATCCAGCGTGCATATAAAAGCTACCGCTTAAGGCAAAATGACAAGAATGTATCAGATACTCCTGCTATAGATGACCGCAGAGATGATCTTACTTCTAAAGGTGCTCACTCTGGCAAAATCGAGGAGAAGGCATCTATTCAGACCCAGATTTAATGACACTTCCCACTTCTACTTTCTTTACATATGTCCCCAAGCACTAAATGTTAACTGATCTTAAGCTGGAGATCAGAAACTAGAGATAATGATAACATCTGTGTGCCCAGACATCTCCATGACAAGCTCAGCTTTAGGGTCAGTCTTCTGATGCATCAGAAAAGACAGCAGCTCAGCGTTGCTGCGGGTAGCTGAACTAGGTTACTGTTGTCTTTTTGGCTATTTAAAATGTTTCTACTTGGCTTGTCTAGTGTGGCCTCTAGTGGAAGATGTGTAGGAGGAAAGGAGAAGAAAGGGAAATAAAGGTCAGCAGCTATACAGTTTTCCTTGTATATTTTATATATAATTTTAGAGGCAACATGTTGCCACCCTTGAGGCTTAGTGGTTAATATGAGATAATTCCTTAAAGTGCAATTGTGCTTCAGAAATAAAAAAGCCCCGCATTAAATCACAAACATGCATAAACAAATGCTGGGAATGGATGGGAGAGGAATAATGCAGGTCTTCAGAAAGTGCCTTTCAGTTCAGTCTTGGGCTAATTTACAAGATCTATTTCTTAAAACTTTTAACTGAAACCTCCCCTTCCATTTTTTGCTTTCTTCCTGTTGCCTTTTTTTATTTTGTTTCCTTTTTTTTTTTTTGTTTGCTTGCTTGCTTGGCTTTGTTGCTGTTCTTTAGTTTTGGATAGTAGATGACATTGTTTCATTGCTCCTGGTTCCTCCTGGCTTGGCAAGCTCTCTGTGAGCTCCCCAGCAGCTGAGATTTCCAGAGCAGGAAGCATAGAAGAAACCACCCTTAATAATGAGTACATTTTCTGTATTTGATTCACATTTATATCTTTTTTAAAGTGCACATTTACTAAAAGGATACAATAAAGAAAAACGTTAATGGACTAAAGCTTTACCTTATTCTAAAAACTGGTGTATTTTTTACCACTTATCCATAGCAGGTGCATGCTATCATTAAATTAGAAGAGTCAAGGGCAACCAGCATGTTTAGGGATTTTCTGTGCCCTGACCCTTAATTTGGAAACTGGCCACTTGAAAGGTCTTTCCATTGCACTTTGTATTTCTTAAAATGTAAAGAAGAAAGTTATCCTTCAAACAATAGGGCTTGTCAATTAACAGATGAAAGTTAAGTTGGTATTTTATAACACCATTATATACACATTAGTTTTAGTGTTCACTTATCTTTTCCTTTCTTTGTTTTCTATCTTGTTATACATCTAAATACTCATGCAAATGTTTTCTAGTTGAGAATCTATGAAATAACAGACATTAGTTTTAACTACTGACATTATTTTTGTTAATATAAATAGTTTTAATTTCTTCACAAAAATTGTTGACTTCCATTCATGTAGTTTGAGAAATGATATTTTCTTCATTTGAATAAAAAACTGATTTCACTGTGCCTATGAAGTCCTCCAGAATTAAAAAAGAAAAAAATATATATTCTACTGACTTAGATAAGAAGCGTTAAATAGGTTTTATGAAACTCAATGCCATTATATCCTAGAGATTGTATTTTGTAATGAACGCATGGACTTGAGCCTTAATTCCTGTAATCTACTTCCAATCTTCAAAACTCTGTGACCTTACCAACTTGCCTTGGATGATCACCCAAGTAAATGTAATTTCAGAATCTGGTGGTTTTTCTGGATGTTGCTTGTTTGTTTGTTAGTTTGGTTTGTTTGGTTGGTTGGTTGGTTGGTTTTTATTAAAGTATTTCCCTTTCACTCTTCACTCTCTGTCATGTGATGGAGCCTAGAGAAGCATGGGAGGTCTAACTGGTGACATGATGACAGCTTCTGTGTAACCGCAATGTCTCAGTTTTCCAACTTCTGGGAATGTCTTAGTGAGGAAAGTGCTACAGATAGTAAGACTGAATCATAACTTGCTTCCATAAATCCCATTAAAACAACACACTGAGTTTGTAAAGTATTTTGCTGTTACCTATAAAGAATGACAAGCAATAGCCATCCAAAAAGTAGAATGTTTCATTTCTGAATGACTGTTACAGAATATCCTTCTTCTGAGATCCCATAGAAAATAATAAATATAACCTGCTAAGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034810-Scn7a:NM_009135:24
Average complexity
IR-S
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
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: