MmuINT0139759 @ mm10
Intron Retention
Gene
ENSMUSG00000034810 | Scn7a
Description
sodium channel, voltage-gated, type VII, alpha [Source:MGI Symbol;Acc:MGI:102965]
Coordinates
chr2:66694810-66697987:-
Coord C1 exon
chr2:66697553-66697987
Coord A exon
chr2:66694916-66697552
Coord C2 exon
chr2:66694810-66694915
Length
2637 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGG
5' ss Score
10.28
3' ss Seq
GGGGCTATAACTTTTTCTAGAAA
3' ss Score
3.12
Exon sequences
Seq C1 exon
ATACTTTACCTCTTTGTGACATTGGTGAGCTCTTTCAGTTACTATGATGCTACATCGGAAGTGAACAAAGAAGCCAAAAACCTTCAGCTTGCCATGGCAAGGATAAAGTCGGGAATAAACTCCATGCTTCTTAAATTAATGTGCACAGAAAGAAGTGTTCCTACAGAAGCAACAGACCAAATATGTGATCCAAGTGTTAAAGAGAATATTTCTGGCCATACTCTTTCTGAACTGAGCAACACCCAAACTTTCCTCAGATATAAGGACCAGAGCAGCAGCACTGAGAAAACTCCAGTGACTGAATCTGAGAGTCAATCTCTGATTGCTAGTCCCAGTGCCTCTGAAACTGTGCCGATTGCTTCAGGAGAATCTGATATAGAAAATCTGGATAACAAGGAGACTCGGAGCAAGTCTGGGAATGGAGGCAGTAAAGAG
Seq A exon
GTAAGGTGTTCAATTATATTCATTTTTTTTTTAGTGTGGATTTGTGGTTTTGTTCAAAAGAAATAAGTCAATGCTGATGTTATAGAGTTAAATTGCACATTTGATTTTAAATCCACCTTACCTAACTACTGGGTTCCATGGTTTTGACCAAATTATGTAAGTGCCCAAGCTTTTGTTTCTTTATCCGAAAATGAAGATATATTTCTTTTAGAGGGAAGAAGTAAGAGAAATAGTAGCGACTTTGCCTAGAGTAAAGTGATATTCTGGAGATATAAGATGGTATAATTGTGGTGATGAAAATCATTTTTAAAGCACATACATACTTTTGTAAAACATCAAGGTATATGATTGGGAGATGTGGATTCCTTGTGTATTATCATCTTCAAGATGTGAGAATAGCTTAAAAGAGTAGGGCATGATTCTTTCTTGCTTGTTAAGAATGAAAGTTTAGTCCATTCATGTCTACCATATATATAAATTAAAGTACATTAAGACTAAAAAAAATAATAAAGTCACTAGTTTGAATTGTGACTAGTTGGTAATTTTATAAATTCCTGACTTAGAAAAAAAATAGCACACACATTAAAAAGTTGTTGTTCACTTAGCTTCTGAAATATTTAGTGTTGTATCCTTTCCACTTAGAAATAACTTAATGCATTATCAAAAGGTAAAGTTCAGTAAGAGCCATTCTTACACAGAGCACTATGTGCTGTATCAGCTTGAAGCTCTGAGTCTTATTGGGCATCATCTCAGGTCAGTCTAAGGCCCCAGAGAAGGACAGATTGCAGCTTCTCCATGTCCCCATCATGCCTGGCAGCCCTTTCATCAAACCTCTGCTGGTTAGGCATATGTGTTCTATTATAATGCTTCAAATGTGTCTTCTGATGCAAGTTCAGGATGAGTAATCAGTAGCCCCTAAACTTCCCTCTGAGCACATCAATATTGTTGGCTTTCTTTATCCTTAATCACAAGATGATTGCAATCCCTGTTCCTCAAACATTCACACGTATCTTTCTTCTCTGAACACTTGGTTTCCATGCAGCTCTACATAGAACTGCTGTATAGCATAGTAAATAGAACCAGGTTTTCATCAGAAAATCTTAATAATATCATTAGAAAGTCTAAAGCACAAAATACAGAATAAAAGAACAATGTAAAATAACTGTAAATATTGAATTTTAGAGTCTGTCAATAATATTGTATGCTTATTTAAGCCTATATTTGGATAAATAATTTCTCAAAGATTTATTCCTTTACATATATGCTAGGTTATATATTTAATTAGTCATTTTGTCGATTATGTAGTCCAAGAATATTTAGTGTACCTTGGTCTAAAAATACAACTAGTAAAGAATGAAAAACACTAATTTAAGAAATATAGTTTCATTTGTATACATTTATCCTTCCTTTGAAATATTATGTATGTACATAAGACTGATCAAACTACTCATCAAGTTGTGAAACTTTTAAAAAATATAGTGTTATATCACAATACATTTTTCATGACATTCTGTAACCTACCAAAGTAAATTATAATTTATATTTTGAGCTCTATGTGATATAATTAAAAGTAAAGCTGTCGAAGTATCATATCAATATCATATGGACAAGTGTTTGATAATATGTATAGCAAGTATGCAAATATTTATATATATATATATACATACATATATATACATACATACATATATATATATATACATATATATATATAATATCTTTCTGCCCACTTTGTTTCTTTGCTCAAGCAACACATTATACTGAAATTACAAATGAATGTGTAAAAACTAAAGCAAAGAAAGCATTCTATTGTACTGATTGTGCATAAGATTACAAGGAATGACCAAGTATCGATAAGTTCTTTTTCCAAAATCTATCTAAATAATCCTGCAGTAATAACATTTCTATATACTCATTGTGATTTGTCTAGATTAGGAAATATCTTTTGGTGCTACTGGCTTATAGGACTCTGGTGCATTTAAAGGATAGTACATGTTTATGTCCATTTCAAAGTCAAGTAAACCAAGTGTCTACCACATGTACAAAGCGATAAACACTTTGACTCAGCAGCCTTGGGCTCTGTCATGGGCAAGTGCAAATGAAGAACCACTCTCTCTCCACGATCTTCCTATATGGCTTTATCCACTTGCCCCACTCTGTCGAGAGACCTCTTCTGTGTGTGCTTCTCTTTTCATATCGTTATAACATCATGTACAAAGTTGACAAGCACAAAACTATCTGGATTGGATTAAGCAGTTACAATGAAATTTATTTTCCACTCAGTGGTAGAATGAATTATTGTGATGTATCTATCTAATTAAAACAACACATATAAGTCCCATGTGAATTGTCTTAAAATTCATAACATAATTATTTTATAAACAATAAGTAAAGTCCTTTATACCTAAACTTTAATTTTATTCAAAGTTATTTTCACTTAAGTATTTCAAAGTAACATATAAAGCAAATATATACATAATGAATTTCATTTCAGGTCAGCCACAACTACTTTAAAATCTTTTAACTTTGATAATATTTCTTTTGTATATCATATTTACTTATGAAAATGAAACAAACCCACAATAATCAAGTTAAACATTGACCGTAACTTTTTGTTGGGGCTATAACTTTTTCTAG
Seq C2 exon
AAAATGAAGCAGTCTAGCTCATCTGAGTGCAGCACAGTTGATATCGCTATTTCTGAAGAAGAAGAAATGGTCTATGAACATGAAAAGTCAAAGCTTCATAAAAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034810:ENSMUST00000042792:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.441 A=NA C2=0.306
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=5.5),PF065128=Na_trans_assoc=PU(60.3=84.8)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(17.2=100)
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
- 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