MmuINT1030767 @ mm10
Intron Retention
Gene
ENSMUSG00000075316 | Scn9a
Description
sodium channel, voltage-gated, type IX, alpha [Source:MGI Symbol;Acc:MGI:107636]
Coordinates
chr2:66537270-66540635:-
Coord C1 exon
chr2:66540264-66540635
Coord A exon
chr2:66537400-66540263
Coord C2 exon
chr2:66537270-66537399
Length
2864 bp
Sequences
Splice sites
5' ss Seq
AGCGTAAGG
5' ss Score
5.87
3' ss Seq
TGATTGCCTTTTTTCCTTAGGGC
3' ss Score
10.2
Exon sequences
Seq C1 exon
TCACCACTCAGCATTCGTGGGTCCTTGTTTTCTGCCAGGCGCAGCAGCAGAACAAGTCTCTTCAGTTTTAAGGGGCGAGGAAGAGATCTGGGATCTGAAACGGAATTTGCTGATGATGAGCATAGCATTTTTGGAGACAACGAGAGCAGAAGGGGTTCACTATTTGTACCCCATAGACCCCGGGAGCGGCGCAGCAGTAACATCAGCCAGGCCAGTAGGTCCCCACCAGTGCTGCCGGTGAACGGGAAGATGCACAGTGCAGTGGACTGCAATGGCGTGGTGTCGCTTGTTGATGGACCCTCAGCCCTCATGCTCCCCAATGGACAGCTTCTTCCAGAGGTGATAATAGATAAGGCAACTTCCGACGACAGC
Seq A exon
GTAAGGATGTTTTCCATAGCTCAGGCATGGCTGAGCTCTTTCTTGTGCATCAGTCATTGTCTCTGCTGGGGGGCCTGCTCTCTGGTCTGTGAATGGCTCTGCATTTCGTGATGCCTCCTCTGTGAAAACACGGGTTTAATTCATAGCTCAGCCCTCAAGTTAGGTGTCATAATCACTTAATTAAAATCTATTTTATGGGGCTAGAGAGATGGTTCCGTGAATAAGAACCATAGGCACAGCACCCAATTCAGTTAGCTCACAAAATCACCCACTGTAATTCTGGCTCTAAGAGATCTGGCTCCCTCTTCTGGCTTCAATGGGTACCTCACATACATGTGCATAACAACACACATACAGACACACAGACACACACATACAATTAAAAATTTTATATCTCATGCTGGAAAATACATTTATTTTATGATTACAGATTTTCTAAAAGCATCGCTTTAGAAAACAGTTGCCTATAATATATATATGCCTATATAAAAGATGCCTATCGTTTATTGAATAGGCTGACCTTCTTAGAAGACAGGTTCCGCTCTGTAAAGACACCTGGATCCCCTGGCACCTACTTGTTTATTTCAGGTTATTTATTTAATACATGCTTATTGCAAGGGACTTTTCCTTGGGTTGTTGATAACAGTGGTAAAAACAGCAAACACGTTCTTTGCTCCATCTGAATGAGCTGAGTCATTACTATCACTGCAAACAGGGGAGATAAGCCAGAATGTTCACATGTCACCATTGTTCATGAGCAGCTCTGACATCTCCACAAAGACCCTGTGCCCTGAGGGTGTGCCCTGAGCCTCCATCTCCACTGTGTCTCCTAAGAGCATTAGGCTTCCAAACCTGTATATAGTTCAGAATCTCTGCACTTATTCCTGTAAACGAATGAAATGCACCACTTTCATTTAAAAATATATCTTGTCTGAGGTCTATCAGTACAAAGTATCCAAAATATATACATTGAAACAAATAAACATAAATTTAAAAATATAGTGATGCTGACATAACAAATTCCAGTCCTTCGGAATCGCTGAAAACTTAGACAATATCACGTTAGGCCTGACTTGAAAACCAGTCTGGAGTTTTCAGGATACATATCTCACCCACTCACTATGGTATTCTGCATTACCAAATATCAGCATGGGCTGCATTAACCCAGCAAGTCTCCACCATCCCTTACACGCCTATGTGTTTGTAGTGGCAAACTGTGTAGTCTTTCAAGTGAGAATTACAGTTCCATCAATGTTATGGCTACACATACATTTCAGTTTGAAAAACAGAAAACTGCATGTGCTCTGGGGGTAACTTGCAACCTGTCTGCTTGCATGGCACAAATTAGGCTGCTCTGTTAAGCTGCTTTTCTGTGGAAGTAGCATGTGACCTTTCTATGAAATGGCACTCAGGCTTTGTCTTCCAATGGTGTTTGTAATCTAAAATGTTATTATGCAATGTATGTCATATTTGAAGCTGAGTTGACATTTTGTTAACTAGTGTTTTATTTAAGAGTTTGGTTTTTTGTTGTGTTTTGGGTTTTTTTGTTGTTGTTGTCGTTGGTTTTTTAGTAGAGAGGGAGAAAAAAACTCAAAAACCACAAAAGTAAAAAAGCTAAAATTATAAAAGCCGAAGAATTACAAATGTGATTATTATAGAGGGTAGGCATAGTGCACAGTTTACAGGTATACGTCTGTCCTTGCATGACAATAAAATCTGTACACTGCACACATGCCCATGTGGGAAAGGATTTGTATAGTCGAATTCTTTTTGATTTCGAAGAATAAAAGTCAATTAGAGCATAAAGCAGAGAAAATGCATCACATGCCTGTACACATATATGCAAATGTGTTGTATGTACACATGTCTATATTCTGATATGTATACATACATACATGACTATATACAACTTTGCAAACTTAAAATTATTTATTCATAGTCATATGGTGAAGTACCTACTGTCTATCCCGTAGCACATACATGCTGGTACATGACAGCTGTAGAGTTGTATAATTGTTTATGTATATTATGTGTATGGGGGTGTTGCCTATACTGTATATGCCTATACTGTATATGCCTATACTGTATATGCCTATATAAAAGATGCCTATAGCTTATTGAATAAACTGACCTTTTTAGAAGACAGGCTCTTCTAAGAAGTATAGTCTTCTAAAAAAAATTAAGTTTGCTGGTGTGCTTGGAAATGAAGCATTTTCACTTAAAGATGAATATGCCTGGTGTGCCTCTGTTCATATTCCTGCATGCCCTCACTTTTAGAGTTGCACCATGGTCACTTCTTTGAGATGGAGACAGTCTCTCCATGCTGCAACTGTTGCCATTGGTCAGAAACACCTTTTTCAAACTGAGTCACTCAGCACTATCTACTCATCATGTCAGCTATAAGAAAAAATTTTTTCTAAAGTGGTTTTCATTAACGTTGACATCATGATAAATAATCTTGGGAGTAATAATTAAAAAAATCAGAGTGTGGTACTCTATCCTTTCTACACACACCTCTACAACTCTCGTCCGGTTGCTTTCATTTGTGGCTTTCCCTTGGTAAATGTTGGATTACATTGTGTAGGCAGAGAGAACACAATAGGGCCATAATGAGAAGAACAGCTGCTTTGTTTCTTACTGGAAACAAGTGTATGAGGCAAGATGTTTTCTTATATGCATCTTACTCATGATGAACATGTGCCCTTTTGAACACAACTAGAAAGTAGCAACATCACCATTTAAATCTAGCAACCAAACCTCTACATTCAATTATTTATTACAACTACCAAGCATGACTTTATTCTTACATATGTTATATTAGAGTTTTGTTCTTAAGATTGGAATTGATTGCCTTTTTTCCTTAG
Seq C2 exon
GGCACAACTAATCAGATGCGTAAAAAAAGGCTCTCTAGTTCTTACTTTTTGTCTGAGGACATGCTGAATGACCCACATCTCAGGCAAAGGGCCATGAGCAGAGCAAGCATTCTAACCAACACAGTAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075316:ENSMUST00000100064:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.600 A=NA C2=0.098
Domain overlap (PFAM):
C1:
PF119333=DUF3451=FE(53.0=100)
A:
NA
C2:
PF119333=DUF3451=PD(16.3=81.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
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]
SPECIAL DATASETS
- 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