MmuINT0139816 @ mm10
Intron Retention
Gene
ENSMUSG00000075316 | Scn9a
Description
sodium channel, voltage-gated, type IX, alpha [Source:MGI Symbol;Acc:MGI:107636]
Coordinates
chr2:66504849-66508674:-
Coord C1 exon
chr2:66508520-66508674
Coord A exon
chr2:66505023-66508519
Coord C2 exon
chr2:66504849-66505022
Length
3497 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
AAATGTGAATGTTTCCACAGGCT
3' ss Score
6.99
Exon sequences
Seq C1 exon
GCTGTGTGAGGAGATTTCCATGCTGCCAAGTTAACATAGACTCCGGGAAAGGGAAAGTTTGGTGGACCATCCGGAAGACCTGCTACAGGATAGTGGAGCACAGCTGGTTTGAAAGCTTCATTGTTCTCATGATCCTGCTCAGCAGTGGAGCTCTG
Seq A exon
GTAAGTGAGCTGATAAGTGGACTCATAAGTCAATATCTTTACCCATACACACATACACACACACACAAAGGAAGGTAAGTATGGCAAACTTTGCTGAAGGTTAATTGGTAGGCTATCATAAACATGGTTCATTCTGATTTCTTCCTCAGCACTACTGTCACTGGTATATAAAAAGACCACTGACTTAAGATTCATTTTCGTTTTTAATAATTGTGTTGCATGTGCACGCATGTGAGGGTGCAAAAACCACCACAAGGGCCAGAAAGGGTCATCTGATTCATCAGAACTGGAGTCACCCAGTGTGAGTCACCCCCTGTGGATGCTGTGAGCCAAATCCAGGTCTTCCACAAGAGCATTATGTTCTTAACCTCTGAGTCATCGCTCCAGCCCCAAAGATATTGATCTTTGGGTGTTAATTTTGTATTCTGCCATGGTGTTGGAAATGCTTATCAACTTTGAGCATTTTGTAGTAGAGTCTGTAAGGTTAGTTTGCTATAGAGTCAAAATCACCTGCAAATCAGGGTTCTTTGACCTCTTCTTTTCCTATTTGCATAGCTTTTATTTCCTTCTTTTTGCCATATTGCTTAAGATAGTATTTCGAAAGCTGCATTTATGGGAATAAAAAAGAGTGGGCTTGTGGTCTTCCTGAGTTCTCCTATCTTTAGTGTGATGCTGACTAACAGTTTGTAAATGCATAGTACTTATTATGTTGAGGGATACTATCTCCATCCTGACTTTTACCATGAAGGCATTTTGGATTTTGTCCAAGAGGCTTTCTTTGCTTATTGAAGCATTCATGTGATTTATGTCTGAGTTGATTTATATGATGAATTACATGTATTTACTTACATAAATTGAACTAACCTGCATCTGTGGAATGAAACCAACTTGGTCATGATGAATGATTTTTTTGATATAATTTTAAATGCTATTTGAAAATAATTTACTGATAGTTTTTTAAATTTATATTTATTATGGAGAAAAACTTGTAAATTCTCTCTCTGTGCCTTTTTGGGGGTAACCCTGTATTCTTGATATACTATATGAGAACAGTCAGGGTCCTCAAGATAATGCCTTCCTTAACAAGTCAGTCTCTTACACATTAAAACTAGAGTGTGTCTTCAAAATGGAAATCAGGACCCTAATATTACCTACTATAGCTCATACTCTTAATAACTAATAAAGTCTCCTGGGTTTATCTTATTCTAAATTATATATGGCCAGTTATTTTAAAGAATATATATATTAGAAGAAGCCATTTTTTAATTAGATATTTTCTTTATATACATTTCAAATGCTATCCCGAAAGTTCCCTATACCCTCCCTCCGCCCTGCTCCCCTACCCACCCACTCCCGCTTCTTGGCCCTGGCATTCCCCTGTATTGGGCATATAAAGTTTGCAAGACCAAGGGGCCTCTCTTCCCAGTGCTGGCCGACTAGGCCATCTTCTGCTACATATGCAGCTAGAGACACGAACTCTGGGGGTACTGATTTGTTCATATTGTTTTTCCACCTATAGGGTTGCAGACTCCTTAAGCTCCTTGGGTGCTTTCTCTAGCATCTCCGTTGAGGGCCCTGTGTTCCATCTTATAGATGACTGTGAGCATCCACTTCTGTATTTGCCAGGCCCCGGCATAGCCTTACAAGAGACAGCTATAACAGGGTCCTTTCAGCAAAATCTTTCTGGCATTGTGAACATATCCCATAATCAGCCACCAAACCCAGACACTAAAGAATATATTTAAAAGGTTAAAGTTTTAAATAAACTTTTGCTCAAAATGTCCAAAAAAGGAGACTGATGTTTTGGAGGAAGCCATATCAACTGAATTAAAAGAATCACACGAAGAAGAAAGGAAACAGCTTTGCAACTATTGGTAGTTTTGCTCAAGGAGTTTTCCTAGTATGATAATGAAGATTTTGAAATTCCTGTCTGTTAAATAAATGCAAATAATAGCTATAATGTAGAAAAATACCATATTTTATAATTTCAATATACATTTCTTTCATAAAATTCCCAAAAACATTCTGAGAAAATATAAAATTTTATCATTTAACAAACAAGAACACTGAGTACAGAGTTTAAAATGTTTCCACATATCTCAATTATAGTAAATGTCAACGTTATAATTTCAAAGCCCCTTCTATAACCCAGACATAGGAGAGCACACCAAAAAGGAAAGGAGAAACAAACAGTACCTGAAATGGGGAGCAGTGAAACCTAAACCCCAACTCTCCCCTTGCCTTTATGTTTCAACATCCACAAAGTTCACCCTGCAAATAGAGACCCTGCATCTGAGTCTGCTGACTGGTCCAATCACAGTGAGGTCTTCTGAATGGAGCATCTTATCTCATCACCAAGACTCAATACTCCTCTCTCTGAACCTGTACCCCAATTCTAAGAGCAGAATTCTTCTTTGACACCAAATCCCTTTCTTGCCATGTTTTGGAGTTACTGATTCTGCTTGGATGGTTTTCATAACTCCTCTAGAACTTGGAGAAAGGCACAGGAAAGTCTTGAGAGCTAGACTCCTTCCCTACCACATGCCATCCCCACCTCCACCCTGCTTACTTTCAGAAGGTCCACAAGGTTGTGCATCTTAGAGGGTCTGCACATTCTTTCTAACCTAAATTCTTGTTTTGCATCAGTATTGCTGTCAACCATGGTAAGAAATGTGCTAATGATGGTTTTTAAAGTATTGACACAGATTTGGCAGTGACGGGGGATAAGAACTGATTAAGTCCATAACCACGGACAGGAAATACGATGTTAATCACTAAAGCTATGTTATTTAGCTCTCATTTCTTCCACCAAGGTGATTAGTGCTTCCATATGAAAGATAAAACCTCATGTAATTCAGACCTATTTTGATCAGCGGCCATTTACAATACCCCCATTACTTCAACTCTCTAAATGTATTTGAATTATTTTCCAAAGAGCTTCAGGCTGTGGGTATCCTATCTTACCCTTGTCATTTTCTTAAAAGTTTTTGAAGAGGATAAATCCTACTAGCATGGAGTAAGAGCCAAAGGAGGTTCCTAACCTAATTGGTGGGTGTGAATTAGAGTGTAGTATTACAAAGGTTTACAAGAGGGCCTGACCCAGGAATAAAGTCTGAAAAGGATCAGGACCCTTTCCGTTTGAAAGGAGAAAAGAACAGGCAGGTGATGTGAAAAAAAAAGTGAGAGAGGGAAAGAAAGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGACCTTAGGCTTTAGAAACCATGATTCTTTCAGAAGACTGTACGTAATTCCATTCCTCTGCTTCTCTGTGACAATGGAAAAGGATGTTAGAAGTAAATTTTATGCAGGAGCTGCAAACCAGAGGAAGGCTAGCCAAGTTGTTTTCACACCATTATTTTATGTGATGTCTCTATCAGAATTGTAATTTCTTCTTCTCCAGTGAAATATAAATTTAACATTACGCATAAGCTGAAATGTGAATGTTTCCACAG
Seq C2 exon
GCTTTTGAGGATATATATATTGAAAAGAAAAAGACCATTAAGATTATCCTGGAGTATGCTGACAAGATATTCACCTACATCTTCATTCTGGAAATGCTTCTAAAATGGGTGGCATACGGGTATAAAACATATTTCACTAATGCCTGGTGTTGGCTGGACTTCTTAATTGTTGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075316:ENSMUST00000100064:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=PD(20.0=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(17.0=67.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
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