MmuINT1030769 @ mm10
Intron Retention
Gene
ENSMUSG00000075316 | Scn9a
Description
sodium channel, voltage-gated, type IX, alpha [Source:MGI Symbol;Acc:MGI:107636]
Coordinates
chr2:66547023-66549121:-
Coord C1 exon
chr2:66548980-66549121
Coord A exon
chr2:66547230-66548979
Coord C2 exon
chr2:66547023-66547229
Length
1750 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
CTCTTTTTTGCTCCCCATAGACA
3' ss Score
10.36
Exon sequences
Seq C1 exon
GCAGTGTCCTGAAGGGTACGAGTGTGTGACAGCTGGCAGAAACCCAGATTATGGCTACACAAGCTTTGACACGTTCGGCTGGGCCTTCTTGGCCTTGTTTCGGCTAATGACTCAGGACTACTGGGAGAACCTTTATCAACAG
Seq A exon
GTGAGCAGCAACAGAAACACGCATGTCTGAAGGCAGTCGGTGTCTGGTGTATGTGTCTCCTGCCTTATGAGCTATTGTAATTGCTGTTGTTTTCATTTTATTTCTGCAGACAGTCTGGGACTCCCTAATGTGCATTATTAAAATTACAGGCAATTTACTTGGCTGATATGAGAACAGATAGTTCTGAAGTCATCAATAATTTTCTGCTGTGTCTGACCAGCGTTAATTTAAGTCTTCCATCTTCTTTGGTATATCCATTGGTCCCAACAAAAAGACCAAAGAACAATGCAATTCTCTTGAGCTGCCTTTGCAGACTCAGCACTTTTGTCACATGCCCACATGTCACATGACTGTACCTGTTAGACTCTCCTGTAATGGGTCCACCATGCTTTAGTGTTGAACACTCTCTACCATGAACTCTCAGTTCTTCTCCAAACTTTCCTTTCTCTTTTCAACTACGTCCTCCTCTGGACTTCATGGCTCTTTAAATAGTACTCAGCTTACAATGTCAGCCTGCCATACAGTAACTGACCCTACACACGGCCGTCTGCTCTAGCATGGATGGAAGGTGCTTGCCATTATGGCCTCTGTGTATTTATTTTAGAGTCTCAACACCCCATCCCCAAAGAAAAGTGGTTGAAATGACTATTTTATTAGTCCATGTAGCAGTAAATTTCTTTTCTCAGAGTTGCTACAGGCTTATTTTATATTTACTTCCATAAACATTATAAATGGCTATGCAATTATATAAAAGGACACTTTGTAGGAAAATAAAAGTAACTGACATAATTCGAGGGCAGAAATGGAATCTTAGAATGCTGTACTGTTGGCCTCACGTACTTTTTCTTGCTCCAACAAAAATATCCACTATTCACAGTCATGAATCTTCATAGCAGTCCCCAGCTTAATAACATAGAAAAGAAGGTCATTTTAACTCAAAATTAAGGACACATGAATAAAACCACTGGCATAATTTTACAAACGGAGTCTCAAGATGGACATATTTAAGTTCAGATATGGAAACTAGTCTTTCTCATACATTGAGAACTTTTGCAGAAAGTTAATGAAAATCAAAATAAATGTTTTCATCCACCTAATAATTCAAGTCTTAGGAATTTATTCAAGAGAAAAACCATAGTTATAATGGAGTGATAAAGCAGATCACAGAGTAACTAAACATTGAGGATTTCAGCAGTAGATAGTTTTTATTAATATCTCTGCACTATTTTGAATTAACCTAAAAGTGTGCTGCATGGCAAGATACACTGCATTTAAAAATTATCAATGATTATTCCAGATTTAAAAAAATCTCTGAGGTCAATAGATTAATTTCTTACATAAGGTATCTGTTTAGGTCAAAATGTAATATGGTTATTTATGCATTTAAAAGGAAAGAATAGAATCTAACCAAAAAAGGGGCCTGTTTCAAAAAGTTAAAAGACAGCATTGGGGGAGGGGTAAAGTTAGTGTTAATTTAAATAATGTGGAAAATGAAGAATTGTTATATCATTATATTTCATTTTAATGAAGAATCAAGCCTTAATGTACATATAACAATGCTGTATCTTTTATATTAAAAAGTTTGTTTAATACTGATTTTCCTCAAAGATATTATCTTTATTTATCTTTCTACAACAAAATTATACAAAAATATCTGGTTTGCACATTCATTATATACTAGCTGCAATAAAAACCTTAGTGAAATTTTTGTATTACTAAAATAATCATGTCTCTTTTTTGCTCCCCATAG
Seq C2 exon
ACACTGCGTGCTGCTGGCAAAACCTACATGATTTTCTTTGTCGTGGTGATATTTCTGGGATCCTTTTACCTGATAAACTTGATCCTGGCTGTGGTAGCCATGGCGTACGAGGAACAGAACCAGGCCAACATCGAAGAAGCTAAACAGAAAGAGTTAGAATTTCAGCAGATGTTAGACCGACTCAAAAAAGAGCAGGAAGAAGCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075316:ENSMUST00000100064:9
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=0.016
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(18.8=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(12.5=44.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCTGAAGGGTACGAGTGTGT
R:
CTCGGCTTCTTCCTGCTCTTT
Band lengths:
343-2093
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