MmuINT0139830 @ mm10
Intron Retention
Gene
ENSMUSG00000075316 | Scn9a
Description
sodium channel, voltage-gated, type IX, alpha [Source:MGI Symbol;Acc:MGI:107636]
Coordinates
chr2:66548980-66550403:-
Coord C1 exon
chr2:66550340-66550403
Coord A exon
chr2:66549122-66550339
Coord C2 exon
chr2:66548980-66549121
Length
1218 bp
Sequences
Splice sites
5' ss Seq
AGGGTATGT
5' ss Score
8.34
3' ss Seq
ATTTTCTTGTTCATCTGTAGGCA
3' ss Score
10.24
Exon sequences
Seq C1 exon
GATATTTTTATTACTTGGAGGGATCCAAAGATGCTCTTCTTTGCGGTTTCAGCACAGATTCAGG
Seq A exon
GTATGTAACCTTTGCTCTACTTTCAGTTTAAGTTTAAGTGTTGCAGAAGAAAATCTCATGCTGAAGACCAAATCTATATTAATTTTCACAAATTTCATGCCGTTGACTTTGCTCATTTTATCTAACAACGAGAACAAAGACTTTACAATGTTTAAAGTTGATACATACTCTGGAAACAAGGCTGATCAAGAGCTAAGACTTCAATCAAAACAAAATACTGGTCATGGAAATCTTGAGAAATAAATAAATAAATATGTATATATGTATATGCATATTTGTATATGTCTATATGAATATATTAGAAATATATATGTATATGTATATATGTGCATATGTATACATGTATATATATGTGTATGTGTATATATATATTTCTTCCTAAAAGCTCATTCAAAGTTAGTTGGCTAGTTTAAGGGTTTTCTTCTTGGAAAGGAGAGTAACAAAACAATCTCTTTCCATCTCCATGTTCTCCATTACTTAACACAGTATGATAACCGAGTTTATGGTTCTGACCACTCTGCATAGGATCCAGTAGACTAGGTTCTGTTTATGCAAATGCCATTTTGCTATTTCTCCATGTGGCACCTTCAGCTTCCAGGGGAGCTCTTCTCCTGCTCTCCCTCCCATCGAGACATCTCTTCATCAGGCTCTGAGAACTCTGCCAACCTCAGAGTCAGCAGTGTTGCCCCTCCCCCAAGTCCACAGGACACAATGTTCATCTAAGACAACTAAAACCCCATCTGGCACCTTTAGGAAGTAAAAAGGTTTAAAGCCACAAATCTTTATGAACATTCACAAATGTTCTATCATTTTTGTTCTTGGGACTAGTTCATTCCAAGAATAACTTTCAGAGAAGATGTTTCACCAGAGGCCTTCATTTCAAACCCTATTGATTTGAGAAGATGAACATAATGTGGCTTATGCCATCTACCATTTGCTAAATGGTGCTATGGACAGATAGTGGGAAAGTCATGTTTTTTAAGTTCAAAATCAATCTTAAGTCTTTGAGGTAAGTTATTTTGTTGTTTCCACTGCAGGAAAGTGTACCTTTAAGAGTTTAAGTAATTTGGCCAAACAATCAATTAGTAAATAATAGAATGGGATTTTATACCCTTTCTTTTGGATCCCAGATTATATGCTCTTCCTCACACTTAAACCTCTGCTCCTTAGCTACACACTGAAGATATTCTGACTTATAATTTTCTTGTTCATCTGTAG
Seq C2 exon
GCAGTGTCCTGAAGGGTACGAGTGTGTGACAGCTGGCAGAAACCCAGATTATGGCTACACAAGCTTTGACACGTTCGGCTGGGCCTTCTTGGCCTTGTTTCGGCTAATGACTCAGGACTACTGGGAGAACCTTTATCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075316:ENSMUST00000100064:8
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:
PF0052026=Ion_trans=FE(8.4=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(18.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGAGGGATCCAAAGATGCTCT
R:
CTGTTGATAAAGGTTCTCCCAGT
Band lengths:
191-1409
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