MmuINT0139815 @ mm9
Intron Retention
Gene
ENSMUSG00000075316 | Scn9a
Description
sodium channel, voltage-gated, type IX, alpha [Source:MGI Symbol;Acc:MGI:107636]
Coordinates
chr2:66404228-66406371:-
Coord C1 exon
chr2:66406064-66406371
Coord A exon
chr2:66404347-66406063
Coord C2 exon
chr2:66404228-66404346
Length
1717 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
TGTCTCTTTTTCCTCCTCAGACT
3' ss Score
11.34
Exon sequences
Seq C1 exon
GCCTCTTAGGTAAGGATCCGAAGGGGAAATAAAACCTACAGGATGAGAAGATGGCGATGTTGCCTCCGCCAGGACCTCAGAGCTTCGTTCACTTCACAAAACAGTCCCTTGCCCTCATTGAACAACGCATTTCTGAAGAAAAAGCCAAGGGACACAAAGATGAAAAGAAAGATGATGAGGAAGAAGGTCCCAAGCCCAGTAGTGACTTGGAAGCAGGTAAACAGCTACCCTTCATCTACGGAGACATTCCCCCGGGAATGGTGTCAGAGCCCCTGGAGGACCTGGACCCATACTATGCAGACAAAAAA
Seq A exon
GTAAGTAATTGAGACTTCAGTGGCGGAGTTCTCTTGATTTCAACCCATACAAAAGATACATGGAGATTAATGACCTCATGTAGTGAGCGTTATATTAAATACACATAAGGATTCTGAGACTATGTCCTTTTTCTAGTAATTTGTTAAACCTGGTAGTGATATTGGCATGCTTATTTGAATTGACTAATTATTCAACAGAAAGTCTACAGTTTTAGGGATGGCATGGTGAACCCTTTCTGGTACTTTTTATAGTCACAGCTATGTTACACTTGTTTAATGTATAGGGTATGTAGGTGAAGTCATGTGACACCTGGTGGAAATCATTTCTCTGGTTCTACTATGTGAGGCCTAGTGAACAAACTCAAGTTATCATCAGGCTTAGTAGAGAATGGCTCTACCTGCTGAGCACTCTGGGCAGCTACTTGTGGTAATACGTTGAGCACAGAGGTCAGAAGGAACTGGAGGTTCAAGAAAGCAGAGCAACTGTAAACATGATATATTATGTAAAGGAAAATCTATTTTCAATAAAAGAAAAAATATTTTAAAACACAAGTCATCCTTTAATTTTTAAATTTCATATGCAATGCAACTTGATCTTGCTAAAACTATGTAATAGTGTAGTAGGTTTCATGTTAGTTTTGATCCCCCTTCTTTGCATTTTATGACACAATTCTTCACCATGTGTTTGTAGAAAGTCCAGTTTGTTGAGATAATATATAACTGAAAAAATAGATATCCCACGTAAGTAAAAACACCCCCTCCCCCACCAAGTTGGTGAAAAAAATTTCTTGTAGTAAGCTTTTTTACACTTATATAAAATGTAAACAAGACAAGAGAAAAAGAGCTCACACAAGATGACCTGAGAGTTATAGGTCAGTGAGAGGCATTGTCACATAAAAACTAGGTCAATTACACCTGAGAGTTGAAGTTGTCCTTTGGCCTTTCATGTGCACATGCACACTCTTGAATATACATCAGAACCCATTAGGCAACTGCATGCAGGTATACACACACACACACAAACACACGCACACGCACACGCACACGCACACACACCAAGGAAAGAAAGGGTACTTTGAGTTCTGACATGACTTAAAATTATGGGAAAAATTTAATGACAATTCTCAGAATGTTTTAAAACTCTCAAGGTACTGTGGTTAAAAAACAGAGATAGATTGTGTCTACCCATTGTTAAAATCTATGTAAGAAAAGAAAGAAAAGTTACATTTAAAAACTAAATGGCAAGTTGACTATAATTATTGAAGAAATCATGTAATGTTTTGGGAGCTCCTTGGACCTGTTCATCTGTCCATCTCACTCTCCCTGGGCTGAATGTGGCTGAGGAGAGCTAAGAGGGTTGTCCAACACATCATCACAAACATGCTTACATCATAAAACTTTTGGGGGTAACTTTATTTTGAGGTTGTTTAGCATGAACTTTGTAGATTACAATGTGCTGTCACAAAGTCTAAAGAGTGGACTTGTATAGAACTACTATATACTCGTATGCAGCTCAGTTCTTATTGAAAACAAACAACCTAGGAGTTCATTGACCAGTGACTAACAGATGCTTCCACACATGGGAAGCCCTTGTAAATCCCCAGGGCAGCTTTTCTTCAGTCCTGCACTACCCCATGGAGGTATAAACTGCTCATAACAATGTGATGGATTAAAGTGTTGGGAGTTCAGCTTCATCCTGTCTCTTTTTCCTCCTCAG
Seq C2 exon
ACTTTTATAGTATTGAACAAAGGGAAAGCAATCTTCCGTTTCAACGCCACCCCTGCTTTGTACATGCTGTCTCCCTTCAGTCCTCTCAGAAGAATATCTATTAAGATTTTAGTGCACTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075316-Scn9a:NM_018852:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.384 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CCTACAGGATGAGAAGATGGCG
R:
AGCATGTACAAAGCAGGGGTG
Band lengths:
342-2059
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: