MmuINT0139827 @ mm10
Intron Retention
Gene
ENSMUSG00000075316 | Scn9a
Description
sodium channel, voltage-gated, type IX, alpha [Source:MGI Symbol;Acc:MGI:107636]
Coordinates
chr2:66562346-66563631:-
Coord C1 exon
chr2:66563540-66563631
Coord A exon
chr2:66562559-66563539
Coord C2 exon
chr2:66562346-66562558
Length
981 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TTTCCCCCCTACATTTTAAGGAC
3' ss Score
10.06
Exon sequences
Seq C1 exon
GTATTTAACAGAATTTGTAAACCTAGGCAATGTTTCAGCTCTTCGAACTTTCAGAGTCTTGAGAGCTTTGAAAACTATTTCTGTAATTCCAG
Seq A exon
GTAAGAAGTGATTGGTGTGGAGCTTTAGACTGCTCAACTCCAGCTGTTTGGGAGTTTTCTTTGTCTGTGTGTGTGTTGTCACTGTGTCTGTGTATAAACTCCCCTATTGCAGATATGTGACAGAGTTTGTGGACCTGGGCAATGTCTCAGCGTTGAGAACATTCAGAGTTCTCCGAGCATTGAAAACAATATCAGTCATTCCAGGTGAGAGTGGGGTTAAACACAAGGGCTGGCTTTGACTGTTTGGAGAAAAGAATTTTCTTCCATCATTCGAACCAAACTGCATTCCTTCTGCTTTCATTGCAATTTTTATTTAAAAAGTCAGCCATTGGGTTTAATCAGTTGCATGGGTCTTGGAGAAGGAAGATGACCACTTGGTTCACATCTCCACTTGAAATTTTTCCTCCTGCCAAAGGATTGGTTTTCTACTTTTTCAGGAAGGAAAATTTCAACTAATCAGAACATCATGCCATTAAGACAATAGGAGATATCTGCATGTAGGCATTGCATGACATTGTTTTACTGACTTCTGTTTCTTACTTGGATGGTTTATCAAGCTGTTTCTTACTTGAAAAGTCGTTCAGTATATGTCATCACTATGTGCTACAATTAGTATCTTCTTTAGTTCCATTATGTAGAGGTGGTTTGTTTGACCATCATTTACTGAATTAGCAGTTACAAAACGATTGATTATATTTGTAAGTGAGTGTGAATATGGTTTCAGCATCCACCTTACTTACCAATTGAACCTGATAATTTCTTGGAAATATTTTACTAGTTTTAACCACTTGTTGTACTTCATAAGAACAAGTTGTACAGATCCACCTTCTGGGACCTGGGGACTTCTCTGGGTTCAGTTATTTAAGGTCAATGACTTGACATAATGCATGCACTCCTAGTTAGGCTTGTGTTTTGACTTGTTTCCCATTGAGAGCCTTTATGTCATTATAAATGCCTCTTTTTTCCCCCCTACATTTTAAG
Seq C2 exon
GACTAAAAACCATCGTGGGGGCCCTGATCCAATCAGTGAAGAAGCTCTCTGACGTCATGATCCTCACTGTGTTCTGTCTCAGTGTGTTCGCACTAATTGGACTACAACTGTTTATGGGCAACTTGAAGCATAAATGTTTCCGGAAGGACCTTGAGCAGAATGAAACATTAGAAAGCATCATGAGTACTGCTGAGAGTGAAGAAGAATTGAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075316:ENSMUST00000100064:6
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(12.4=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(28.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTAACAGAATTTGTAAACCTAGGCA
R:
TTTTCAATTCTTCTTCACTCTCAGCA
Band lengths:
302-1283
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