MmuINT0139804 @ mm9
Intron Retention
Gene
ENSMUSG00000023033 | Scn8a
Description
sodium channel, voltage-gated, type VIII, alpha [Source:MGI Symbol;Acc:MGI:103169]
Coordinates
chr15:100803185-100805147:+
Coord C1 exon
chr15:100803185-100803391
Coord A exon
chr15:100803392-100804853
Coord C2 exon
chr15:100804854-100805147
Length
1462 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TGCTGTGGTCCCTTTCCTAGGCT
3' ss Score
9.25
Exon sequences
Seq C1 exon
ACCTTACGAGCGGCTGGGAAAACGTACATGATCTTCTTTGTCTTGGTGATCTTCGTGGGTTCTTTCTATTTGGTGAACTTGATCTTGGCTGTGGTGGCCATGGCTTACGAAGAGCAGAACCAGGCAACACTGGAGGAGGCAGAGCAGAAAGAGGCAGAGTTCAAGGCGATGCTGGAGCAGCTCAAGAAGCAGCAGGAGGAGGCGCAG
Seq A exon
GTGAGTGGGCAGCCCTGCGTGCCCCGCCTTCTTCCGGGTCTCAGAGGCTAAGGCTCCCACTGATTGGCTGATTGCCAGTGCACACGCTCTTTTATTGACTTTCTCAACTCAGCATTCAACTCCTGTGGTGACTGGAAGCGAGCGACAAGCAGTTTCTGCTGTGGCACTGTCTGGTTTGTTTATTGGCTCAGGGTTGGAGACTGAACACAGAGCTTCGTGCATCTGTGCACTGGGCAATACCCCACACCTACCCACTTTCTGATTAGAGAAACACTGGGATACCCTTGATGGGTTCACTATGGCCAGAGAATATTATTTCTAACTTAAAACAAAATACAGGGGCCTGGGGAGAGAACGCAGACAGTGAAGTGCTTGCCACAGAAGGGTGAGGACCCAAGTTGATCCCCAGAATCCACACAAAAAGCCAGACATGGTGGCTCCCTGAAGCCGTGTCCATAGGTGGAAATAGGTGGGTCCCAGGGGTCCTGGCCAGCCAGCCTAGCCTACTTAGTGAGTTCCAGGCTAGTGAGAGACCCTGTCTCACAAAACAAGGTGAGTGGAATCCTGGGTTGACCTCTAGCCTCAACCATATACATTTGCACACACACATATACACACATACACACAGGCACACACACACAAATACACACACATACAAATACACACACATAGAAATACACAGACACACAAAAATACACACACATGCACACACAAATATATACAGATAGATACACACAAATATATACAAATACAGACAATACACAAAAAATACACACACATACACACACATATACACAACACACACATATTTAAGGAGGTGAGAGACACAGTGAGACGGCTCAGTGGGCGGTCACGGGAGCTTTCCACATGAGCCTGGTGACCTGAGCTTGATCCCCAGAATGCAAAAACTGACTTTATAAAAGTTGTCCTTTGATATCTGTATGCACACACATAGACACACTCCCACGCACATACATACAATAATAAATAGGTTTTAAACACTTAAAATGAAGATGTTGGCAAAAAATAAAACTTAGAAACAATTTGTTATTCTATTACTGTTAATATGTAACTTCCTACTTGTATATATGAGTCACATGAGTCACACACACACACACACACACACACACACACACACATTGCAGTGTTTGCCCGCTACTGTGTAATATCGTTTCTAAGCCTTCATTTCCATTGTCACTCACTTCATCCTTTGGTATGAAGACAGCAGCCAGGTCCTTACCTGGGATGCTCAGAATAAATCTCCAGCATGCTCACCATGAGATGTGCTGGCCATCTTGGCCTGAGTACCAGGATGCAAGTTCACAGAGAGTGGAAGCAGCCAGTGCTGACCTCAGCCTCCTCCAGCAGGATGGGCTTCCCCATGTCCGTGTCTGTTAGTGTCTGATTGGGTGGCCCCAGATAATGCTTCTGACCAGGTCTATTGCTGTGGTCCCTTTCCTAG
Seq C2 exon
GCTGCTGCAATGGCCACTTCGGCGGGCACCGTCTCAGAAGATGCCATTGAAGAAGAAGGGGAAGATGGGGTAGGCTCTCCGAGGAGCTCATCTGAGCTGTCTAAACTCAGTTCCAAGAGCGCGAAGGAGCGTCGGAACCGACGGAAGAAGAGGAAGCAGAAGGAGCTCTCTGAAGGGGAGGAGAAGGGGGACCCCGAGAAGGTGTTTAAGTCAGAGTCGGAAGATGGCATGAGAAGGAAGGCCTTCCGGCTGCCAGACAATAGGATAGGGAGGAAATTTTCCATCATGAATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023033-Scn8a:NM_011323:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.068 A=NA C2=0.857
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(12.4=44.9),PF057587=Ycf1=FE(24.9=100),PF0310514=SPX=PU(19.9=55.1)
A:
NA
C2:
PF057587=Ycf1=PD(29.7=82.7),PF0310514=SPX=FE(50.8=100),PF119333=DUF3451=PU(29.5=68.4)
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:
GAAGAGCAGAACCAGGCAACA
R:
GGCCTTCCTTCTCATGCCATC
Band lengths:
342-1804
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: