MmuINT0139795 @ mm10
Intron Retention
Gene
ENSMUSG00000023033 | Scn8a
Description
sodium channel, voltage-gated, type VIII, alpha [Source:MGI Symbol;Acc:MGI:103169]
Coordinates
chr15:101032185-101033582:+
Coord C1 exon
chr15:101032185-101032322
Coord A exon
chr15:101032323-101033477
Coord C2 exon
chr15:101033478-101033582
Length
1155 bp
Sequences
Splice sites
5' ss Seq
AAGATAGGT
5' ss Score
2.1
3' ss Seq
TCTCTGCATTCTCTCTCTACTTT
3' ss Score
2.35
Exon sequences
Seq C1 exon
CCGGACGAGCAGCCTGATTATGAGGGCAACATCTACATGTACATCTACTTCGTCATCTTCATCATCTTCGGCTCCTTCTTCACCCTCAACCTGTTCATCGGTGTCATCATCGACAATTTCAATCAACAGAAGAAAAAG
Seq A exon
ATAGGTTTCCTCCCCGCGCCGCCAGCTGCAGAGGCCAGCCCAGCTGAGAGGCACTCTGCCTTGTTTCTAGAGAAAGAATCAGTGTCTCTGTCTCTGTCTCTCTCTCTCTGTCTGTCTCTCTCTCTCTCTCTCTCTCTGTCTCTCTGTTTCTCTCTCTCTCTCTGTCTCTCTGTCTCTCTCTGTCTCTCTGTCTCTCTCTGTCTCTGTGTCTCTCTCTCTGTCTCTCTGTCTCTCTCTCTGTCTCTCTCTCTCTGTCTCTCTCTCTGTCTCTCTCTGTCTCTCTGTCTCTGTCTCTGTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCGTTGCCACCCTATGGTAGCACCGGCCCACTGTCCAGCCCCAGACAACCCCTTTTTGTTTGAGGCTGGACTTTGCAGTGTGTGGTTTACAACATTTCCCTGAAGTTTCGCTTTCTGGAGGCTGCCCCTGATGGGACTCTCTGCCAGAAGGAGGGACAGAGAAAAGAGGCAGATAGTACCACGGGGAGATGCAGATGTGACACCTGTAGCATGGTGGGAGTGGAGAGGTCACCCTCATAGGACTCACTTCCTTGTGGGTAATGGTTCTCCTAAGGTACACTGGGAGACTTAGACTTAATTCTAAGCTGCCTTTTTATACCACAAGTTCCAAATTCTGAATTTCATTAAAAGTGAATTTGCTGTTGGCTGCTCCAAAATACTTTTTTTTTTTTTTGTAATGTTTGGGAGGGCCACAGGGCACAGTGCACACAGGGTACACCTTTGACACAAGCACTCAGGAGGCAGAGGCAATTCTCACTCAAATTCTCACTCCATAGTTCCAGGCCACCCGGGATTACACAGTGAGACCCTGTCTGGTGTGACTGTGTGACTGCCCTCTCATCCCTTGCTCTCGCTCTACTTCCTGCCCTGAAAGCCTGTAGTCAGACGGCCCTGTCTCAAGACTTGGCCTGGGAGATTCCAGACACCCCCACTGAAACTGGCAGCTGTCTCTGACTGGGATGACTGGCCCCATGAGAGTCCTCACCACCGGTGACCTCTGGAGGGAAAATAGAGTCCTTCCTAGCCTCAGTGGTGCTCGGTCGCACCTCCAGAGCTGGTTGTAATTGTCCCCTCTCTGCATTCTCTCTCTAC
Seq C2 exon
TTTGGAGGTCAGGACATCTTCATGACAGAGGAACAGAAGAAGTACTACAACGCCATGAAGAAGCTAGGCTCCAAGAAGCCACAGAAGCCCATCCCCCGACCTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023033:ENSMUST00000108909:24
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=PD(15.2=76.1)
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:
CGGACGAGCAGCCTGATTATG
R:
AAAGGTCGGGGGATGGGC
Band lengths:
241-1396
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