MmuINT0142246 @ mm10
Intron Retention
Gene
ENSMUSG00000043535 | Setx
Description
senataxin [Source:MGI Symbol;Acc:MGI:2443480]
Coordinates
chr2:29161472-29161865:+
Coord C1 exon
chr2:29161472-29161573
Coord A exon
chr2:29161574-29161749
Coord C2 exon
chr2:29161750-29161865
Length
176 bp
Sequences
Splice sites
5' ss Seq
TGAGTAAGT
5' ss Score
8.82
3' ss Seq
GATTTTTAAATTTATATTAGAAA
3' ss Score
4.46
Exon sequences
Seq C1 exon
GAAACTGTGGAGATATAAATTTAGTACGACTAGGTCCAGAAAAGTCTATTAATACAGAGGTCTTAAAATTCAGTTTGGACAGCCAAGTCAACCATAGAATGA
Seq A exon
GTAAGTGTTGGCCTTTTTGCATTGGTGTTCTGCTGCTGTTGTATGACAAAGTAATGATGGGGGCACTAGTGGCATTTTGGGGACCCTACAACTATTCTAGCTTCTTTCTCCTTATGTTTGTGTGTGCCTGTGTGAATTTTGCTAGAAATAACATGTGATTTTTAAATTTATATTAG
Seq C2 exon
AAAAAGACTTGCCTTCTCATATTCAAGAAATGCTTAGAAGAAAAGAAATTCTAGATGCTCAACTTGATGAGCTTTCTCGTCAGCGAGCTCTGTGCCGAGGTGGGCGGGAGATGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043535:ENSMUST00000061578:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.021 A=NA C2=0.128
Domain overlap (PFAM):
C1:
PF130861=AAA_11=FE(11.9=100)
A:
NA
C2:
PF130861=AAA_11=FE(13.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAATTTAGTACGACTAGGTCCAGAA
R:
CTGCATCTCCCGCCCACC
Band lengths:
202-378
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