MmuINT0142239 @ mm10
Intron Retention
Gene
ENSMUSG00000043535 | Setx
Description
senataxin [Source:MGI Symbol;Acc:MGI:2443480]
Coordinates
chr2:29124992-29125963:+
Coord C1 exon
chr2:29124992-29125549
Coord A exon
chr2:29125550-29125851
Coord C2 exon
chr2:29125852-29125963
Length
302 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGG
5' ss Score
10.17
3' ss Seq
AGTTTTTATTTTAATTTCAGAAA
3' ss Score
6.63
Exon sequences
Seq C1 exon
GCCACTCAGCGGTCAGGCCGGTTGTTCCCCGCTGCTGCACTTTCCACCTCCCGTCCGCCCCCATGGTCCGCCCCCTTGGTGTACCACAACAAGCCGGCTCTGGCGGGGGCGGGCTGAGGGCGGGGTCCGCTCTCGCGGCAGCGGCGGGTTGGGCGTTGGGCGTCGCCTTGCCCTTCCGTCTGCTGTTCTAGCGGGGGGCATGGAGGTGGGTTAGCGCGCTGCAGCCGGGCCTAGCCGGGGTGAGACGCGCCGCGGACAAGCCGCGAGCGGGCGAACGAGCAGGAGAGGAGAGCGCGTGCGCGGTGAGGGGCGCGCGGCTTACTGCCGTTGGGAACTTGCGCGCGGCCTGCGGGAGCGGGCGCCTGCTGTGACCCTTCTGGAGAGCTGCGTTTGGTGAGAGCGGCGGCTTGCCGCTGCTACCAAGGGCGGGCAGCGCTTGGTGTTTCCTGCAAGCGAGGCCCGCCCCCGGATCTCTGCTGTTCTGGCATCAGCACCGCCGGCCCTGGGCAACGATGTACAGCGAGGACCCTTAGCTTCGGGGCGAGGGAGGCCTCCCGG
Seq A exon
GTAAGGATCCGACCCTCTGTCCTGGCGTCGCTTCCGCATGGGCACCCGGACGCCCTCCCCGCCGTACCAGGCGTTGCGGTGTGGACAGCCTCCCGTACGCCCACAGCGGATGTGATCAAGTGCCTATTTGGCCCCTGGAGGAGAACAGTCCCTAGGGAAGTTGGGGGGGGGGATCAGTGTTAAGCCGTTCCCCCCAGTAGTGTGTGGATCTAACCTGACCTAGGTAACTCATTAGATGACACAAGGCCCAGGTGAGATGCATAATGTAAGGGACATTTTATCAGTTTTTATTTTAATTTCAG
Seq C2 exon
AAATGTTCTTTTTGGGGGCCAAAGTGTGAATCTGTCTGAATGCAGAGCCACATCTCACAGATAAGCCCAGCAATCACAAAGAGCATCACTTCTCTGTAGGACCTTGGTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043535:ENSMUST00000061578:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGAACGAGCAGGAGAGGAGAG
R:
TCTGTGAGATGTGGCTCTGCA
Band lengths:
348-650
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