MmuINT0142253 @ mm9
Intron Retention
Gene
ENSMUSG00000043535 | Setx
Description
senataxin [Source:MGI Symbol;Acc:MGI:2443480]
Coordinates
chr2:29027836-29029241:+
Coord C1 exon
chr2:29027836-29027928
Coord A exon
chr2:29027929-29029076
Coord C2 exon
chr2:29029077-29029241
Length
1148 bp
Sequences
Splice sites
5' ss Seq
TGAGTATGT
5' ss Score
4.43
3' ss Seq
CTTTTTTCATCTTTTTAAAGCTC
3' ss Score
9.27
Exon sequences
Seq C1 exon
ATTGACTGAATCCATTCGATGTTCATCAGAGTGGCCATTTCAGCCCTACCTCGTGTTTGATGTTGGAGATGGTTCAGAACGACGGGATAATGA
Seq A exon
GTATGTTTTTGTTTTCCTTCATTCTTCAGTAATGGTCTCAGAATCATTAGCTTATAAGCTTTTCCTATACATGTCTCTCTAGTACCAAGGTATCTGTGTTGATAGCTTCCTCTTTTCTGTATAATTGGTCAGTACTCTCAGGTGACCAGTAAGTCCTTGAACGGTCATAACTGTGAGAGACCCCATCAAAAGTTGATGATTGTGATTTCATAGGAAAGCAGGCATAAGCCAGATAGTCCTTGAAATTTTGAGTTGTGAAGGATTGTGTTGGGTACCTATAAAATGATAGCAAAGTGGAGGTGGGTGGTGTGTTGCTAGGTAGCAAATATATCAGAAGAGCCAAGGATTGCTCTGAATAGAGGAGTTTAACAGCCTGGAGGTATTGTTTATGAACATGTGCATAAAGACTACCCTGTTATGTGGAAAATGTGAAAAAACAAAATAAAACCCCACAGATTCTAAAGTGAGACTAGGAAATGGGTCTAGATAGAATATTCCTTGCAGTGAAAAATAAAGAGGTTCATATGGTCTTCAAGAGTAGAGCAGAAGATGAAGAGCCTAACCCCAAGCACATTATAAGACCAGAAAGCAGCAAGGAACTTGATAGAGTCTGAATCTGACAAATAAAGACGGTCTAGGAGAAGGAGCTATCTTCCTGGGATGTTACAGTGTAGCATGGCTGAAAGCATGACAGTAGTTATTGGGTGTTAATCCTTAGGGAAACAAGGACCCATGTTGGTAATGGTTGGATCTACTTTGGCAATGAAAGGACACACACGTGGGGGTATGGACTGTGAGAACAGGATATTGGAGCCAGCAGAGAGGATAATGAGGTAGCTTTCATGCCATTCAGCCCTAGTGGGCTATGTTGTTAATGTTTAGTTGTCTGGGTGACATCTTTTCAGCTTTGTGGTTTATTGGTTTAAACTTAGCTGACTACAAATTTCTTTCTTACAACCACTTCATGGATTGGACAGTTATTTATAGTTACTCATATGTATATAAATCACTATTATATCTTCTTGATATTGCTGCCTGACTAGAGGGAAAAGCACCTATGCATATTCTTTAATGGGAACTAACTAGAATTAGTGAGCAATTAGACAGCTGTGAGATTTGACACCTTGTCTTTTTTCATCTTTTTAAAG
Seq C2 exon
CTCATATATAAATGTTCAAGAAATAAAGTTGGTGATGGAAATAATTAAACTTATTAAAGAGAAAAGAAAAGATATTTCCTTCCGAAATATTGGCATAATAACCCATTACAAGGCTCAGAAGACGATGATCCAGAAGGATTTGGAGAAAGAATTTGATAAGAAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043535-Setx:NM_198033:22
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.016 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF130871=AAA_12=FE(15.3=100)
A:
NA
C2:
PF130871=AAA_12=FE(27.2=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:
TGACTGAATCCATTCGATGTTCA
R:
CAAATTCTTTCTCCAAATCCTTCTGG
Band lengths:
246-1394
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: