MmuINT0142240 @ mm10
Intron Retention
Gene
ENSMUSG00000043535 | Setx
Description
senataxin [Source:MGI Symbol;Acc:MGI:2443480]
Coordinates
chr2:29144603-29150107:+
Coord C1 exon
chr2:29144603-29148721
Coord A exon
chr2:29148722-29150007
Coord C2 exon
chr2:29150008-29150107
Length
1286 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
TCTTCTTTTGCTTTGTGTAGGTG
3' ss Score
9.77
Exon sequences
Seq C1 exon
GATTCTGGGTGGAGATCAGCCATTTGTCCAGATTATTGTCCAAACATGTATGAAGAAATGGAAACATTAGCCAATGTACTTCAGTCAGATATTGGTCAAGATATGCGTGTTCATAACAGCACCTTTCTGTGGTTCATACCTTTTGTTCAGTCACTCATGGATCTTAAGGATTTGGGTGTGGCTTACATAGTAGAAGTTATTCATCATCTATACTCAGAAGTCAAAGATGTCCTCAACCAGACAGATGCTGTGTGTGACAAAGTCACTGAATTTTTTATTCTGATTTTAATATCAGTGATTGAGCTGCATAGAAATAAAAAATGCTTGCATCTGCTGTGGGTGAGTTCTCAGCAGTGGGTAGAAGCTGTTGTGAAGTGTGCCAAGCTTCCTACTACCGCATTTGTCCGGAGTTGTGAGAAGTCACCTGGAAGTACCTCCAGAGGAGCAGCAATAATGTCGTCCTTGGCGTTGCATTCGGTGCAGTCTAACTCTGTCCAGCTTGCTTGTGTACAGTTGATTAGAGGTCTCCTCAAAGAAGGTTATCAGCTTGGTCAGCAAACACTTTGTAAGCGGTTCTGGGATAAGCTTAACTTATTCCTTCGAGGAAATTTGTCTCTGGGTTGGCAATTGACTGGTCAAGAAACCCATGAGTTACAAATGTGTTTGAAACAAATAATTAGAAACATAAAATTCAAAATGCCCCAATATAGCACTTTTGGGGATTCAACTTCTACATTTAAAACCCCTCCATCTTTTAAAGAAGAAAGTGATAAAATAGACAGGAAGCATAAAAAAAACATTTATTGTTTGGAAAATTGCAGTCCAGTGTCTTCTAAAGAGCCAATGAAAGCTGACACCCATCGAGTATTGATGAAAGTAAATACTACAGAAGAGGAGAACTTCAAGCAGCATTACATTGATTTGAATGAAGAAGAGCAAGAGCCTCTTCCAGCTGAGTTGTGCTTGAAGCAGAAAAGTGAGGCCCTTTTTTCTGAAAGTGCTCAAGAGCAAGTTAAAATTAGCGCAGAGAAGTCTGGGAAAGAAAGCTCTTCATATGCACCATCAAATAGTACTTCAAGAAATGGTCCAGAATGGGGATGTGACAGAGGAGTGATAATGTCAGCACATTCATTGACTGATTCTAGCAGTGATTTTATGGAACAGGTATCTACATCAAATGAAGATGTCTCATTAAAGGATGGCTCTGTTGGTAAAACTTCAAAACCAAGTTTCAAATTACAGAAAGATGAAATTTGTGCAAAGTTATCACATGTCATAAAGAAGCAAATCAGGAAAAGTACTTTGGTAGATAATATTATCGATCTAGAGGAAAATACAGCTATATCTGACCTTGAGAACTGTTCAGGAACAGATGGAGGAGCTCTAAAGGAAGATAGTATTGGACACAATGTCCCTTCAGACCCTGTTCTGGATGACAAGCATGAAGAGCAAAAATCTCAAAACAGTTCATTATTCAAGAAAGAGATAAAGAGTGAGGAGTTGGATAATAGTAGTTCTGATGATGAAGACAAGCTTCAAATCCAGGAAGGCCGTGCTGACGATGATTTGGTATCATTTACAGAAGTTACTGATACACTGGTGAAAGCTCCATGTGAGGGTCATGTAAAGATGGTAGTTGAATCAAGAGATAAGGAAATGAGAGAGAGTACAGCGTTGACTTCTAACTTGGTAGAAGGACAGGTGCCTCATGACAGTAGCAAGCCTTTGGTTGCAGGTCGTCAAATAGACCTCTGTAACATAACTTTAATATCTCAAACCACTGTTATTCAATTTCCATCAGGTTTAAGTAAACAGAATTCATTTCAGCTACAAAAAGGTGATAAAAGATGTTTGACAGCTAACCAAAACAGTGCTGCCACCTGCCGTGGACAAGTTATTGTGATTTCAGATTCTGACGAAGAAGAGGATGAGGATGAAGATGAAAGAAGTAGTAGTGAGGAAAACATCAAACAGAGTAAAGCATGCATAGGGAAAGACTGCTCAGAGCATCGTAGCTTGGCAGTTAATGCCAGTGTGGAGAAGCAGCTTGTAAAAGAGGAAGAAAGGTACCCTGTAGAATTTGAAGACTCTGAATCTCAGGTTTTTGAGTTTGAAAGCTCATCTGAAGTCTTTTCAGTTTGGCAAGATCATAAAATAGACAGCAAAAACTCCCTTCAAGGGGAACAGAAGAGCTATGTAACTCATGTAGCTGATAGTACAAACAATAACTTGGGTTGTGGTGACTCTGTGTCTGAAGAGGTTGTTAGAAACAAAGCAGAGGGAGTTAAAGAGCATGCAGGACCACATAGTAGTGTTTCTGCTGAGGAATTTTGTAAAACTGGAGTAAAAAAACCTAAGAGGAAACGCTATGACAAAGTTACAGCTGAAGATCCTCAGAGGCCTTCCTCTTCTGTTGGAACTGATCAATTGCCTGATCGCAGAGATCTTACTGAAAGTGATTTAAAGAGTGCAGACATGGGGATGGCAACTCCCAGTTCAAGTGTTGAGAGAGATTCTACAATTTTACAGAAGTCTACAAAATCTCGAACTCACTCAAAACCTGTTAGGAAAGTTCCAGCCTCTAAGGCAACTAAGAAAACACATTCAGACACCAGAAGAGGACAGTCTAAGAGTTCATGTTACATAAGTTGTAGAACTTCTCCTGCTATTGTGCCACCAAAGAAGCTTCGTCAGTGTCCAGAGCCAACTTCAACAGTTGAAAAACTTGGTCTGAAAAAAGCCCCTAGGAAGGCATTTGAGTTGTCCCAGAGGTCTCTGGAGTGTATAGTCCAATTACGTGACCACGGGAAGACTGTTGGAGTAGTTGACGCCCCCAAGAAAGCTAAATTAATTTCTCCTCAGACTCTTTCTATCAAAAATAATAAGAAGCTTCTGACAAGCCAGGATCTTCAATTTCAAAGGCTTATGAGATCCAGATCACATAAAAAACGAGACTTTGATTACAAAAATACTGATACTGTAAGAGTGTCACGCATAGTACAGGGATCAGATGTACTTGAAGCAGACTCTGATGAGCCAGATGATCATAGAGTAAGTGAGCCACTTGCCATCAGTAATGAAAAACAGTTAGCAAAATGCATGCTTTCCAAAACAGAAGTGGCAGAAGCCTCTTCTGATCCTTGGGTGACAGGTATAACTTGTCTTGTGAACCAGTGTGAATCTAGAGTGTTAAGTGGAGGAGTGCCAACAGATGTGGTGATGGTCTCTGCTTCAGAGGACCCTGTGGATGGAGGTGCTGTCACAGTTCAAGTTGGGGAGGTGGCATCTGTGAAAGCTGCAGAGCCAGCGTCTAGTAGTGATACAGATGATGATGACAACTTATTCCTAACACAACATGATCCTCAAGATATGGATCTGTGCTCACAGTTGGAAAATAAAACCATTATCGTGGCTCATAAAAAAGATACAGTTCAGAGAGAAGATTCTTTAAGTCGGCCTCAGTTGGAGTCTTTGAGTATCACAAAGTGTAAATACAAAGACTGTGTCGAAACTACAAAAAACCAGGGTGAATACTGCCCAAGACACTCTGAAGCTAAAGCAGCAGATGACGGCCTGTTCCGTAAACCTGGCTTGCCTCTTTCTGTAGCCAGGCCCTTGAGACCTACTACTACCAAGATATTTAGCTCAAGCAGCGCTTCACGAACTGCCAATCTTTCCAAGTCTTTGGAAAGTACTACACTTCAGCAGTCAGCACTAAAAAATAAGTCAAGTGGAGCGCAGCCTAATTTGAAGGTGACACCACCCTCTTCCATGGGTTCTCAGAAGCCAGTGGCTGAGGTGAAAAGTCTATGCAATATTTTTCATTTTCAGACTCCAAGCAGTTCCAGCAAACAGAGTTGCAAGCTTACATTTAGTGAGAACAGGCCTACATCAGCTGCTTCTCCAGTGAATATTCTCTTGCCATCGCAGTCTATCTTTGACACCTTCATTAAAGAGGTCTTAAAATGGAAATACCAAATGTTTTTGAACTTTGATAAGTGTGGTGCTCCAACAAGTCTCTGTCAGTCTATCTCAAGACCTGTGCCTGTCCGATTTCAAGATTGTGCAGAATATTTTAATGTTTTTCTACCTTTGATTATATTGAATGCTTTTGAAACA
Seq A exon
GTAAGTATTCTTTAATTCTTTGCCCCTACTGTAGATAGAGAAATGGTTATAAGCATATAGCCTGCTTTCTAAGTTTCTATAAGTTTGAGTCTATACTCACTTCAGTGAGAAGGTATTGGAAGATTTGGAGTTGGTCAGTATTTAGACCAGGGACTAGTAATACACAGTAGCTTATCCTTACCCAACATCCTTGGTTGTTGGGTAGAGAATAAACTGTGGAAAGGCTAACAGGTCTAGTAGACTAGTTATAGGTTGGTTACAGCTACTTGGGGGTAAAATGATAGTGGCTTTGGGTGGTAGCTGTGGAGATGGAAAGGCTATAAGGGTACATTTTAGAATATATGACTGATGAGTGGAAATTGAAAAGATGACTCTGTTTGGAGGCTTAACCTGGTTATGTTATGTTTACTGTCTGCCAGGAGTGAGGTAGAACTTGAGTTCACCTCTCCTGGTTTCTAGGCTGGAGCAGTACATGGCAGGAAAGCTCCTCTGGATGTTTCTAGCCAAAAATGGTGCAGAGTGTGATGATGGGGTTGTGTGTGTCGTTCCCCCGCCCCCCCAAAGAGGAGTAGCTGCTTGGTTAACTTTGAGTAGAAGCAGCTCAGCACTAAGAATTGTTGGTTACCAGGAACTGATGGCCAGTTGCAGATTTAGCTACTTGACTCAAAAAGTTATTGTAAAACAAAACAAAGTCTCAAAGGTCATTTTTTTTGTTGTTTGTTTGCTTGTTTAAAAAATGTTAAATATAGCCTTTTTACACTAGTAATTTTTCTTTCATAAATTTGGGCTTAGGAGTAGTCATTTTTAACTCACAAAAGATCTCAAAGATACTTCTGGGTTTGATTTGAGCCTTTGGAAGACTACTAGTACGTGTGACATATAGAAACCAACAGGAAGAGTGCTTGTGCCAATATTGCAGAGGTTGAGAGAAATGTAGGTCAGATAATCGCATTGTGAAGTAGGTACTACCAGTAAGATCTAGCATCGCATGAACAGTATCAGAACCACAGGTGACTGCTGAACATGAAAGGTGTCTTATTTCAACTGAGGAATAGTATTTTTTAGCCTTTAAAAGTTCAGTTAACAAATATAACCAAATGTGACTAATGGCTGCTAAATTGGGCAGGACAGTTGTGGACAACTTTATAAACCTCACAGACTGACTCTTAGGTTTTCACTTGGGATCTGTTCTGTTTTCCTTTAGCCCACTGGAACATTTTGCTGTTTGTTTGTAGTAGCTTTTAGCATGTTCTTTATTTCTTAGTTTCTTCTTTTGCTTTGTGTAG
Seq C2 exon
GTGGCACAGGAATGGCTGAGCTCTCCAAATAAAGAGAATTTCTATCAGTTGCAATTACGAAAATTTCCAGCTGACTATAAAAAATACTGGGAGTTTCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043535:ENSMUST00000061578:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.429 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CCAGTGGCTGAGGTGAAAAGT
R:
GAGAGCTCAGCCATTCCTGTG
Band lengths:
358-1644
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