MmuINT0142254 @ mm10
Intron Retention
Gene
ENSMUSG00000043535 | Setx
Description
senataxin [Source:MGI Symbol;Acc:MGI:2443480]
Coordinates
chr2:29173557-29176975:+
Coord C1 exon
chr2:29173557-29173721
Coord A exon
chr2:29173722-29176876
Coord C2 exon
chr2:29176877-29176975
Length
3155 bp
Sequences
Splice sites
5' ss Seq
AGGGTGACG
5' ss Score
2.31
3' ss Seq
TTTGTGCCTTTTATAAACAGACC
3' ss Score
8.65
Exon sequences
Seq C1 exon
CTCATATATAAATGTTCAAGAAATAAAGTTGGTGATGGAAATAATTAAACTTATTAAAGAGAAAAGAAAAGATATTTCCTTCCGAAATATTGGCATAATAACCCATTACAAGGCTCAGAAGACGATGATCCAGAAGGATTTGGAGAAAGAATTTGATAAGAAAGG
Seq A exon
GTGACGTATTTTTACATGTATTTCTGGTATTTAGGTTGAATTAGGTTGTTTCTTAACAGGACTGGGGGACTGGGGTTGAATCAGGGTCTTTGTATTCTAGGCAAGTGCTCTAACGTCTCTGTTATATTGCCCAGTCTTTTTATTATTTTTGTGATCATGTCTGTAAGTTTCCCATTTGCTGTCCTCCTGCCTCAGCCACCAGGCCCTACTAAGATTGTGGTTTTGTCTCCTTATCTCTACACTAAAATTAAAGATTAAAATCTGGAAAGTCTAGCCAGGCGTGGTGGCGCACGCCTTTAATCCCAGCACTCGGGAGGCAGAGGCAGGCGGATTTCTTGAGTTCGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTGGGAAAACTAAGGAAAAAAAAAATCTGGAAAGTCAGTGTCAGGTGTGTGGTGAGAAACATTTAACTCCAGCACTTGGAAGGTGGAGGCAGGACGATCAGTCAAGGTCATCCTTGGTACCGTAGTTTCTTTTCCCGTTACTATGACAAAATATTCTGACAAAAGCATTAAAGGGTTTATTTCACCTCACAGTTTATTACAGCCCATCATGATGGGGGAATCAAGGCAGCAAGACTCTGAAGCATCCAAGCAGCAGCAGAAGAGCAGTGAATTTATGCATGCTAGTGATGAGCTCGGTTCCTCCACTGTTACACAGTCCGGGATCTCCAGCCTAGAGAATGGTGCCACCCACACTGGGTGGGTCTTCCCAACTCAACTAACACCATCAATAAATAACCCCCAGAGACATGCCCCCAACCCATTTCTTAGGCTAGTACAGGTTTTACCAAGTTGACTATTAATACTAATCATTATATTCTGCTGCATAGTGAGTTCAAGGCTGACCTGGGCTATGTGATCCCCATCTCAACAAAACAGTCTGGAGAGAGATGGCTCAGTGGTTAAAAGCACTTGCATTGCAATCATAAAGATCAGAGTTCAGATCTCAGTACTTAGACAACAAGCTGAGGGTTGTTTCTTTGTAACCACAGCTCTGACTTGGGCAGAGATGGGGATGTTTTGGGGTTTGCTGGCTTCCAGGCTGTCTGAGAAAGCATGTGCTTTCAAGCTGCTTCTTGTGGCCTTTCCTCACATGCACACATGCACTGTTACTCCTAAGATAAAATACCAAAACTAGCAACTTTTAAAGTTTCTTATCTAGAAACACACAAAACTGACTTTAGAGAAAATTTTAAAAATCCGGAGATTCTATCTCTCTCTCTCTCTCTGTCTCTCTCTCTCTCTCTCTATCTATCTAGCACACCTCTCAGTGTAGTGACCAAAACCTGAAAAACAGGTTAGACTTGACTGCTGAGTTTCGCCAAATGTCAATCCACAGTCAGCACTAACACAGCTGTGTGTCTGCAGTCCTTGCACTCTGGAGTCTGAGGCAGGAGGATCTAGAGTTTTAGACCAACCTGGGCTACGTAGGTAATACCCTATGTGAAAACAGCAGAAAAAGCCAGTAATACTTAGGACTTGACAAAAGCCTAATAAAACTTCCTGGTTTTCTTTTTTTAATTTATGTAAAGCAGGCACACCGTGGTGTGCATATGGTCAGAGAACAACTTTCAGTAATTGGTTCTGGATAGAACTCCAGTCATCGGCTTGGTGGCAAGCTGCCTTACACGTTTTGAACCATGTTGCTGGCTCCAAGGACACTGTAATTTTTTTATGACACCAAAGCAGAGAAGGTGTTACAAGAGCCACAGGACCGATAACACTAATGATTGTAGATTTAAGAATGCTAAATGGACAGCTGCAGACTGAATCCAGAGCATATTAAGGGACTGTATATCATGACCACATGAAATTTATCCCAGAGTGCAGTGTTGGCTAACTATCTTGCTGGAATAAGAGAAGGAAGCAAGAGTTGGCAGCTCACTCTTGGAGCCTCCATACTTGGGAATACAGGGCAGGATAAACATAATGAGCTTGAAGCCACCCTAGGTTTCTGAATGGAGACTGTATCTTAAAGAACAGACAATTAGTATGGCATGTGGGTCACCTTCTCAATCTAACAGATGACAGAAAAGACTTAACAAAGCCTATCATCTTTCACAACAGAAAAAACTATTAGGAGTACAGAGAAAATTTCTTAACTTGATTGTCTATGGAAAACACATAGGTAACATTGATCTGTCATGGTTCAGCAGTCTTTCCTGTAGACCACGGAGGACATTTTTCTTACTACTTCTGTTGTCCATTGCAATAGACACTCTAGCCAAAGCAAGACTTTGTTGTGTGTAAGTCTGTAAATAATTCAGCATGGTTATATATAGATCCAGTTAATGAAGCTACATAAAGAAGCTCTTAGGGTTAACACTTGAGTTTAAGAGACTTGTAGAATACAGGATCAATATGTAAAAAGTGGTTGTCGGTTAATAGTCTGCTCAAGAAGTTAGAAACATTCTATTTATAATAAATAGCACCAAAAGTAATAAAATACTTAGAAGTAAATAAGACCAGTAGTAGTATAAGATGTATCCACTGAAAACTACAAAGCATGTTACAAGAAAAAATTAAATACTCAGGACACAGGAAGAAGGTCGTGGATAAGAAGACACAGCCCCAGTGGCTGTACTCAAAGAAGACTGGTACTTTGTCTGCCAGAATTCCACCCGCCTCTGACAGAAGTCAAGCTGATGAAGCTATAGAAGACTCTGAAAGGCCTAAGGAAACATACATACAAATATATATAGCCTCAGACTAGGAGATGGTTTCTTATGGACTTCATAAACACTAAGAATTGTGTTTCAGAAGATGCCATCAAAAGAATGAAGGATGTTATGCTGACCTCAAGCATATCTGAATGTACTGTCCTGTCTGGAACATACAACAAACCTTACAACTCGGGACATTCGGATTTTGGTTTTCACAACAGTGTTTTTCTCTCTGTAGCCCTGGCTATCCTGGAATATACTCTGTAGACCAGGCTGACCTCAGAGTCTCTCTGCCTCTGCCTCCAAGTGCTAGGATCAAAGGTGTGCGCCATCACTGCCCGGAATCCAATGAAGAGTTTTAAATACTGCCTATGTGCATGTATTTCATAATTTAAATGTTTTAGTAAACTTTGTGCCTTTTATAAACAG
Seq C2 exon
ACCTGCAGAAGTGGACACAGTAGATGCCTTCCAGGGCCGGCAGAAAGACTGTATCATCGTTACCTGTGTCAGGGCAAGTGCTGTGCAAGGCTCAATAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043535:ENSMUST00000061578:23
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=0.147
Domain overlap (PFAM):
C1:
PF130871=AAA_12=FE(27.2=100)
A:
NA
C2:
PF130871=AAA_12=FE(16.3=100)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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