MmuINT0142247 @ mm9
Intron Retention
Gene
ENSMUSG00000043535 | Setx
Description
senataxin [Source:MGI Symbol;Acc:MGI:2443480]
Coordinates
chr2:29017270-29018569:+
Coord C1 exon
chr2:29017270-29017385
Coord A exon
chr2:29017386-29018497
Coord C2 exon
chr2:29018498-29018569
Length
1112 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
GATTTCAAAATTGTTTTCAGAGG
3' ss Score
4.88
Exon sequences
Seq C1 exon
AAAAAGACTTGCCTTCTCATATTCAAGAAATGCTTAGAAGAAAAGAAATTCTAGATGCTCAACTTGATGAGCTTTCTCGTCAGCGAGCTCTGTGCCGAGGTGGGCGGGAGATGCAG
Seq A exon
GTATGAACCCCCTCCCCATGTGAACCTTGCAGAAGTGGCTTAGACATGAACTAGTCGATGGGTGTGTCATGCTGCTCTCATTGATGTGGTGTGACTCCATGATATGCTGGAGTAGTATGGCTAATGTCAGGCTAATGTTAGCGAGCTCTTCTGTAAATACTGTTTTATAGACCATAGTCTATATCTGTAGTCTCTGTGACAGCTCCTCAGCTTGATTGTGGCTCTAAAGCCATGCAGCTGTATTGCAGTTAAGATTTATTTATAAAAGTAGATGGCATATTTTATTATTAGGCACTTTACTGTTGAGTTAAACCCATTTTAGTGGCTGGAGAAATGGCTCACTGCTTAAGAGCACTGACTACTCTTCCAGAGGATCCAGGTTTGGTTCCTAACATCCACATGGCAGCTCACAATAAATTAACTACAGTTCCAAGGATCTGATGGTGTCTTCTGGTTTCCTCAGACAGACTCTTGGCACACACGTGATAAACAATGCAAACAAAACACATGTAGACATAAATAAAAACAACCAACATTTATAATTAGATTGAGACAGAGAATTTACTGGCTCATATACTCAAAAGAGTCAAGTGTGACTTAGCTTTTAGTATGTTTGTATCAAGAAATGTATCTGGCAACGTTTTGCCACCTTTTGCTTTCCCTTTTCTATGTATCTCAGCCTTTTCTTTTCCATGAGAAGTCAAGTGCCAGTACTTTTGGGCACCATCACTCTGGCTTAAAATACCATGTGTCTGTTCCAAGGATACACTCTGATTAATCTCTGCTCGCCAAGCAGATCTAACCCCTGATTTGATTTAGGGGAAGGGTGTCATGCCTGCAGTATGTTACATGCTCAGCACTGTTGCAGGATTGTTGTGTACCTTAGACATGAATGAAGGATTGAAACTCCGAGGCTTGAGACAGCAAACGCGTGTGGAGACATAATTGAGCCCATCAGGTGTGTAGAGCAGGGTTGGGGCTTGGCTGGTAGGGAAGAGAGCAGGAATTCAGGGAATTCACGGTTAAGATGCTCTTTACTCTCCTAAGGTGTGAAGTGTCTGAGAGCTTTCTAAAGTGCTTGGTTTTCACAGTGATTTCAAAATTGTTTTCAG
Seq C2 exon
AGGCAAGAATTAGATGAACACATTGCCATAGTCTCAAAAGAAAGGCAAGAACTTGCTTCGAAAATTAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043535-Setx:NM_198033:17
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.167 A=NA C2=0.167
Domain overlap (PFAM):
C1:
PF130861=AAA_11=FE(13.3=100)
A:
NA
C2:
PF130861=AAA_11=FE(8.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGACTTGCCTTCTCATATTCAAGA
R:
TCTTTAATTTTCGAAGCAAGTTCTTG
Band lengths:
183-1295
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: