MmuINT1031023 @ mm10
Intron Retention
Gene
ENSMUSG00000015697 | Setdb1
Description
SET domain, bifurcated 1 [Source:MGI Symbol;Acc:MGI:1934229]
Coordinates
chr3:95354542-95356202:-
Coord C1 exon
chr3:95355934-95356202
Coord A exon
chr3:95354694-95355933
Coord C2 exon
chr3:95354542-95354693
Length
1240 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
TGCATGTGTTCCAATATCAGGGA
3' ss Score
6.72
Exon sequences
Seq C1 exon
GGCCAAAGCATGTCCTCCCTCCCTGGGTGCATGAGTTTGGCTGCAGCGCCAGCTGCAGCTGACTCTGCAGAGATTGCTGAGCTGCAGCAGGCGGTGGTTGAAGAGCTGGGTATCTCTATGGAGGAACTTCGTCAGTACATTGATGAGGAACTGGAAAAGATGGACTGCATACAGCAGCGCAAGAAGCAGCTCGCAGAGCTGGAGACGTGGGTACTACAGAAAGAGTCTGAAGTGGCTTATGTTGATCGGCTGTTTGATGATGCATCCAG
Seq A exon
GTAGGGATTCCAGGAAGCAGAAGTAAATGTCCATCTGTGTCCTCCTTGGAGTGACTGTTGTTGTCATTGTCCTAAGCACTTTATACTTTGGCGACTTCAGTCAGGTGGGGCCTTACTCTTCCTCTGAGTTTGTAATGCAGAGTTGCAACAGAACACTTTTTCCCTGTGGGTAGCTGCTATGTGATCAGCAGTAGTTAGGTTAAAGGCTTGAATTCCCTTCTCTTCCTCCTGGACTGAACTTCCTTCCTAAGATCCCCAGAAAGTGAAGATTGTAGAGTTGCTGTCTTTTCTGTTTTTCTGAGACAGAATCCCAATACCTAAATCTTGCTGGCCTGCAACTTGCAGAGATCTGCCGACTTTTGCCTCCTAAGAGCTGCAATGAAATGATCCTAGCTTATGCTTGTTGAGTTGATTGGGGTTTCATTCGTTCATCCATTTTTGATACAAAGTCTCTTTACGTAGAATTGGCTGCCCTAGAACTCACCATATAAACCATATTGAGCTGGACTCATAGAGACCCATCTGCCTTTGTTTCTCCAGTGGTGAGATTAAAGGGATGTTTCACAGCACCCAGCAAAATGAAGTTGATATTTAAAGCTGTCTTCTTAGTTCCCAAAGCCACATAGATAATAAATATCAGATATTAGGACTTTTGTAACAGCAGGTGGAAAATTGAAGTCTAGAAAATTGTTTCATAGAAGAATTACATGGAAACAAACATTCTGTGGAAAAGCATTCTAAATAGGTACTTTGGAACATGTAGAGCAAACAGTCTATATTTAAATATACATAATTTCCTGTTACTGTGTTGTGTTTTGTATGTGGGGGGGGTTGTTTTTTGTTTTTGTTTCTGTTTTTGTTTTGTTTTATTTTTGAGACCGTTTCTTTGTAACTCTGGCTGTCCTGGAACTACCTCTGTACACCAAATTGGCCTGGAATTCAGAGATCTGCTTGCCTCTGCCTCCTGAGTGCTGGGTTCTGTTTTTGTTCTGTCTAAAGGTTTCTTACTCTGTAGGCCATGCTGGCCATGAACTGTATTGACCATGAACTCTATTGACCATGAACTCTATTGACCAAAGTGACCTCAAACCTAGCTAGTCTTGGTTCCTCAGGCTAAGGACTAGGATTACATGTGTGAGCTCAGAGGCTAGGTATTGTATAAATGTATATACATTGTAATGCTCTTGTACTGCACTGTCTCCACTGGCTTTGATCTTTTCTGCATGTGTTCCAATATCAG
Seq C2 exon
GGAAGTGACTAACTGTGAGTCTTTGGTGAAGGATTTCTACTCTAAGCTGGGACTACAGTATCATGACAGTAGCTCTGAGGATGAAGCTTCCCGGCCCACAGAGATCATTGAGATTCCTGATGAAGATGATGATGTCCTCAGTATTGATTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015697:ENSMUST00000107170:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.419
Domain overlap (PFAM):
C1:
PF072276=DUF1423=PU(67.8=89.7)
A:
NA
C2:
PF072276=DUF1423=PD(31.3=69.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCCTGGGTGCATGAGTTTG
R:
GGGAAGCTTCATCCTCAGAGC
Band lengths:
343-1583
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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