MmuINT0142207 @ mm9
Intron Retention
Gene
ENSMUSG00000015697 | Setdb1
Description
SET domain, bifurcated 1 [Source:MGI Symbol;Acc:MGI:1934229]
Coordinates
chr3:95141071-95142954:-
Coord C1 exon
chr3:95142268-95142954
Coord A exon
chr3:95141188-95142267
Coord C2 exon
chr3:95141071-95141187
Length
1080 bp
Sequences
Splice sites
5' ss Seq
TAAGTGAGT
5' ss Score
6.43
3' ss Seq
TCACCCTTTTCTCTCTGCAGATC
3' ss Score
13.74
Exon sequences
Seq C1 exon
GTCACCTTTGGCCTCAGTAACATCTACCCCAGCATCTGCAGCCCCTCCAGTCCCTCCAGTCCCACCAGGGCCTCCAACCCCTCCAGGGCCTCCAGCTCCTCCAGGGCCTCTAGCTCCTCCAGCCTTCCATGGCATGTTAGAGCGGGCACCAGCTGAGCCCTCCTACCGAGCCCCCATGGAGAAGCTTTTCTATTTACCTCATGTCTGCAGTTACACTTGTTTGTCCCGGATCAGACCCATGAGAAACGAACAGTATCGGGGCAAGAACCCTCTATTAGTTCCACTTCTGTATGACTTCCGGAGGATGACAGCACGGCGCAGAGTTAACCGCAAAATGGGCTTTCATGTAATCTATAAGACACCCTGTGGTCTCTGCCTTCGGACGATGCAGGAGATAGAGCGCTACCTTTTTGAGACTGGCTGTGACTTTCTGTTCCTGGAGATGTTCTGTTTGGATCCATATGTTCTTGTTGACAGAAAGTTTCAACCCTTTAAGCCTTTTTACTATATTTTGGACATCACCTATGGCAAGGAAGATGTTCCCCTGTCCTGTGTTAATGAGATTGACACAACTCCCCCACCCCAGGTGGCCTACAGCAAGGAACGCATTCCTGGCAAGGGTGTTTTCATTAACACAGGCCCTGAATTTCTGGTTGGCTGTGACTGCAAGGATGGGTGTCGGGATAA
Seq A exon
GTGAGTTGGTGGGGTGTACAGGCATTGCTGTCTCTGCCTTCAGGTTTATTACAGTTGCTTTTCTTTTCTTTTTTATTTGTATTGCTTTCCCTGTTTTCCTTTACCTCCTCTTTCAGCTAGAGTTCTGCTAAGGTCATTATGAAATACAGATACAGAAACTGGGTACAGTGGCACATACCTGTAACTTCAGAATTTGAAATTCAGCATTGTGGCAGTTTCATCTTGAGTTCTGGGCCAGCCTAGGCTTCATAATAACTTTGAAGCTAGGCTGAGCTAGCTACGCAGTGAGATCTTATTGAAAGAGAGAGAGAGAGAGGGAGAATGAATGAACATGAGATAGGGAGACCAGGGTCTGATCGTCTTAAATGTCCCCAGGAGTAACCCTGGAAATGTAGGGGTTATGTTCTGTTCCTGTCTCCTCTTGCTGTTTCTGTCTCCCCTTAACCTTTCATCCTTGTGTTCACCATTTAGATTCTACTTTATTCTCACTGTATCTTACTCATGCTTTTTCTCACTACCTTTACCTTATCCCCATCCTCTGTTATTGGTTGATTTTTGCCCTAAGGTAAGGTTTGTTGAGGGAGTCCCTGGTGACTAAGGATGAGGCCTCGAAAGTTCCTCGCAAGGGAAAGAGTTTCCATAACCAAGATCTGCTTAAAAATATGGCTTTAGCTCCACCTTTCCTACAGCTCGGCCTGCTTCATATTCAGCATGGCCCTGGAGGTTAGAGCCTTTGGTATTTCTCACATTTTAGGAAGTCCTTGCCAACAAAGTCACTCAGCCAGTGCACCTCCTGTGCACTCAGCCAGTGGTACCACACATGGGCACCTTGGGCCTGGCAGAGCCTGACCTGAGATGAATGACTGCAGCTAGCAAGTCCTAAGTTGTGGACTCAACTCAGTTTTGATTTAAGACCGCTCAAGCTGGCCCAGAACTTACTAGCTGAGGATAGCAGTTAACTCCTGATCCTCCCACCTCTATGTCTCAGATATTGGATTACAGATGTAGATCACTGTGTCCAGTTCCCATCCTCATGAACCTCAGAAAACCACAACTCTAGTCACCCTTTTCTCTCTGCAG
Seq C2 exon
ATCCAAATGTGCCTGCCACCAGCTAACTATCCAGGCCACAGCCTGTACCCCAGGGGGCCAAGTCAACCCTAACTCTGGCTACCAGTATAAAAGACTAGAAGAGTGTCTGCCCACAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015697-Setdb1:NM_001163642:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.226 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0142914=MBD=WD(100=32.6),PF0503311=Pre-SET=PU(49.6=24.8)
A:
NA
C2:
PF0503311=Pre-SET=FE(33.9=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:
GCAGGAGATAGAGCGCTACCT
R:
GCTGTGGCCTGGATAGTTAGC
Band lengths:
342-1422
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: