MmuINT0142235 @ mm9
Intron Retention
Gene
ENSMUSG00000071350 | Setdb2
Description
SET domain, bifurcated 2 [Source:MGI Symbol;Acc:MGI:2685139]
Coordinates
chr14:60036246-60038398:-
Coord C1 exon
chr14:60037838-60038398
Coord A exon
chr14:60036363-60037837
Coord C2 exon
chr14:60036246-60036362
Length
1475 bp
Sequences
Splice sites
5' ss Seq
CATGTGAGT
5' ss Score
7.83
3' ss Seq
CCCCACTGCCTTTCTTTTAGAAA
3' ss Score
8.45
Exon sequences
Seq C1 exon
ATCTCCAGGAAAAAAAGTATTCCTCCCTGTGAAGAATAAAGCTGACAATTTAGTGAAAAAGGAAGCCCCACTGCATATATCTTTCCATCGCCATATCTGCTCCAGGACTTGTCTAATGGAAACCCCACTGTCCTTGAAGGGAGAAAACCCCCTGCAGCTACCAATCAGATGTCACTTCCAAAGACGACATGCAAAGACAAACTCTCATTCTTCTGCCCTCCATGTGAATTATAAAACGCCCTGTGGACGGAATCTACGAAACATGGAGGAAGTTTTCCATTACCTGCTTGAAACAGAGTGTAACTTTTTATTCACAGACAACTTCTCTTTCAATACTTATGTCCAGTTGACTCGGAATCACCCAAAGCAAAATGAAGTTGTTTCTGACGTGGATATTAGTAATGGAGTGGAATCAGTGTCGATTCCTTTCTGTAATGAAATTGACAACAGTAAACTTCCACGGTTTAAGTATAGAAATACAGTATGGCCCCGAATATATCATCTGAACTTTTCCAACATGTTTTCTGATTCATGTGACTGTTCTGAGGGCTGCATAGACAT
Seq A exon
GTGAGTAGAAAAACATGGCGTCTCAAGCAATCTTTTGCATGTAGACATATTTGCTTCGTCCTACTGTGTTCCATTTGCCATTCTGTCTGTCTAAATAAAACAGTGGACAAATTGTCTAAAATAGATGAAAAAAGATACCCTGTTTCATAACTCCCCAAAGTGGCTATTTGCAATTTATTTTCTCTAAGGATGAGCAAATTTATTGCCATAGTTATAACAGCAATTACAGTACCATTGATGAGTGTCATGTATGCCCAAATACTTTAAATACATTCTCTTCATTGTCACAGACTCCTGTTTTAGGTAGTATATTTCTGTCATACAAGTAAAGAAGAAATAAAGAAATAAAGTCTGTCTGTCTGTACTTTCCCCACATACTCTAAAGCATGACCCTTGATCTGTTAATCAATATGGCTCTTCAGTTAATCAATATGGTAAGCAGTGGGATCTGCTTGTCATTTTTCATTTCATATTCTGAGGAAGGTAGTAGAAACGATACTACAGCAGTTTCTTCCTTTACAGTGGCTTCAGTTCCTGTGGCTAACTGTAGTACAAAAATATTGTGCTGGAGAGATGTTTTAGAGGTACTGGCTGCTCTTCCAGAGGACCCAAGTTCAGTGCCCAGCAACCACGTGGTAATTCACATCCAGTGCCAAGGGAACTGCTGCCCTCCCTAAACAGCTGTGTGGCATGCAAGTTGTGCGCAGATATACAGCAGACAGGATAAAAAGTTAGGTGGAGAATTTTCTATACACTTAAATCATAAGTATTAAACTACATGCTGTTTGGAGTCATGTGATGGAACGCCCCACTTCATCCCACTTGGAATGTGAATCATCTCTGTCCACCGTAGTCATGATTTGCCAGTTAGTCACTTAACAGCCACATTGATTACCAGATCAAGTGTTGTATTTGGCAGTGCATTCTAGTAAGGCTCACTTTATTTAATAATGAGGACACAAGTAATGATATATATAAAAAAAAACAAAGCATGTAAGGGGATATTAATTCTGATAACATGTGGTAGTGTTTCACAGTATGTGGGGAAAGCACAAATAAATAGACTTTGGTACTGATACAAGATGTTAAGCATTCAGGGGTCTTTAAATATACCTCAGATAATAAGGGAATAACTATTAAAATAATCTGTGGTAGAAGAACATAACTAAGACTATCAAGAAATGAGCATCTGCTGAGGAAGACACTCATTTTGAAAAGTTAAAAGCCCATGTAATTAAATATATGTTTCAAGGTCAGAGAGCTCAGTGTGGTTTATATCAGTTGTAATGAGCCTGTGGTTGGTGTGATTTCAGATAGGCCTACCTTGTTTAGAGAGGTTTCCATATAGTCCTTGAGCAAAACCTCTCTTATAAATAAAAGTCCACCATTTTTAATGTCATTTACAGTTTTACTGAGTCTCATAACTTGCTGATTTTTTTTTTCTCACTTCTCTATCCCCACTGCCTTTCTTTTAG
Seq C2 exon
AAAAAAATGTGCATGTCTTCAGTTGACAGCAAAGAATGCCAAGGCATGTCCCTTGTCATCGGATGGAGAATGTGCTGGATATAAATACAAAAGACTGCAGAGGCTCATACCTACTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000071350-Setdb2:NM_001081024:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.016 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0142914=MBD=WD(100=38.8),PF0503311=Pre-SET=PU(49.1=29.8)
A:
NA
C2:
PF0503311=Pre-SET=FE(34.2=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:
CCCTGTGGACGGAATCTACGA
R:
TGCTGTCAACTGAAGACATGCA
Band lengths:
354-1829
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: