MmuINT0086115 @ mm10
Intron Retention
Gene
ENSMUSG00000054611 | Kdm2a
Description
lysine (K)-specific demethylase 2A [Source:MGI Symbol;Acc:MGI:1354736]
Coordinates
chr19:4322387-4325046:-
Coord C1 exon
chr19:4324337-4325046
Coord A exon
chr19:4322551-4324336
Coord C2 exon
chr19:4322387-4322550
Length
1786 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGC
5' ss Score
8.27
3' ss Seq
AATTCTCTTCTGTCTTACAGGTG
3' ss Score
11.71
Exon sequences
Seq C1 exon
AAGCGGAAAATAGAAGAGAGTGATGAAGAAGCTGTACAAGCCAAAGTCTTACGGCCCCTGAGGAGCTGCGAGGAGCCTCTCACACCCCCGCCTCACTCACCTACTTCCATGCTGCAGCTCATCCACGACCCGGTTTCTCCCCGGGGTATGGTGACTCGGTCATCCCCTGGGGCTGGCCCCAGCGACCACCACAGTGCCAGCCGTGATGAACGCTTCAAACGGCGGCAGTTGCTGCGGCTACAAGCCACCGAGCGCACCATGGTACGGGAAAAGGAGAACAATCCCAGCGGCAAAAAGGAGCTGTCTGAAGTTGAGAAAGCCAAGATCCGGGGATCGTACCTCACTGTCACTCTACAGAGGCCCACCAAAGAGCTCCACGGGACATCCATTGTGCCCAAGCTGCAGGCCATCACGGCCTCCTCTGCCAACCTTCGCCCTAACCCCCGCGTGCTAATGCAGCACTGCCCAGCCCGAAACCCCCAGCATGGGGATGAGGAGGGGCTTGGGGGAGAGGAGGAGGAAGAGGAGGAGGAGGAGGAAGATGACAGTGCAGAGGAGGGGGGTGCAGCCAGGCTGAATGGCCGGGGCAGTTGGGCTCAGGATGGAGACGAAAGCTGGATGCAGCGGGAGGTCTGGATGTCTGTCTTCCGCTACCTCAGCCGCAAAGAACTTTGTGAATGTATGCGAGTGTGCAAGACATGGTATAAATG
Seq A exon
GTGAGCAGGGATGCAGGGGCAGGGGGTAGGTGACAGGGCTTCTATGTGCACCTTGATATTGTCAGTCATAAATAGACCTGCTCTGTGGGTACCGTTAAAAATGAGTCCATTGTACCTGCAGATGTTAGGGGAATTGGAGCCTTTGCCTCTTCTGCCTGCCCTTTGTTTCCCTGTCTCAGCTGCGGGGAGGGAAACCAATTTAAGGAATGGATTTTTGTACAGTCTTACAGGTTGTGAGCTTGTCTTCCCCTCCTAACTAACCTTGTGCTGGTGGAGAATCTGTGACAAGCTGTTATTGCACCAAGAGGAGTGGGCAAACTTTCTAAACTTGAAGGTGTTCTAATATTCTGGTTCTAGTACTCCTTGGCCTTCCCTTCAGTGTTCGCTCCAGTTTAATCATCCCCCAAACTTGAATTATTCCTTTCTTCAACAAGTGGAGCCCAGTTCTGAAGCTGAGACTTAATTGTCCTTCCTAATGGAACATTTCTCCTCCAGTTTAACAGACATTTAGTAGGGAAATCCCAAGAACTAATGAAGAGATTGCTATGGAGCATTGTGAGGTTTTCTAGAAGGGTGTATAATTTTTATTTTGGTTACACACTATTACTGTTGTTCCTAAAATTTGGTGTCTTGACCAGCAAAATATGTCTAGAAACTTGTCATAGTATGGTAGTGCCAGAGTGTAGTGTTACAGGTATGATCCCAGCGTCCATGAGACACAGGCAGAAAGATCTGCAGTTTGGGGTGAGCAAAGGCTGCATAGCTGCAGACCAGTCTGCTAAAGCATGAGAAGGACGGAAAAGCAGACCCCAGGCTGCTAAATCAGAGCCTCGGGGATGGAGTGTGTATGCATGTTAGGTTTTGGGTTTTGTTGTTTTGTTTTTGTTTTGTTTTGTTTTTGTTGTTTTTTTATTTAAGGACTCCTACCATCAACATTTGGTGTGCTATCAGTGAGACTTCTGTCAATTGTAATACCTTTATCAGTACAAATCTTATTTCTTGACTTGAAATTTATGTGATCTACCCAGATTATCTTAATTTCTTTTTGTCAAGCAAGTAGGCTTCCTAGTCTCTAATCCTTGGTTTCCAGGCCAAGGCACATGAGACTCCCAATACATATTTCCTTGTGTCCTGCCAGGCAGGCTGACCTGGAGACTATAACATTGTAGAGTGGGAAGGCCTCTCACTTTCAGTTTTGGATGGACTGGCTAGATGTTAAGCTAGCAGGGAACCAAATGACTTAGTGTGAAAGAGAGCTGTCTAGATTGATAGAAACCTCACTTGGCCTGAGACAGTAGTAAGCTCACGGCAAGATGTGGTGATGTTGGGTAGCATCCTTCATCTCCCTCAGCTCCATGTAACTATAACTAACAAGGGAAAGAAGCAAGCTAAGAAATTCTAGGCAGTAAGAAGTCAAAAATCTTGTAACCAAGTTAAAGATTAAAGTCTATATCTAAAAATTATTTAAATGTTTTCTTTTTTTTACACTGTATAATAGGAGCCATACCACTTTAGTACAAAGGAAGAGAATACAGCATACTATTGTGTAGACTTGCCAAACCATGCCCAACCTATCCTGGATTTGTAAAGTGTCTAGTTATAAAGGGGTGGGGGCAGTTTTTGCCTGACTCTGAGGTAGAAAATGACAGAGATTTCTGGTTTTCTAGAGAACTTAACAGGAATGACCTTCAGGTATTGAGACTTTGCTAGAAATTTTCCAGCACAGTACCTTGGGAGCGTCTTTGACAGGAATAGCAAGTTAGTTAAATTCTCTTCTGTCTTACAG
Seq C2 exon
GTGCTGTGATAAACGACTTTGGACAAAAATTGACTTGAGTAGGTGTAAGGCCATCGTACCACAAGCTCTCAGTGGTATCATCAAGCGGCAGCCAGTAAGCCTCGACCTCAGCTGGACTAACATCTCCAAAAAGCAGCTGACATGGCTGGTCAATAGGCTGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054611:ENSMUST00000047898:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.797 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0064628=F-box=PU(72.3=14.3)
A:
NA
C2:
PF0064628=F-box=PD(25.5=21.4)
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:
AGAGGAGGAGGAAGAGGAGGA
R:
GCCATGTCAGCTGCTTTTTGG
Band lengths:
347-2133
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