MmuINT0086114 @ mm9
Intron Retention
Gene
ENSMUSG00000054611 | Kdm2a
Description
lysine (K)-specific demethylase 2A [Source:MGI Symbol;Acc:MGI:1354736]
Coordinates
chr19:4324337-4326898:-
Coord C1 exon
chr19:4326809-4326898
Coord A exon
chr19:4325047-4326808
Coord C2 exon
chr19:4324337-4325046
Length
1762 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
CTTTTCTATGCATTTTGCAGAAG
3' ss Score
8.14
Exon sequences
Seq C1 exon
ATGGATGGAGAGGGGTTGCTGAACGAGGAATTGCCAAATTGCTGGGAGTGTCCAAAGTGTTACCAGGAAGACAGCTCGGACAAAGCCCAG
Seq A exon
GTAAAGGAAATGTTCAGTCTGGCCTTTGCAGTAGTATCCAAGGGCTTTCTCTGACCCACGATTATTTTGGTTTTATTTATTTGATATCTTTTTATCCTCCCTTTCTGGTTATTCCCCTTCCCCCTCCAGTTTGTTGGGGTTTGTTTGTTTGTTTTGCTTTTGTATTTTTGTTTTGTCTTTAGTTTTGATTTTTATATTACTAATTAACTGTTCCACTTAGGAGTCCTGATGTCCTTTTTATTCTTTAGGGTACTAGAAAGGCAGGAACCATCCCTGGGCTATTGAGTTGGAGAATTAGGTATGCAACTTTGTCCTGAGGAATGTAACTATGTAACTAGAGGGGAGCCAGGCTTGGCCTATGGTGCTGTTACTTACTGGATTCATATACTAGAGTATCCGGTTAAGCAGGTTTACTTTTTTTCTTTTTGGGTCATCTTTAGCTCTTTGTCCTTACTTGCCCCGTGCACCCAAATGTGCAATTCAGAAGCAGACATTCTACTAGAGAGAATAGAGACCAGCTTCATGACCTTAGCCCAGGACATCTAAGGTTGTTGCCCTAATGGTTACCAGTAGCATCAGTATGCCAAAAGGACTCTGGTTACTCAAGCTGGCAAGGCTAGATCTGCTAAGAGCAACAGACAGTAGAAGATGGCTGCCTCCTGTCAGTTCTTCAGGGATCCTGCACAGGCACGAGGAAGAAGCCTAAAGGAAATTGATTATCTTTATCTTTATTTCTTCCACTTGGGTTCTGGGGCAGTAGAACTTTTAGTTAACATTTCTTGTTTGCTATTTTGAGACAAAGTCTCACTGTGTAACCTTAGCTGGTCTCGAATTCAACTATGTAGATCAGGTTGGCTTTGAACTCAAAGAGATCCAACTGCCTCTGCCTCCCCGGTGCTGAAAATCAAGGTGTGTGTACCATGCCTGGCTGGTTGAAATATTTTTGAGAATGAGGGTTCTTATTCCACATTCTTGGACTAGCAACTTTTAAATTTGTCTTTACTGGTGCTGTTGAGAATGGCAGATGCTGTGGCTTTGCTACGTTTTAATATTCTGTGCAAAATAGCCTCTAGAACAAAGATGGTCATTGCCTCAATATTAACCAAGAATGTAAAGAACAAAAGAAATATAGACCAAGAGTGTTGCTGGTGACAGAATGTCTCCTTATGGAAAATCTTACTTATTAACAGAATATTTAGTGGCATATGTTGATTGAGTTTTGTCTCAGCATAGTCAAGGGTGGTCGCAGGAAAGGACAGGTTTCAGAAAAGCACGGGTACTACAGGATGAGGTCTGGACCTAGCAGGATTCTTCACCATAATCATAATGAAGTCTCTGCGGTGGCTTGGTTCCTGACAGAAAGCTGGATTGAGATACTGCAGAATGTACACAAGTGGTAGAGTTGTAACGCTAAAATAACCTTTTTACCAGAGTTACCAAAAAATTGAGGTGCAGTGAATATGATAGAATGTAGAATCAGAGCCTTGTATTCTAGATTTCATTCCTCTGTACGTGGCCACAAACCTTTTCTCATGGGTAGGTTTCCCAAGTGACCATTTAAGGATTTTGTGTACTGAAATTACCATTCTATGGCCTGGGTTCACATGTGAGCTCAGTTGCTGATCTTGGCAGTCTGAATCACCAGCTTAGAGGAAACAGACCCCTTAAGTAGCAGTGACATGGCTTCTCTCAGATTCTACGTATTATTTAAAGAGTTTAGGGGGAAAAAAGCAGTGGTGTTTCTTTTCTATGCATTTTGCAG
Seq C2 exon
AAGCGGAAAATAGAAGAGAGTGATGAAGAAGCTGTACAAGCCAAAGTCTTACGGCCCCTGAGGAGCTGCGAGGAGCCTCTCACACCCCCGCCTCACTCACCTACTTCCATGCTGCAGCTCATCCACGACCCGGTTTCTCCCCGGGGTATGGTGACTCGGTCATCCCCTGGGGCTGGCCCCAGCGACCACCACAGTGCCAGCCGTGATGAACGCTTCAAACGGCGGCAGTTGCTGCGGCTACAAGCCACCGAGCGCACCATGGTACGGGAAAAGGAGAACAATCCCAGCGGCAAAAAGGAGCTGTCTGAAGTTGAGAAAGCCAAGATCCGGGGATCGTACCTCACTGTCACTCTACAGAGGCCCACCAAAGAGCTCCACGGGACATCCATTGTGCCCAAGCTGCAGGCCATCACGGCCTCCTCTGCCAACCTTCGCCCTAACCCCCGCGTGCTAATGCAGCACTGCCCAGCCCGAAACCCCCAGCATGGGGATGAGGAGGGGCTTGGGGGAGAGGAGGAGGAAGAGGAGGAGGAGGAGGAAGATGACAGTGCAGAGGAGGGGGGTGCAGCCAGGCTGAATGGCCGGGGCAGTTGGGCTCAGGATGGAGACGAAAGCTGGATGCAGCGGGAGGTCTGGATGTCTGTCTTCCGCTACCTCAGCCGCAAAGAACTTTGTGAATGTATGCGAGTGTGCAAGACATGGTATAAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054611-Kdm2a:NM_001001984:16
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.083 A=NA C2=0.802
Domain overlap (PFAM):
C1:
PF058836=Baculo_RING=FE(38.2=100)
A:
NA
C2:
PF0064628=F-box=PU(72.3=14.3)
Main Inclusion Isoform:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGCCAAATTGCTGGGAGTGT
R:
TTTTGCCGCTGGGATTGTTCT
Band lengths:
355-2117
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: