MmuINT0086112 @ mm9
Intron Retention
Gene
ENSMUSG00000054611 | Kdm2a
Description
lysine (K)-specific demethylase 2A [Source:MGI Symbol;Acc:MGI:1354736]
Coordinates
chr19:4328128-4329222:-
Coord C1 exon
chr19:4328953-4329222
Coord A exon
chr19:4328260-4328952
Coord C2 exon
chr19:4328128-4328259
Length
693 bp
Sequences
Splice sites
5' ss Seq
GCAGTAAGT
5' ss Score
9.07
3' ss Seq
TGATCTTTGTCTTTTTGTAGCCC
3' ss Score
9.15
Exon sequences
Seq C1 exon
CTTAAATTCCCTACCAGGCCAAAGGTGAGGGTTCCTACAATTCCCATCACAAAGCCTCACACCATGAAGCCAGCTCCACGCTTAACACCTGTAAGGCCTGCTGCAGCCTCCCCCATTGTGTCAGGAGCCAGGCGGAGAAGAGTGCGGTGCAGGAAATGCAAAGCTTGTGTGCAAGGAGAATGTGGAGTCTGCCACTACTGCAGGGACATGAAGAAATTTGGTGGACCTGGACGCATGAAGCAATCCTGTGTCCTCCGACAGTGCTTAGCA
Seq A exon
GTAAGTGATCCGAGTGAAAATTTTGCAAGGCTTGGTATTGGTGCCAGAGAAATTGTGTATATGTAAAGTCAGGGAGACTTAACTGAGATGGGTTTAGAAGGAAGATGTCTTTTTTGGTTTTTTTGGGTTTTTTTTTTTTTTTTTTTTTTTTTTAAGAATTATTTATGTTGCAGGGCGTGGTGGCACACGCCTTTAATCCCAGCACTGGGGAGGCAGAGGCCAGCCTGGTCTACAAAGTGAATTCCAGGACAGCCAGGGCTATACAGAGAAACCCTGTCTCGAAAACAAACAAACAAAAAAAATTTATTTTATGTATATGAGTAGTACACTGTAGCTGTCTTCAGACACACCAGAAGAGCACATTGAGTCCCATTACGGATGGTTGTGAGCCACCATATGGTTGCTGGGATTTGAACTCAGAACCTCTATAAGAGCAGTCAGTGCTCGTAACTGCTGAGCCATCTCTCCAGCCCCCTGAAGGAAGTTATCTTAATAAGAAAAGACAAGCCAACAAAGAGTGAATTAATTGCCTTTGATGGTCTAGTTTCTAGGCAGTTCAGTCCCAAGTCTTTGTCAGTCATTACTATCTTGTCTTTGTACACCCCAAGTGAACCAAGTCTCCTATCTTCATTTAAAGGGACTATGAAATTTAAAGGTTCAAAATCTGGTCTTCTGATCTTTGTCTTTTTGTAG
Seq C2 exon
CCCAGACTGCCTCATTCAGTTACGTGTTCTCTCTGTGGAGAAGTAGATCAGAATGAAGAGACCCAGGACTTTGAAAAGAAACTCATGGAATGCTGCATCTGCAACGAGATAGTTCATCCTGGCTGCCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054611-Kdm2a:NM_001001984:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.333 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0200815=zf-CXXC=WD(100=52.2)
A:
NA
C2:
PF058836=Baculo_RING=PU(50.0=86.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAAGCCTCACACCATGAAGCC
R:
GGAGGCAGCCAGGATGAACTA
Band lengths:
350-1043
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: