MmuINT0086107 @ mm9
Intron Retention
Gene
ENSMUSG00000054611 | Kdm2a
Description
lysine (K)-specific demethylase 2A [Source:MGI Symbol;Acc:MGI:1354736]
Coordinates
chr19:4394792-4397077:-
Coord C1 exon
chr19:4396311-4397077
Coord A exon
chr19:4394893-4396310
Coord C2 exon
chr19:4394792-4394892
Length
1418 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGA
5' ss Score
8.51
3' ss Seq
TTGTAAATTTGGATCCTTAGGAA
3' ss Score
6.38
Exon sequences
Seq C1 exon
TGAGAATCTGACGGGTTCAAAATGGCGGCGGCTGCTTCAGCGGATCCTCCTGTGTGAGGGAAACAACACCCCTCCCCGGCAGCGGCGGCGGCGGCGGCGGCGGGCCGCAGAGCACCTTTCCAGTTCCCGGGCCCGTCGCGGTTGTTTCCCTCCCGGGCAGTGGGCTCTTCGCGTGGAAGGGCAACGTCAGGGGGCCCATCCCCCGGAGTCCCTCCTCTGCTACTGGGGAGTAGCTGGGGGTGTACGGGGGATCGTCCCGCAGCGCGGAGCCCCGGCTCAGGGGACGACGCAAAGGCAGCCGAAGGCCCCCGGTCAGGGCGCTTCGCTGCTCCCGCCCTCTCCGCCCCCCGGGGCCGGGGCCCGCGTTCCGGGGGGCCGGGCGGCGCGGGGAGCGTCGGCCGGGCGGGTCTCAGCTGATCGGCCGCGGTTCCTGGGCTTCGGTAGCGGCTGTGGCCGGCTGAGGGTACCGAGAGGAGGGTGTTTCCCGCGGCCCGGTTGACCCGGGTCTCGGGCTGGGGCTGCTGACCGCCAGCTTGGGGGAGTAGCCGAGTGGTCTTGCTTCCCTGACGCCTCGGACGCGGAGTCTGTAAAAGCCAGAAGAGGAGGTTTGATTCAGTAACTGTTTCCTCTTTTCCGGGTCGCTCTGACCCTTCTCTGGATACTGGGTTAATACACAGAAATACCGAAGACGACGTTTGGGATTTTATTTTGTCTGTGTTTGGAATTTTACTTCTCTCTTGGACAAGAACTCAAGAACAAAATCCTCG
Seq A exon
GTGAGATTTCCCCTCCCCCCTCCCCCGCCCTGGGAAGTTTGGTTCCCGGTCTTATCTAAAGACTTAATGTAAAGTTTTTATTTCTTTGCAAGGGGTGAGCCACAGAACGCCTTTTCCCTAGGGGAGCAGTCGAGGTTTACCGCTTTGCTGTCCGGCCCTGGGGTGCAGACTGTGTCCCTCGCGACCGAGGCCGAGGAGGGCAGTGCCACGAACTGCTCTCGCAAACTATGTCATCGGGTCCTCTGAAAGGATTTTGTTAACGTGGCCGTATTATATTTACAAGAGAGAAAAAAAACATTTGTATATCCAATTAGAAGCCATTATTCTGGAGAAAGATATTTAGAAAAACGAAAACCCTTGCTTGGTGTTGTGGATTGATTGACGTGCCAACCGGCCTTTATTTAATGGATGTTTCACCCGTATCCATATATCGAGACGTTTCATTTATTATTTACTCATCTAGATTAGATGGTATTTTTGCCTCCGTTTGCAACTCTCAAATTTGTTCTGTAGTTGTCCACCTTGAGGTGGATGGTAGTTTGGGGAAGGCAGTTCCTTACTAGAAGGATATGGGACATTGGTTTGAAGTCTTTCTGTAAAACCAAATTTTTCTTGCCCTCTTTTTTTTTTTTTTTAATGAAAGTAACCTCCCCGTTTTGCTTATAATTTGTTATTACCTGTTTGAGAACTCACTGGTTTAGGGTCTGGCTTAGTTTTGTGTGTACTTCACCTTCACCTGGCCATTCAGCACTTTAGAAATAAAAGTCCTTCCTGGGTTTGGTGCTGCACACCTTTGCCAGCACTGGGCAAGCAGAGGCAGTCGGGTCTCTTGTAAGTTGGAGGCAAGCCTGGTTGGTCTATGTTGTAGTTCCAAGACCACCAGGGCTATGTAGAGAGATCCTGTCTCAAAACAACAAAACTTAAACACACACACACACCAGCAAACATACAGAAGAAGAGAAGTAAAAGTCCTGAGCCTTTTCACCTGCATTATATCTGTGTAAGGGTCCCTTAGAACTGGAATCAGACAGTGACCTGCCATGTGGTTGTTGAGAATTGAACTCGGATCCTCTTGAAAAGCAGCAGTGCTGTTAAGCACTGAGCCATGTCTCCAGTCCCCTCTATCTATCTATCTCTTTATCTATCTATTGCTAATGTTAGCAGGAAGAATTTTGCTAGTTGCAATCCCATGAGCAGAAACAAATGATGTGGCTGGTCCTAAGGAACTGAAACCAAAGTCTCCTTTTGCTTAGGTCTTATTTTATAGTTGTGATGTGATTAATATTGACAAGACATGGCACCATTTGCCCAAGAGGATAAAGGATTCTCAGAGTCTTTAACTTAATGAGAAGGGGAGGTATAAGTTCCATAATGAGTTCTTATTTCTCTTCATTTCCTTTGTAAATTTGGATCCTTAG
Seq C2 exon
GAAGAGGAAGGCATCCCTGGAGTGGTTTCTTTACTGTACTTCCATCAGAAGAGTGAGAGATGGAACCTGAAGAAGAAAGGATTCGGTACAGCCAGAGATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054611-Kdm2a:NM_001001984:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.900
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTTCGGTAGCGGCTGTG
R:
TCCAGGGATGCCTTCCTCTTC
Band lengths:
354-1772
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: