MmuINT0086126 @ mm9
Intron Retention
Gene
ENSMUSG00000054611 | Kdm2a
Description
lysine (K)-specific demethylase 2A [Source:MGI Symbol;Acc:MGI:1354736]
Coordinates
chr19:4348646-4350330:-
Coord C1 exon
chr19:4350177-4350330
Coord A exon
chr19:4348762-4350176
Coord C2 exon
chr19:4348646-4348761
Length
1415 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
CTCTATTCCCTGTTTTCCAGGTT
3' ss Score
9.53
Exon sequences
Seq C1 exon
GTCTTCTGGCTCATCCCCCCTACAGCCCACAACCTGGAGCTGTACGAGAATTGGCTGCTATCAGGGAAACAGGGAGACATCTTTCTGGGTGACCGGGTGTCAGATTGCCAACGAATTGAGCTCAAGCAGGGCTATACCTTCGTTATTCCCTCAG
Seq A exon
GTAAGCAAAGTAGGGGAAAGTAGGTTGCTTTCTAAGTTTCTTAAACAATGCCGATTATGAACAAGGCTCTGAATTCAGTGTCCAGTGAAGCATGTATGTGCATGACTGTACAGTCAGCAGCAAACAATGGTGTTTTCCTGTTGTTATGAAGTACACACAGAGAATATGTATTTAAAAACAAATAACAAGGCCTGGAGAGACGGCTCAGTGATTAAGAGCACCAACTGCTCTTCCAGAGGTCCTGAGTTCAATTCCCAGCAACCACATGGTGGCTCACAACCATCTGTAATGGGATCTGATGCCCTCTTCTGGTGTGTCTGAAAACAACTATACTGTACTCATGTAAATAAAATAAGTAAATCTTAAAAAAAGAAAAATTTAACAAAAGCAGTGCTTAATACTGGTACAGTGCTTCTCAAATGTATTAACTTGGACTAAATATTAAGCCTAGTAATCCAGAGTTTTTACATGTGATGTGTCTGTCCTCTCTAGTGAGAAGAACAACTTTTCCCACCTGAGTGGGGAATGCTGAATCAGCGTTTTTGTTTTCTAGGCAGGGTTTCTGTGTAGCTCCGGCTGTCCTGGAGCTTGCTATGTAAAATAGGCTGCCTCTGCCCTTGCCTCTTGAGTGCTGTGATTAAAGGTGCACACCACCAAGTATGAGTAAATTGTAGATATTTTCATTGCATCTTAATTCTAAATAAATGCATATAAAAAGAACAAATTTTGGAGTCCCTATCTTTTTGAGAATTCTGGCTATGCATTTGCCTGCTCAGTACTACTTTGGTCAGATACTTAAATCTGTTTTTATTTGATAAAACTACATGAGAATATTAATAAGCTGTCCTGTGTGGAGCTGGCACATAATTGGTGCTTCAAAAAAAAGGGTAGCAGCATTTATTTAAAAGTTTCTTGCACTGAGGGAGTAATAACATGATGGTAGAGTATTTGCTTAGCATGCATAATACCCTGGGTTTTATCTCTAACAATAAAAAAAAATTAAAAATTCTCACATTTTTTACCGAGTATGGGATCATGCACTTACAGTCCAAGCTATTTGCATGTTTGAGACCAGCATGAGCAGCATTTTATGGCCCTGTCTTAAAAATAAATAAAACTTGTTCCATGTGTATATATACATACACACACACACATATATATATGTGTGTGTATATATATATATTCTCATTTAATGCTCACCATTATATATAAAATATAGTCTATGCTAGTTTTAAAGAGAAAATTAAGGCTTTGAGAGATAAGTAACTTAACCAACCATAAAGGAGTCTGAGCTATGGATCAAGGACATGTTTCCAAAAAAAAGAGAAAAATATAATCTAAAAGTCTTGTACTATTCTGAAGAAAGTATATTGCAGTATGTGCTTTCAATCCTGACTCTATTCCCTGTTTTCCAG
Seq C2 exon
GTTGGATTCATGCTGTGTATACTCCTACAGACACATTAGTGTTTGGAGGCAATTTTTTGCATAGCTTCAACATCCCCATGCAATTAAAGATATACAGCATTGAAGATCGAACACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054611-Kdm2a:NM_001001984:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0237317=JmjC=FE(50.5=100)
A:
NA
C2:
PF0237317=JmjC=PD(17.8=46.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCTTCTGGCTCATCCCCC
R:
CCGTGTTCGATCTTCAATGCTG
Band lengths:
270-1685
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: