MmuINT0086120 @ mm10
Intron Retention
Gene
ENSMUSG00000054611 | Kdm2a
Description
lysine (K)-specific demethylase 2A [Source:MGI Symbol;Acc:MGI:1354736]
Coordinates
chr19:4361977-4362914:-
Coord C1 exon
chr19:4362776-4362914
Coord A exon
chr19:4362056-4362775
Coord C2 exon
chr19:4361977-4362055
Length
720 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGT
5' ss Score
8.68
3' ss Seq
ATTTTTCCCCATGGTTTCAGATT
3' ss Score
8.45
Exon sequences
Seq C1 exon
CGTGGTACCATGCGTCGTCGCTATGAAGATGATGGCATTTCAGATGATGAAATTGAAGGGAAAAGAACTTTTGACTTGGAAGAGAAGCTCCAAACCAACAAATATAATGCCAATTTTGTTACTTTTATGGAGGGAAAAG
Seq A exon
GTCAGTATCATTTTGATTCAGACCCTGAACTCCTTGATGTAAGAGTCATCAACTTGAGATTTTAGCAACTGTGCAACGTTAAAATATCACCTGTTGATGTTAATTTTACTCATAATGCTCATTCTCTGCCAGATTTGAAGTAATCTTTTATTAGAACAAGAAGGTTACTGGGAAAAACACCTTTTTCTGAATTCTTGGCTTGAGTTTAACTAAAAATGGCACAGGTATGATGGCACATGCCTGTAGTCATTGCACTTTGGAGATAGAAACAGAAGGATCAGGAATGGTCTATGTATAAGTTATAATGTATGTATAAGTAATGGTAAGTTAAGGCCAGACTCTGCTACATGAAACTTTGGATAGAAGGAGAGGGAGAAAGATATCAAAACAAAAAAGTACAATGAAATTTCTTTTATGATGTTGGATTCCTTATGTGTTATGTAGCCTTGACCCTTAGGAAACTGTGGAAAAATTGGACATATAATGTTCAAACTATTTTAGCCATTAAGAGACATAATTTCTAGTTAGAATGTATGAAGTGACTCATTAACACAACTACCTACAAGCCCTGATTTTTCAGTATACTTTCCATATTTAATAAGAGATGTAAAATATTGTATGCACAGAGTAACAAACACTATAAATACCTTTTTACTTAAAATTTCCTTCATAGTTTTTTTCAATGATTCTTCTCTTTCTAATTTTTCCCCATGGTTTCAG
Seq C2 exon
ATTTTAATGTAGAGTATATCCAGCGGGGTGGCTTGAGAGACCCTCTCATTTTCAAGAATTCTGATGGACTTGGAATAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054611:ENSMUST00000047898:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.231 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CGTGGTACCATGCGTCGTC
R:
TTCCAAGTCCATCAGAATTCTTGA
Band lengths:
214-934
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