MmuINT0086128 @ mm10
Intron Retention
Gene
ENSMUSG00000029475 | Kdm2b
Description
lysine (K)-specific demethylase 2B [Source:MGI Symbol;Acc:MGI:1354737]
Coordinates
chr5:122987662-122989099:-
Coord C1 exon
chr5:122988868-122989099
Coord A exon
chr5:122987807-122988867
Coord C2 exon
chr5:122987662-122987806
Length
1061 bp
Sequences
Splice sites
5' ss Seq
TTGGTGTGT
5' ss Score
3.29
3' ss Seq
CTCTGGTTGGGTCCCCGCAGCGT
3' ss Score
7.45
Exon sequences
Seq C1 exon
AACTGCTGAAAATGGTTTCCTAGGACTTTGCAAACGGATCTGCTTAAGTGTTGGTGCAAAACTTTGTAGATATCGGCTCTGGCTTGCTCTATTTATTTATTTTTTTGCTTTCTTTTCTTTGGTCTTCCCTCCTTTCCCCCTCCGCCAAAATGCAGGGGGCAGGAGTGTTGACAATTAATTGGTGAACTCTCCTAAAAAAATGGAGGCAGAGAAAGACTCTGGAAGAAGATTG
Seq A exon
GTGTGTAGCTTTTTTTTTCTCCCCCAAATCTGTATCTGGTATATGATCGATTTATCTATCTATTTATTTTTTTGGTTGTTTCTTGCTGCCTTTTCTTTCCTTTTCTGTATTTTGCAAGAGGACCGGAAAAAAATAATAAATTGCATGCAAAAGGAAGCAAGCAGCTTACTCCTCCAGTCTCTTGTGAGGCTCAGGGTCTCAGACACTTAAGTGGGGAGGAGGCAACGCCGAAAGGCGTGGAAGGGACTGAGCGGGCTCGGGGTTCGCCTGGGATCTGGGGGGCTGCGGGGCTCGGTGCTGAGCGGCGGAGGGAGGAGGAAGAAGGATGCGGGGAGTGGTGGGGGAGTCTCCTTAGGAAGTGAGTGTGCGCGCGCGCTCGTGGGGAGATGAGGCAGCTGCTGGTGCGTTTTGGGGTCTCTGATAGAAGCTTTGTGGTGGGCTGGCTGCCTCTCTCCCCCCACATTCTTAACCTCCTCCCCTCCCCTCCTCTTCTTGCACTAGCGGTCGGTCGGCGGGGGCCGTTAGGGTCTCAACCCTTCCGTTTCAGCTTTCCAGCTTTTCTGTAGCTCGGGAGCAGCTCCAGCCTTAGTAATGCCGCCGGCCCTGGGTTCCGGCTTCCCGGGTTGGCCGCCGTGGCCGCCAGGGCTGCTGTTACCGCGGAGCCGGTTGCTGCAGCGGCTTCTCTCGGGGCCTACATCTGCCCCGCCAGCTCATACCCGGAGCCCCCTTCAGGGGTTACATAACCAGGCTCCCAGTCGAGTGGGCAAAGCTTAGCACATCACTTGGCGTGGGGGCAGAGGAAAGCCCCCAAATACCATTTCCATAGCTTCCAAAGATGCAAGAAGGGATTGCTTCGTTTAAGGGCAGTCGGGCCTTGGGGGTGTGAGCCCCTTTTTCTGCTTTCCAGCATCTTTGGCATTTGCGCAAAGTTGCTCAGATTGCAATGCTGGGGTGCAGTGGGCGCGCGACTCTTGCACCTGTTCTTGGTGGGCCCAGGGTGAGAGGAGACCCCCCCAAGTCCTCTCAGTAATGTCCGGGGTTCTCTGGTTGGGTCCCCGCAG
Seq C2 exon
CGTGCGATTGACCGCCAGAGATACGACGAGAACGAAGACTTGTCGGACGTGGAGGAAATTGTCAGCGTCCGTGGCTTCAGCCTGGAGGAGAAGCTACGTAGCCAGTTATACCAGGGGGACTTCGTGCATGCTATGGAAGGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029475:ENSMUST00000046073:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.273 A=NA C2=0.053
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:
GGACTTTGCAAACGGATCTGC
R:
GCCTTCCATAGCATGCACGAA
Band lengths:
351-1412
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