MmuINT0115819 @ mm10
Intron Retention
Gene
ENSMUSG00000038718 | Pbx3
Description
pre B cell leukemia homeobox 3 [Source:MGI Symbol;Acc:MGI:97496]
Coordinates
chr2:34370824-34372044:-
Coord C1 exon
chr2:34371721-34372044
Coord A exon
chr2:34370898-34371720
Coord C2 exon
chr2:34370824-34370897
Length
823 bp
Sequences
Splice sites
5' ss Seq
AAAGTTGGT
5' ss Score
1.99
3' ss Seq
TTTTGCTATTTGTTTTTTAGGAA
3' ss Score
11.91
Exon sequences
Seq C1 exon
CGGCCGCCTCCCCCTCCCCCTCCCCCTCTTTCTTCTCCTCCCTCGCCGCCGCCGCCGCTGCCGCCGCCGCCGCCTCAGCCTTCGCCTCCGCCGCCGCCGCCCGCTCCCGCCCGCGCGCGGCGGGATGGACGATCAATCCAGGATGCTGCAGACTCTGGCCGGGGTGAACCTGGCCGGCCACTCGGTCCAGGGGGGTATGGCTCTGCCGCCTCCCCCTCACGGCCACGAAGGGGCGGACGGCGACGGCAGGAAGCAGGACATCGGCGACATCCTCCACCAGATCATGACCATCACCGACCAGAGCTTGGACGAGGCGCAAGCAAA
Seq A exon
GTTGGTGTCGTCTCATTAAGCATCTTTTGTGTGTGTACGGGAGCCGGGCTCGGGTCCCGGCTGGCTCCCGGGACCCGGGCCTCAGTTGCGGGCGGGAACTTTCTCCGCCCGCCGGGCACTTGCTGTGTCCCCCATCGCGCGGGCAAAGTTGCTCGCCGGGCTCGGGACAAACTCGATCATTGCTTCGTCCGTGCCCTGCTGCCCGCCCCCCTCCCCAGATTTAAACCTCCCGCTCGGACCCCAGCGCGCTCCGCGTCCCAGCCGGGTCCGTGGCCGCACCGCAGGGAAGTGCAACTTTCTCCGCCTGCCCAGACTCCGGGCACCCACTCCCCTCGGCCCAGTCCGGGGTGACCGGCTGCTTCCCCGCACAACCCTGTGCGGGAGCGCCAAGTTCTCTAGAGGGAGGGCCGCTTGGCAAACTTTGCGGAGCTGTCACCCGCTGATTATTAGCCGCCCGCTGGCCGCTGCGCCCGCTCCTCTTGTGGAGCTTGGGCGTTGGGGTTCCCTCCGCTCCGGTCTGGTCCCTTGGGTCCCGCCGCGGCCCCCGGAGCGGAGCCTCATGCACGGGTCACTCCTGTGTACGCCGAGGCTTCTGTCGAGCCAGCAGATGGGTCACGCTGCTATCGGGCTGGAGCTCTCAGCCGCTAGAGCTTGCCGCCAGTTGCGAACTAGTAAACTTGAGTTTTTGTTGACTTCCCGTGGTTCAAAGGAGCTTTTCCAAACTGGGGGCCGGTTTTAAATCTTGGGTCTAACTTAAAGGAAGGCGCCATATTATTCCAATAGGTGATGCTAATACCTTTGTGTTTTGCTATTTGTTTTTTAG
Seq C2 exon
GAAACATGCTCTGAACTGTCACAGAATGAAACCGGCGCTCTTCAGCGTCTTGTGTGAGATCAAAGAGAAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038718:ENSMUST00000040638:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.801 A=NA C2=0.142
Domain overlap (PFAM):
C1:
PF037928=PBC=PU(14.7=43.3)
A:
NA
C2:
PF037928=PBC=PU(29.6=94.1)
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:
TCTTTCTTCTCCTCCCTCGCC
R:
TCACACAAGACGCTGAAGAGC
Band lengths:
355-1178
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