MmuINT0115816 @ mm9
Intron Retention
Gene
ENSMUSG00000034673 | Pbx2
Description
pre B cell leukemia homeobox 2 [Source:MGI Symbol;Acc:MGI:1341793]
Coordinates
chr17:34731746-34732298:+
Coord C1 exon
chr17:34731746-34731899
Coord A exon
chr17:34731900-34732209
Coord C2 exon
chr17:34732210-34732298
Length
310 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGAG
5' ss Score
2.57
3' ss Seq
TCTCTCTCTGCCCTCGAAAGGCT
3' ss Score
5.81
Exon sequences
Seq C1 exon
GTTTCCAACTGGTTCGGTAACAAGCGAATTCGCTACAAGAAGAATATTGGGAAGTTCCAAGAGGAGGCGAACATCTATGCTGTGAAGACAGCCGTGTCAGTTGCCCAGGGGGGCCACAGCCGCACCAGCTCTCCAACGCCCCCTTCCTCTGCAG
Seq A exon
GTGGAGCCCACCGCCACGCTGGCTGGCTGACTTGAGTGTTTCTTGCCTTTGCTTCCACTTGTGTCTGTGCAGGATGATAGCAAGGAGGACTTTGGGGTGGGGTGGGGGAAGACCAGGCTAAGATGGGGTGGCAATGTCAAGGGGTAGCCTGTTGTGAGGGAGGGCCTGCTGTTCTGTGGATAATCTTCATATACTCCGAGTCTAGTCCCAGAGAGTGAGCTTTCTGGAAGCTCAGGGTTGGGTTTCCCTCCTGTCCCCCATCAGAGGGCCCTGTGCTTTTTCTGATTCTCTCTCTCTCTGCCCTCGAAAG
Seq C2 exon
GCTCTGGCGGCTCTTTCAATCTCTCAGGATCCGGAGACATGTTTCTGGGGATGCCCGGGCTCAATGGCGATTCCTACCCTGCTTCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034673-Pbx2:NM_017463:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.327 A=NA C2=0.500
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(21.7=25.0)
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:
TCCAACTGGTTCGGTAACAAGC
R:
TGGGAAGCAGGGTAGGAATCG
Band lengths:
239-549
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: