MmuINT0115824 @ mm10
Intron Retention
Gene
ENSMUSG00000038718 | Pbx3
Description
pre B cell leukemia homeobox 3 [Source:MGI Symbol;Acc:MGI:97496]
Coordinates
chr2:34176749-34178342:-
Coord C1 exon
chr2:34178177-34178342
Coord A exon
chr2:34176862-34178176
Coord C2 exon
chr2:34176749-34176861
Length
1315 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
CTTAACTCTTTCCTTTCCAGGTT
3' ss Score
11.89
Exon sequences
Seq C1 exon
GTATCCAACTGGTTTGGCAACAAACGAATCAGGTACAAGAAGAACATCGGCAAATTTCAAGAGGAGGCCAATCTCTATGCTGCAAAAACAGCCGTGACAGCCGCACATGCAGTGGCTGCAGCCGTGCAGAACAACCAGACCAACTCACCCACCACGCCAAACTCTG
Seq A exon
GTGAGTACGGCTTGCTCACTCCCTACTCAGCCAGACAGGCATCTGCCACAGCCTCCCAGCCCACAGACTCTGAAGCTTCAGCCTTACTGGGTGCACAGTGGGGCTCTCGGGAGATTTGCATTTGCTTGCAGGCTTGTTCTGGAGATGGATAAATAAGGCCACAGCCTGTGCTGGTAAACCCACTGTTCACAGTCAGTGCCACTTGCTCCTGTAGATTCTAGAACCATTATACCAGTCATGGCCTTTAATTCAGCAGTTAGACAAAGGTCCATCATATACTGTGCTGCCCATCCCGTTAGGGTTATTGGTGATCTGTCAGAGTGAAGCAGCAGGATGTGCTGGTTGCTGGGCAGCTGAACGTTGGGCTGAGATGTTGCTGTGCTTCCTGTGTTCTTGACTTCAGGCTCGAGGTGCAACCTGTATCTGTGCCATGTGGCTTGCTGGGCTTATATATAAGGAGATGGGTTTTTTGGTTTTGCTTTTTGTGGTAGTAAGGATTGAACCCAGGGTTTTGCATAAGCAAAGCTTAGTCCTTTGCCATTGATCTACATAATTACCACCCCCCCTTTTAAGATAGTCTTATTAAATTGTCCAAGAAAGCCTTGAACTCACTTTATAGCTCTGTCTGGCCTCAGACTTGTGATTCCTCTGCCTCAGCTGCATAGGTGGGATTGCATGTGTGTGCCGCCACAGCTGGCTATAAATGCACTACTTTTGACTCCTTACACAGAACATTCTATTTAAGTTTTCTGTGGCATTTATGACAGAGATTGAAGAAATGTCTTTAAATTATGGGGAACTTGGCTGGCAGCGAAAAGTGCAGCTAGCCCAGTAGAAGAGTTGAAGGGTCTTGGAGGCTTTCTAGGGAGATTTAAATATATATATATTTAAAAGTCCAGGGAAGGCTGTCTGTTTTATTATACCCCATCATTTCTAATGGGAAAGGAAGTGTTATAGCTAGGAGAGAGTGTCAGAAAACTGTGTCTTCTCCAGGTAATTCTCCACCAAAACAGCAGCATTGACGAGCTCCTTTGACTAAGTCTGGAGAGAAATGGAAACAAGGCTAGGGCCAGCTCCTGCGTGCTTTCAGTCTATTTTGATTTGTCTCTGGTTTTTCATTTGGGTTCGCCCTCTATAATGTTCTTCCTGTGTGTAGTGTAAGTAGCAGGACCTTCCAGAGCTCCTTTAATGTTCTGTCCTTCTAAAGCTGGAAATGCCTCTCCCTTCTGCCTCTCTTGCTCTCCCTACCTCTAGGTCTTTGGGGGTTGTGTGTGTAGCTCGCTGTTATTCAGCTACTTAACTCTTTCCTTTCCAG
Seq C2 exon
GTTCTTCTGGTTCTTTTAACCTCCCAAATTCTGGGGACATGTTCATGAACATGCAGAGTCTGAATGGGGATTCTTACCAAGGGTCCCAAGTCGGAGCCAATGTGCAGTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038718:ENSMUST00000040638:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.330 A=NA C2=0.789
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(21.7=23.2)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCAACAAACGAATCAGGTACA
R:
GTGACTGCACATTGGCTCCG
Band lengths:
262-1577
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