MmuINT0115832 @ mm9
Intron Retention
Gene
ENSMUSG00000031860 | Pbx4
Description
pre B cell leukemia homeobox 4 [Source:MGI Symbol;Acc:MGI:1931321]
Coordinates
chr8:72393928-72394583:+
Coord C1 exon
chr8:72393928-72394081
Coord A exon
chr8:72394082-72394476
Coord C2 exon
chr8:72394477-72394583
Length
395 bp
Sequences
Splice sites
5' ss Seq
CAGGTGACG
5' ss Score
7.66
3' ss Seq
TGACTGCCCATTTCTCACAGGTC
3' ss Score
9.51
Exon sequences
Seq C1 exon
GTCTCTAACTGGTTTGGCAACAAAAGAATCCGGTACAAAAAGAATACAGGGAAGTTTCAGGAAGAAGCCACCATGTACACAGGGAAAGCATCCACAGTCACCAAGGCCCGGCGTCCCAGGGGTCAGAGCAGCTGCCAGTCCACACCCAGCCCAG
Seq A exon
GTGACGAGGCCATTGGCTTTAACTTAAGCTTTCTGTGAGGTTAGGTGGGACCTAAGCTACCCGATCCGTGTAGATAGCCAGTGCCAGCAGAGGGACAGACAAGAGTGTCTTAATTTCACAGGCCAGCATCACCTACACAAGGCCAGGGGAAGTACAGGTGGCTGGATGCTTTAGGGGGTCAGATCCAGAATCTGTCTGTCTGCCTCCCCTTTCTTCCAAGACAGGCTTTCTCTGTGTAGAACTCACTCTGGAGACCAGGCTGCCTCCCGAGTGCCACCCCCACTTGGCCCAGAGTCTCTCTCGATGAGGGACTGAGCAGATGCTACCAGAAATCCCTGTGACTGCTGACCCAGATTCTGCTGTGACACCCCCAACTGACTGCCCATTTCTCACAG
Seq C2 exon
GTCCCTGTGGCCCCTTGCCACTGACCAATGGAAGTGACGTGGTTCTCACTCTGCGGACCCTGGCCTTCCTCCAGCCCCCCACTGGGGGAGTCTGCCTACAGCCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031860-Pbx4:NM_001024954:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.510 A=NA C2=0.194
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(21.7=25.0)
A:
NA
C2:
PF037928=PBC=PD(3.5=5.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCTCTAACTGGTTTGGCAAC
R:
CTGTAGGCAGACTCCCCCAG
Band lengths:
255-650
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: