MmuINT0115830 @ mm9
Intron Retention
Gene
ENSMUSG00000031860 | Pbx4
Description
pre B cell leukemia homeobox 4 [Source:MGI Symbol;Acc:MGI:1931321]
Coordinates
chr8:72388723-72390502:+
Coord C1 exon
chr8:72388723-72388913
Coord A exon
chr8:72388914-72390366
Coord C2 exon
chr8:72390367-72390502
Length
1453 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGG
5' ss Score
7.2
3' ss Seq
CTGGGCATCTCTGTCTGTAGGCG
3' ss Score
7.65
Exon sequences
Seq C1 exon
GCCTGTCGTGAGTTCACCACACATGTCACCAACCTTCTCCGGGAACAGAGTAGGGTGAGGCCTGTGTCTTGCAGGGAGATGGAACACATGGTGAACACCATCCAGAGCAAGTTCAGTGCCATCCAGAGGCAGCTGAAGCAGAGCACGTGTGAGGCTGTGATGACTCTACGCTCACGGTTCCTGGATGCCAG
Seq A exon
GTCAGGGGCTGCGTGCCACTGGGGTCCCCGAGGGTTGGCCCTTAGATAATAGAAGCAGGATCAGAGTAGGATAGTTCCGATGTTTATGTCATAGTGTTGCAAGCGCTAATCCCATGTTCTCCCTACCACTGAGCCCAGCCAAGCTCTGTCTTGTTTTTAAGTCTGTCCAGAGGGTCTAGCCAAGGCCTCACATAGCTTCTTTATGAGAAGACCCAAAGTACAAACTGCTGGTTTGTTGTGTGTGTGTGTGTGAATGGCAGGTGAGTGTGTCATGGCACAGCGCGTGGACAGCAGAGGACAGCCTCAGGGTCTCTGCTGTTTTCCACTGGATGTGTCAGGCCAGCTGCCCAGTTCAGAGGATTCTCCTGTCTGCCTCCTGTCGTGCCTGCCTGTGGAGCTCTGTGACTACAGACATGTGCTGACATTATGGCTCCACATGGGTCAGGGAACCCAGACTCGGGTCTTCTTACATGTTCCTTACCTACTGGGGCATCTGTAAAGCCCCTGATTGACCGGGATTGCTCACTCAGTTAAGTGTTCGCTGTGCAGTCAGAAGGACCTGAGTTTGCACACCCAGCACCCACATAAAAAGCCAGAAATAGGCCAGCAATATGGTGCAGGGGGTAAAGGAACTTGCTGCAAAAGTCTCAAAACCTGAATTTGATCCCAGAAATGACCTGAACCTGCAGGAATAAGGGTTCTAAATGTTGAAGTGTTAAGTAGGAGGGTCGAGAGGAGATAAGCAATAGCTGGGACCAGGAGACCTTGCATAAGTGACGACTTCTGCTAAGAGAGTTTGTTCAGAAGTACATCACCCTATATACTATTTTCAGAGGGGAAATGGCAAGGCTGGGAGAGAGCAAAGTCAAGCAAAGAGTACATAAGGTGCTCAGACAGAGCTGCTTAAGGACCGACAACCACAGCCTGGGGGCAGAGCCAGGTCCCCGGAAGCTGCAGTCTTGGCTTCTCTGAGGCTCTGGACAGGCACACAGAGCTAGTGTTCTCTTTGTCCTCTCATCTGGGTCTCTGGTGTGTGCACACACACAGACATACACACACACACACACACACACAGACACACATAAACACACACATACACACACACACACTTCTACACACACAGACACTTACACACAGACACATACACACACATACACTCACACATGCACACACACACACACACACAAAGACTTTTTAAAGCCAGGAGCTGCTGCAACCCAGGCACTGGAAACATGGAGACGGGCTGGTCCCTAGGCCTGCTGATCACCTCTGCCCAGTGAGTGAGCTCCAGGTTCAGTGCGAGACCACACCTCAAAGAAAGAAGATGGAGAGTGATGGAGGACACAGGCACCCACCCACCTCTGGCCTGTACATGCACAGGAGATTAGGGACATGAGAGATGTGACTCTACCCCAGCAGGGAAGCACTGCAGACTGGGCATCTCTGTCTGTAG
Seq C2 exon
GCGCAAGCGGCGGAATTTCAGCAAGCAGGCCACAGACGTGCTGAATGAATATTTCTATTCCCATTTGAGCAACCCTTACCCCAGTGAAGAGACCAAAGAAGAGCTGGCCAGGAAGGGTGGCATCACAGTGTCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031860-Pbx4:NM_001024954:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.076 A=NA C2=0.302
Domain overlap (PFAM):
C1:
PF037928=PBC=PD(31.1=95.3),PF070286=DUF1319=PD(31.6=85.9),PF040917=Sec15=FE(67.7=100),PF083976=IMD=FE(51.2=100),PF0004624=Homeobox=PU(0.1=0.0)
A:
NA
C2:
PF040917=Sec15=PD(0.1=0.0),PF083976=IMD=PD(26.8=71.7),PF0004624=Homeobox=PU(75.0=97.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGTCGTGAGTTCACCACAC
R:
CTGGGACACTGTGATGCCAC
Band lengths:
326-1779
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: