MmuINT0115811 @ mm9
Intron Retention
Gene
ENSMUSG00000034673 | Pbx2
Description
pre B cell leukemia homeobox 2 [Source:MGI Symbol;Acc:MGI:1341793]
Coordinates
chr17:34729416-34730590:+
Coord C1 exon
chr17:34729416-34729719
Coord A exon
chr17:34729720-34730516
Coord C2 exon
chr17:34730517-34730590
Length
797 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGT
5' ss Score
9.1
3' ss Seq
CTCCTCCCGTTCCTCCTAAGGAA
3' ss Score
8.28
Exon sequences
Seq C1 exon
AGCGGCCCCAGCGAGTTTGGGGGGGAAGTCACCCGGCGGGGGGAGGGGCGAGCAGGGAGGGGGCCTCAGGCCCCCCCCCAGCTATGGACGAGCGGCTGCTGGGGCCGCCTCCTCCGGGCGGGGGCCGTGGGGGTCTGGGGCTGGTAGGTGCGGAGCCCGGGGGCCCTGGCGAGCCTCCCGGTGGCGGAGACCCCGGTGGGGGAAGTGGGGGGGTCCCGGGAGGCCGAGGGAAGCAAGACATCGGGGACATTCTGCAACAGATAATGACCATCACGGACCAGAGCCTGGACGAGGCCCAGGCCAA
Seq A exon
GTGAGTGCCCCCACCCCGGGACCCCGCTCACAGCTCTGAGTCCTCTGCAAGCCCCCCTCCCCCAGGGCCCTCTCTGGATCTTGCAACTCTTTTCTTTCCTTAGTTCTAGTGTTCTCTCAAAGCTTGCTTTGCCCCTAGGCCCTAAAGCCTCCTCCACAGAGCGAACCCCAGGTGGTCTCACTCCCTCCTAACCTTTTGCTGACCCCTACAGTCAACTCTGGCCCATCTCTTGGCTCCCAGACTTAGAAACTGTTCTCAGCCAAAGCTGTCTTCCCTAACTATCCGGCTAGCCCACCCCATTCTCCGCGTACGGATCCAGGATCTCCACACATTCCCTTCCACGGAGGTCGGGGCCTCCAAGAGTCCTCAACAGCCTTCCCCCTGCTCAGCCCACACATTCTGTACTGAACTCCCAGGTAGCAGGGCACCCCCCCCCCCACCTTTCTCAGGCCCCCTACCGCCTCACACTGACAGCCTCCGGTTCTCTACTCCACAACCTACCTAGTCACCTTTATTTCTTCAGTCATCTCTAGATCCTTGCTCCATCTTTTTGCTTGAACCATCCCTCTTAGCCTCAGCCCGCCCATAGTGACTTTAGCCCCACTGCCTGCATCTTCTGCTTCCTGTGACCCTGCCGCTTCCCGAAGCTATGGCAGCTGATCTCAACTATCCCTCGGACTCCACTCTACCCCGATTCCCACTTAACCCCCTCGCAGATTATGCCCCCACCTTGCACCCTGGCACCCCTCTCGTCTTTCTCCTGCCTGAACCCTTTCTCTCCTCCCGTTCCTCCTAAG
Seq C2 exon
GAAACATGCCCTAAACTGTCACCGAATGAAACCTGCCCTGTTTAGTGTCCTGTGTGAAATCAAGGAGAAAACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034673-Pbx2:NM_017463:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.231
Domain overlap (PFAM):
C1:
PF037928=PBC=PU(14.1=37.8)
A:
NA
C2:
PF037928=PBC=FE(12.6=100)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGCTATGGACGAGCGGCT
R:
TCTCCTTGATTTCACACAGGACAC
Band lengths:
294-1091
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: