MmuINT0115809 @ mm9
Intron Retention
Gene
ENSMUSG00000052534 | Pbx1
Description
pre B cell leukemia homeobox 1 [Source:MGI Symbol;Acc:MGI:97495]
Coordinates
chr1:170113661-170115199:-
Coord C1 exon
chr1:170115087-170115199
Coord A exon
chr1:170113751-170115086
Coord C2 exon
chr1:170113661-170113750
Length
1336 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
GTTGTTGTTCCTCTGTCTAGGTG
3' ss Score
9.68
Exon sequences
Seq C1 exon
GTTCTTCCAGTTCTTTTAACATGTCAAACTCTGGAGATTTGTTCATGAGCGTGCAGTCACTCAATGGGGATTCTTACCAAGGGGCCCAGGTTGGAGCCAACGTGCAATCACAG
Seq A exon
GTAGGGACCCAGCCAATATGCCACCAGGTGGATTCAGTAGAGTGTACCAGCCTTCAGTTTTCTCAGCGTCCTGCTCCTGTCTGGACAGAAAGAAGGAGAAAGAAAGGGAGGGAAAGGCAGACAGGCAGTAGTCAAATCAAATCAGAGTAAACTGAAACAGAACAAAGACAACCATTATCATAGGGGATGGTGACCATGCTTCGGCTCTGGCTTGTCAGTCACACTAGGAAGGTAGGAAAGGAACAAACACAGAATGAGGTGAAGGAGGCCTGTGAGATGGGGGGAACTGGAGTCTCCGTTATTCATCAGAGGAAAAGGAATTTCAGCCCATTATCTCTTCCACGTTTCCCTCTCATCTGTTGATGTCCCATCTTCAGGATTTGCTAACATCGAGAAGTCATCCAGGGTCAGGCAGATGCATAAGTATGCCCTGCTTTCGTCTTAAGCTTTAAAATTACCAAAACCATCTTGACTTAACACATACACTTAGTCACCCTTGAGGTCAATGGACTCGAGTTTCTGATGATAAAAGCATAAATGGAACCAAAAATCAAGTCATGTGCCAAACCTCTGTGCTTCTTAGTGTAACCATCTACCTTCAAGACAGATACCTCAGGAAGCCATCCTGCTATCTCAGCATGAAGCGTGGTCTGAGAGATTGAAGTCATATGCTCTGGGTCACAATGACTTGGGAAGATAGGAGTCACATCTCCTTATCTGACACATGGAACAGAAAATGTTACATGCCTGGAAGAGAAAGCTGGCTGGTGACTCAGCCCCTTGTATAGGAAGCACTGCCTAGAATCAAATTTGAGGTGATACAGACAGGTTCTGGTCATGTGACTAAATGACTTACCATCATCAAAATACTGATTTAAAAAGCAAAAAACCAAAAAAAAAAAAAAAAACCAAAAAAAAAAAAAACCTTGGGTCTTTATCCCAGTTCCCTCTCTCTATGACATGGCTGTCCAAGACTAAAGAAATACCTCGACTTGAGTTGCACAAGATAATCTATAGGGAAGAAAGTGGGGGAAGGAGACGCTTCTGTCCTCTTCCCTCCATTTCCTATAGCTCCACAGCTCCCTGTCCCCTCACACAGCCTTGTGCAGTCTGTCTCAGTTTCAAGTTTCTTTTATTATTTTTACTAAACTCATAAGTGACAATGGATTTGCCATCCGGGGGAGTCCCAGCCTCATGCTTAAGACTTTCCCCCAGGAAGAGCATCTTCAAAATCTTCACTGTGTGGCATGTCCTATCCGTGCCTGTAAGAAGATGATGTGCTGTGTGCCTTTCTCTCTCTGACTAATTGCCTTTCTGTTGTTGTTCCTCTGTCTAG
Seq C2 exon
GTGGATACCCTTCGCCATGTTATCAGCCAGACAGGAGGATACAGTGACGGACTCGCAGCCAGTCAGATGTACAGTCCGCAGGGCATCAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000052534-Pbx1:NM_183355:7
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.500 A=NA C2=0.813
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0157913=DUF19=FE(17.6=100),PF0004624=Homeobox=PD(4.1=6.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTCTTCCAGTTCTTTTAACATGTCA
R:
ATGCCCTGCGGACTGTACATC
Band lengths:
199-1535
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: