HsaEX0045750 @ hg38
Exon Skipping
Gene
ENSG00000185630 | PBX1
Description
PBX homeobox 1 [Source:HGNC Symbol;Acc:HGNC:8632]
Coordinates
chr1:164811990-164821626:+
Coord C1 exon
chr1:164811990-164812149
Coord A exon
chr1:164820072-164820184
Coord C2 exon
chr1:164821537-164821626
Length
113 bp
Sequences
Splice sites
3' ss Seq
CCTCACTCTTTCCTTTCCAGGTT
3' ss Score
12.04
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
Exon sequences
Seq C1 exon
GTATCAAACTGGTTTGGAAATAAGCGAATCCGGTACAAGAAGAACATAGGTAAATTTCAAGAGGAAGCCAATATTTATGCTGCCAAAACAGCTGTCACTGCTACCAATGTGTCAGCCCATGGAAGCCAAGCTAACTCGCCCTCAACTCCCAACTCGGCTG
Seq A exon
GTTCTTCCAGTTCTTTTAACATGTCAAACTCTGGAGATTTGTTCATGAGCGTGCAGTCACTCAATGGGGATTCTTACCAAGGGGCCCAGGTTGGAGCCAACGTGCAATCACAG
Seq C2 exon
GTGGATACCCTTCGCCATGTTATCAGCCAGACAGGAGGATACAGTGATGGACTCGCAGCCAGTCAGATGTACAGTCCGCAGGGCATCAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000185630_MULTIEX2-2/3=1-3
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence exclusion
Show PDB structure
Features
Disorder rate (Iupred):
C1=0.333 A=0.468 C2=0.624
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(21.7=24.1)
A:
NO
C2:
PF0004624=Homeobox=PD(4.1=6.7)
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTGGTTTGGAAATAAGCGAATCC
R:
CTGATGCCCTGCGGACTGTA
Band lengths:
242-355
Functional annotations
There are 2 annotated functions for this event
PMID: 26705333
Forcing inclusing of exon 7 in ESCs (deleting PTBP1 binding sites) induces expression of many neural genes, including Phox2b (highest change).
PMID: 32156753
Pbx1 is expressed throughout the olfactory bulb dopaminergic neurons. The exon 7 inclusion isoform (Pbx1a) is the primary isoform in olfactory bulb mature dopaminergic neurons, while the exclusion isoform (Pbx1b) is mostly expressed in SEZ cycling neural stem cells progenitors and immature migrating neuroblasts in the subependymal zone and in the Rostral migratory stream. Pbx1a, but not Pbx1b, specifically rescues the olfactory bulb dopaminergic neurons terminal differentiation in Pbx1 KO mice.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development