DreEX0053794 @ danRer10
Exon Skipping
Gene
ENSDARG00000101131 | pbx1b
Description
pre-B-cell leukemia homeobox 1b [Source:ZFIN;Acc:ZDB-GENE-070424-11]
Coordinates
chr6:2175076-2180702:-
Coord C1 exon
chr6:2180543-2180702
Coord A exon
chr6:2177486-2177598
Coord C2 exon
chr6:2175076-2175165
Length
113 bp
Sequences
Splice sites
3' ss Seq
GCTGTCTGTGCTCCTCTCAGGTT
3' ss Score
9.4
5' ss Seq
CAGGTACAG
5' ss Score
8.68
Exon sequences
Seq C1 exon
GTGTCTAACTGGTTCGGAAACAAGCGAATCCGATATAAGAAGAACATCGGAAAGTTCCAGGAAGAAGCGAACATGTATGCGGCCAGAACGGCTGTGAACGCGGCGAGCGTTTCTGCACACGGCAGTCAGGCAAACTCTCCGTCCACTCCAAACTCAGCAG
Seq A exon
GTTCTGCAGGCTCTTTTAACATGTCAAACTCTGGCGATTTGTTTATGAGTGTTCAGTCTCTGAACGGGGACTCGTACCAGGGCTCTCAGGTGGGGGCCAATGTTCAGTCACAG
Seq C2 exon
GTGGATACCCTTCGCCATGTTATCAGCCAGACAGGAGGATACAGTGACGGCCTCGCAGCAAACCAGATGTACAGTCCGCAGGGCATCAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000101131_MULTIEX1-1/2=C1-2
Average complexity
S*
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence exclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.333 A=0.526 C2=0.867
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(21.7=24.1)
A:
NO
C2:
NO
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTGGTTCGGAAACAAGCGAA
R:
ATTGATGCCCTGCGGACTGTA
Band lengths:
243-356
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]