DreEX0053789 @ danRer10
Exon Skipping
Gene
ENSDARG00000100494 | pbx1a
Description
pre-B-cell leukemia homeobox 1a [Source:ZFIN;Acc:ZDB-GENE-000405-1]
Coordinates
chr2:19065215-19073524:-
Coord C1 exon
chr2:19073365-19073524
Coord A exon
chr2:19069379-19069488
Coord C2 exon
chr2:19065215-19065304
Length
110 bp
Sequences
Splice sites
3' ss Seq
TCCTTCTCTCTTCCTCTTAGGTT
3' ss Score
11.95
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
Exon sequences
Seq C1 exon
GTATCCAACTGGTTTGGAAACAAAAGGATCAGATACAAGAAAAATATTGGAAAATTCCAAGAAGAAGCCAACATGTACGCTGCCAGAACCGCCGCTAACGCAACCAGCGTCTCCACCCACGGCAGCCAAGCCAACTCGCCTTCCACACCAAATTCGGCCG
Seq A exon
GTTCTGCTGGCTCTTTTAACATGAACTCCGGGGATTTGTTCATGAGTGTTCAGTCTCTGAATGGGGACTCATACCAGGGGGCCCAAGTGGGGGCCAACGTTCAGTCACAG
Seq C2 exon
GTGGATACTCTTCGCCATGTTATCAGTCAGACAGGAGGATACAGTGAAAGCCTTGCTGCCAGTCAGATATACAGTCCACAGGGCATCAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000100494_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=0.463 A=0.486 C2=0.600
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(21.7=24.1)
A:
NO
C2:
NO
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:
TGGAAACAAAAGGATCAGATACAAGA
R:
TTGATGCCCTGTGGACTGTAT
Band lengths:
235-345
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]