HsaEX6010288 @ hg38
Exon Skipping
Gene
ENSG00000106331 | PAX4
Description
paired box 4 [Source:HGNC Symbol;Acc:HGNC:8618]
Coordinates
chr7:127611535-127613091:-
Coord C1 exon
chr7:127613022-127613091
Coord A exon
chr7:127611945-127612000
Coord C2 exon
chr7:127611535-127611676
Length
56 bp
Sequences
Splice sites
3' ss Seq
GATTCACTCTCATTTTATAGGTG
3' ss Score
10.09
5' ss Seq
CAGGTACTC
5' ss Score
7.04
Exon sequences
Seq C1 exon
GTCTGGTTTTCCAACAGAAGAGCCAAATGGCGTCGGCAAGAGAAGCTCAAGTGGGAAATGCAGCTGCCAG
Seq A exon
GTGCTTCCCAGGGGCTGACTGTACCAAGGGTTGCCCCAGGAATCATCTCTGCACAG
Seq C2 exon
CAGTCCCCTGGCAGTGTGCCCACAGCAGCCCTGCCTGCCCTGGAACCACTGGGTCCCTCCTGCTATCAGCTGTGCTGGGCAACAGCACCAGAAAGGTGTCTGAGTGACACCCCACCTAAAGCCTGTCTCAAGCCCTGCTGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000106331-'8-14,'8-12,9-14=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (No Ref, Alt. Stop)
No structure available
Features
Disorder rate (disopred):
C1=0.701 A=1.000 C2=1.000
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(19.3=45.8)
A:
NO
C2:
NO
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTCAAGTGGGAAATGCAGCT
R:
GCTTTAGGTGGGGTGTCACTC
Band lengths:
148-204
Functional annotations
There are 2 annotated functions for this event
PMID: 11263967
PAX4v was generated by alternative splicing lacking the exon 7, and containing intact paired and homeo domain followed by novel 35 amino acids. PAX4v reversed the wild-type PAX4 mediated repression of the insulin promoter in cotransfection assays. PAX4v may play a role to antagonize the wild-type PAX4 function in human insulinoma.
PMID: 23129807
FLAG-tagged Pax4 suppressed the insulin promoter by �60%, whereas its exon 7-skipped isoform Pax4v had only a minor effect. Coexpression of Pax4v with Pax4 compromised the suppressive effect of Pax4 on transcription, suggesting that an increased Pax4v/Pax4 ratio could relieve Pax4-suppressed insulin expression.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains