RnoEX6012892 @ rn6
Exon Skipping
Gene
ENSRNOG00000008020 | Pax4
Description
paired box 4 [Source:RGD Symbol;Acc:620433]
Coordinates
chr4:55736614-55737716:-
Coord C1 exon
chr4:55737647-55737716
Coord A exon
chr4:55737041-55737096
Coord C2 exon
chr4:55736614-55736755
Length
56 bp
Sequences
Splice sites
3' ss Seq
GATTCACCTTCACCTTATAGGTG
3' ss Score
9.1
5' ss Seq
CAGGTACTT
5' ss Score
8.17
Exon sequences
Seq C1 exon
GTCTGGTTTTCCAACAGAAGAGCCAAATGGCGCAGACAAGAGAAGTTGAAATGGGAAACACAGATGCCAG
Seq A exon
GTGCTTCTCAGGACCTGATGGTACCAAAAGATTCTCCAGGGATCATCTCTGCACAG
Seq C2 exon
CAGTCCCCTGGCAGTGTACCCTCAGCAGCCCTGCCTGTGCTGGAACAATTGAATCCTTCCTTCTGTCAGCTGTGCTGGGGGGCAGTACCAGACAGATGTTCCAGTGACACCACATCCCAAGCCTGTCTCCAACCCTACTGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000008020-'6-10,'6-9,7-10=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence exclusion
No structure available
Features
Disorder rate (disopred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(19.3=45.8)
A:
NO
C2:
NO
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
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:
GGCGCAGACAAGAGAAGTTGA
R:
ACATCTGTCTGGTACTGCCCC
Band lengths:
141-197
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]