RnoALTA0028137-2/2 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000013670 | Pax3
Description
paired box 3 [Source:RGD Symbol;Acc:620431]
Coordinates
chr9:84097890-84099529:-
Coord C1 exon
chr9:84099294-84099529
Coord A exon
chr9:84098017-84098019
Coord C2 exon
chr9:84097890-84098016
Length
3 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
ACCCGTCTCTTCTCTTAAAGCAG
3' ss Score
7.76
Exon sequences
Seq C1 exon
TGTCTACACCCCTCGGCCAGGGCCGAGTCAATCAGCTCGGAGGAGTATTTATCAACGGCAGGCCTCTGCCCAACCACATCCGCCACAAGATCGTGGAGATGGCCCACCACGGCATTCGGCCTTGCGTCATCTCTCGCCAACTTCGCGTGTCCCACGGCTGTGTCTCTAAGATCTTATGCAGGTACCAGGAGACAGGCTCCATCCGACCTGGCGCCATTGGCGGCAGCAAGCCCAAG
Seq A exon
CAG
Seq C2 exon
GTGACAACGCCTGACGTGGAGAAGAAAATTGAGGAATACAAAAGAGAGAACCCAGGCATGTTTAGCTGGGAAATCAGAGACAAATTACTCAAGGACGCTGTCTGTGATCGGAACACTGTGCCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000013670-2-2,2-1-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (disopred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0029213=PAX=PU(57.9=92.4)
A:
NA
C2:
PF0029213=PAX=FE(34.1=100)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGCAGGTACCAGGAGACAGG
R:
CAATTTTCTTCTCCACGTCAGGC
Band lengths:
92-95
Functional annotations
There are 2 annotated functions for this event
PMID: 15688409
DNA binding analysis demonstrated that PAX3 Q- (taking internal NAGNAG) isoforms exhibit higher affinity than corresponding Q+ isoforms for class I sites and no difference for class II sites. This results in different transcriptional activity.
PMID: 15688409
DNA binding analysis demonstrated that PAX3 Q- (taking internal NAGNAG) isoforms exhibit higher affinity than corresponding Q+ isoforms for class I sites and no difference for class II sites. This results in different transcriptional activity.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]