HsaALTA0006095-3/3 @ hg38
Alternative 3'ss
Gene
ENSG00000135903 | PAX3
Description
paired box 3 [Source:HGNC Symbol;Acc:HGNC:8617]
Coordinates
chr2:222295528-222297213:-
Coord C1 exon
chr2:222296978-222297213
Coord A exon
chr2:222295655-222295774
Coord C2 exon
chr2:222295528-222295654
Length
120 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
AGGTCTTTTTGCTCACAAAGGGG
3' ss Score
3
Exon sequences
Seq C1 exon
TGTCCACTCCCCTCGGCCAGGGCCGCGTCAACCAGCTCGGCGGTGTTTTTATCAACGGCAGGCCGCTGCCCAACCACATCCGCCACAAGATCGTGGAGATGGCCCACCACGGCATCCGGCCCTGCGTCATCTCGCGCCAGCTGCGCGTGTCCCACGGCTGCGTCTCCAAGATCCTGTGCAGGTACCAGGAGACTGGCTCCATACGTCCTGGTGCCATCGGCGGCAGCAAGCCCAAG
Seq A exon
GGGGACCGTCCCAGAGGATTCAGCGAGGAGCATCCCGACAGGCCCAGAGGCGGTGGGGCCGCCGCCACCTGGCCCAGGGTACCGGGTACCAACGCCTGCCCGCCTGTTCTCTTAAAGCAG
Seq C2 exon
GTGACAACGCCTGACGTGGAGAAGAAAATTGAGGAATACAAAAGAGAGAACCCGGGCATGTTCAGCTGGGAAATCCGAGACAAATTACTCAAGGACGCGGTCTGTGATCGAAACACCGTGCCGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000135903-2-3,2-2,2-1-3/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (disopred):
C1=0.153 A=NA C2=0.015
Domain overlap (PFAM):
C1:
PF0029213=PAX=PU(57.9=92.4)
A:
NA
C2:
PF0029213=PAX=FE(33.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
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:
AACCACATCCGCCACAAGATC
R:
TGTCTCGGATTTCCCAGCTGA
Band lengths:
247-367
Functional annotations
There are 1 annotated functions for this event
PMID: 15688409
This event
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]
SPECIAL DATASETS
- Autistic and control brains