HsaALTA0006095-2/2 @ hg19
Alternative 3'ss
Gene
ENSG00000135903 | PAX3
Description
paired box 3 [Source:HGNC Symbol;Acc:8617]
Coordinates
chr2:223160247-223161932:-
Coord C1 exon
chr2:223161697-223161932
Coord A exon
chr2:223160374-223160376
Coord C2 exon
chr2:223160247-223160373
Length
3 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
GCCCGCCTGTTCTCTTAAAGCAG
3' ss Score
7.03
Exon sequences
Seq C1 exon
TGTCCACTCCCCTCGGCCAGGGCCGCGTCAACCAGCTCGGCGGTGTTTTTATCAACGGCAGGCCGCTGCCCAACCACATCCGCCACAAGATCGTGGAGATGGCCCACCACGGCATCCGGCCCTGCGTCATCTCGCGCCAGCTGCGCGTGTCCCACGGCTGCGTCTCCAAGATCCTGTGCAGGTACCAGGAGACTGGCTCCATACGTCCTGGTGCCATCGGCGGCAGCAAGCCCAAG
Seq A exon
CAG
Seq C2 exon
GTGACAACGCCTGACGTGGAGAAGAAAATTGAGGAATACAAAAGAGAGAACCCGGGCATGTTCAGCTGGGAAATCCGAGACAAATTACTCAAGGACGCGGTCTGTGATCGAAACACCGTGCCGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000135903-1-2,1-1-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (disopred):
C1=0.165 A=NA C2=0.017
Domain overlap (PFAM):
C1:
PF0029213=PAX=PU(57.9=92.4)
A:
NA
C2:
PF0029213=PAX=FE(33.6=100)
Other Inclusion Isoforms:
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGACTGGCTCCATACGTCCT
R:
ATGCCCGGGTTCTCTCTTTTG
Band lengths:
107-110
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)