BtaALTA0021268-2/2 @ bosTau6
Alternative 3'ss
Gene
ENSBTAG00000009950 | PAX3
Description
paired box 3 [Source:HGNC Symbol;Acc:HGNC:8617]
Coordinates
chr2:111226270-111227967:-
Coord C1 exon
chr2:111227732-111227967
Coord A exon
chr2:111226397-111226399
Coord C2 exon
chr2:111226270-111226396
Length
3 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
GTCTGCCGGTTCTCTTAAAGCAG
3' ss Score
5.94
Exon sequences
Seq C1 exon
TGTCCACTCCCCTCGGCCAGGGCCGGGTCAACCAGCTTGGAGGTGTTTTTATCAACGGCAGGCCACTACCCAACCACATCCGCCACAAGATCGTGGAGATGGCCCACCATGGCATCCGGCCCTGCGTCATCTCCCGCCAGCTGCGTGTGTCCCATGGCTGCGTCTCTAAGATCCTTTGCAGGTATCAGGAGACTGGCTCCATCCGCCCTGGTGCCATTGGTGGCAGCAAGCCCAAG
Seq A exon
CAG
Seq C2 exon
GTGACAACGCCTGACGTGGAGAAGAAAATAGAGGAATACAAAAGAGAGAACCCCGGCATGTTCAGCTGGGAAATTCGAGACAAATTACTCAAGGACGCGGTCTGTGATCGAAACACCGTACCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000009950-1-2,1-1-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (disopred):
C1=0.228 A=NA C2=0.000
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
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCCTGGTGCCATTGGTG
R:
CATGCCGGGGTTCTCTCTTTT
Band lengths:
92-95
Functional annotations
There are 3 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.
PMID: 15688409
Four isoforms due to 3nt (Q, HsaALTA1001031) and 6nt (GL, HsaALTA1001032) insertions/deletion. The relative DNA binding affinity for each isoform is: Q-GL- > Q+GL- > Q-GL+ >/= Q+GL+ for class I sites and Q-GL-, Q+GL- > Q-GL+, Q+GL+ for class II sites. This results in different transcriptional activity.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development