Special

BtaALTA0021268-1/2 @ bosTau6

Alternative 3'ss

Gene
Description
paired box 3 [Source:HGNC Symbol;Acc:HGNC:8617]
Coordinates
chr2:111226270-111227967:-
Coord C1 exon
chr2:111227732-111227967
Coord A exon
NA
Coord C2 exon
chr2:111226270-111226396
Length
0 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
TGCCGGTTCTCTTAAAGCAGGTG
3' ss Score
5.43
Exon sequences
Seq C1 exon
TGTCCACTCCCCTCGGCCAGGGCCGGGTCAACCAGCTTGGAGGTGTTTTTATCAACGGCAGGCCACTACCCAACCACATCCGCCACAAGATCGTGGAGATGGCCCACCATGGCATCCGGCCCTGCGTCATCTCCCGCCAGCTGCGTGTGTCCCATGGCTGCGTCTCTAAGATCCTTTGCAGGTATCAGGAGACTGGCTCCATCCGCCCTGGTGCCATTGGTGGCAGCAAGCCCAAG
Seq A exon
NA
Seq C2 exon
GTGACAACGCCTGACGTGGAGAAGAAAATAGAGGAATACAAAAGAGAGAACCCCGGCATGTTCAGCTGGGAAATTCGAGACAAATTACTCAAGGACGCGGTCTGTGATCGAAACACCGTACCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000009950-1-2,1-1-1/2
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=0.228 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 Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
ALTERNATIVE
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