Special

MmuALTA1002178-1/2 @ mm10

Alternative 3'ss

Gene
Description
paired box 3 [Source:MGI Symbol;Acc:MGI:97487]
Coordinates
chr1:78193740-78195486:-
Coord C1 exon
chr1:78195251-78195486
Coord A exon
NA
Coord C2 exon
chr1:78193740-78193866
Length
0 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
CGCCTATTCTCTTAAAGCAGGTG
3' ss Score
5.29
Exon sequences
Seq C1 exon
TGTCCACCCCTCTTGGCCAGGGCCGAGTCAACCAGCTCGGAGGAGTATTTATCAACGGCAGGCCTCTGCCCAACCATATCCGCCACAAGATAGTGGAGATGGCCCACCATGGCATTCGGCCTTGCGTCATTTCTCGCCAGCTTCGCGTGTCCCATGGTTGCGTCTCTAAGATCCTGTGCAGGTACCAGGAGACAGGCTCCATCCGACCTGGTGCCATCGGCGGCAGCAAACCCAAG
Seq A exon
NA
Seq C2 exon
GTGACAACGCCTGACGTGGAGAAGAAAATTGAGGAATACAAAAGAGAGAACCCGGGCATGTTTAGCTGGGAAATCAGAGACAAATTGCTCAAGGACGCTGTCTGTGATCGGAACACTGTGCCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004872-1-2,1-1-1/2
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=0.215 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:
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGACAGGCTCCATCCGACC
R:
ATGCCCGGGTTCTCTCTTTTG
Band lengths:
107-110
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]


SPECIAL DATASETS

  • Ribosome-engaged transcriptomes of neuronal types
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types