DreALTA0019660-2/2 @ danRer10
Alternative 3'ss
Gene
ENSDARG00000010192 | pax3a
Description
paired box 3a [Source:ZFIN;Acc:ZDB-GENE-980526-52]
Coordinates
chr2:47576550-47577635:-
Coord C1 exon
chr2:47577400-47577635
Coord A exon
chr2:47576677-47576679
Coord C2 exon
chr2:47576550-47576676
Length
3 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGA
5' ss Score
9.45
3' ss Seq
TGTTACCATTGCAATAAAAGCAG
3' ss Score
-1.19
Exon sequences
Seq C1 exon
TCTCTACGCCTTTAGGTCAGGGCCGCGTGAACCAGCTCGGCGGAGTCTTCATAAACGGGCGCCCTTTGCCCAATCACATCCGCCACAAGATAGTAGAGATGGCCCATCACGGCATACGACCGTGCGTCATCTCCCGGCAGCTGCGAGTCTCACACGGATGCGTGTCCAAAATTTTATGCAGGTACCAGGAGACCGGTTCCATTCGGCCCGGGGCTATTGGTGGCAGCAAACCCAAG
Seq A exon
CAG
Seq C2 exon
AGCACAACTCCTGACGTGGAAAAGAAAATCGAAGAATACAAGAGAGAAAATCCAGGGATGTTCAGCTGGGAGATTCGGGATAAACTTCTGAAAGATGGAATCTGCGATCGGAATAACGTTCCTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000010192-1-2,1-1-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (disopred):
C1=0.215 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 Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTATTGGTGGCAGCAAACCCA
R:
ATCCCGAATCTCCCAGCTGAA
Band lengths:
104-107
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]