GgaALTA1026129-1/2 @ galGal4
Alternative 3'ss
Gene
ENSGALG00000003782 | Pax-7
Description
paired box protein Pax-7 [Source:RefSeq peptide;Acc:NP_990396]
Coordinates
chr21:4444786-4445737:+
Coord C1 exon
chr21:4444786-4445021
Coord A exon
NA
Coord C2 exon
chr21:4445611-4445737
Length
0 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
GCCATTGACCACAAAAGCAGGTT
3' ss Score
-0.46
Exon sequences
Seq C1 exon
TGTCCACCCCGCTGGGCCAGGGCCGGGTGAACCAACTCGGAGGGGTTTTCATCAACGGGCGCCCACTGCCCAACCACATCCGCCATAAGATCGTGGAGATGGCTCACCACGGCATCCGGCCCTGCGTGATCTCCAGGCAGCTGAGGGTCTCCCACGGCTGCGTTTCCAAAATCCTCTGCAGGTACCAAGAGACGGGCTCCATCCGGCCCGGGGCCATCGGGGGCAGCAAGCCCAGG
Seq A exon
NA
Seq C2 exon
GTTGCGACTCCCGACGTGGAGAAGAAAATCGAGGAATACAAGAGGGAGAACCCTGGGATGTTCAGCTGGGAGATCCGGGACAGGCTGCTGAAGGACGGACACTGCGACCGCAGCACTGTGCCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003782-1-4,1-3-1/2
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=0.253 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
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTGCGTTTCCAAAATCCTC
R:
TTTCTTCTCCACGTCGGGAGT
Band lengths:
108-111
Functional annotations
There are 1 annotated functions for this event
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]