GgaALTA1026130-2/2 @ galGal4
Alternative 3'ss
Gene
ENSGALG00000003782 | Pax-7
Description
paired box protein Pax-7 [Source:RefSeq peptide;Acc:NP_990396]
Coordinates
chr21:4445608-4446717:+
Coord C1 exon
chr21:4445608-4445737
Coord A exon
chr21:4446583-4446588
Coord C2 exon
chr21:4446589-4446717
Length
6 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
CTTGTCTTTGACTGTCTGAGGTT
3' ss Score
1.27
Exon sequences
Seq C1 exon
CAGGTTGCGACTCCCGACGTGGAGAAGAAAATCGAGGAATACAAGAGGGAGAACCCTGGGATGTTCAGCTGGGAGATCCGGGACAGGCTGCTGAAGGACGGACACTGCGACCGCAGCACTGTGCCCTCAG
Seq A exon
GTTTAG
Seq C2 exon
TGAGTTCGATTAGCCGTGTGCTACGCATCAAATTCGGGAAGAAAGAGGAAGAGGAGGACTGCGACAAGAAGGAGGAAGACGGGGAGAAGAAGGCCAAGCACAGCATAGATGGCATCCTGGGCGACAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003782-2-6,2-5-2/2
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=0.000 A=NA C2=0.727
Domain overlap (PFAM):
C1:
PF0029213=PAX=FE(34.1=100)
A:
NA
C2:
PF0029213=PAX=PD(6.3=18.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAACCCTGGGATGTTCAGCTG
R:
GCACACGGCTAATCGAACTCA
Band lengths:
101-107
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]