HsaALTA1001031-2/2 @ hg38
Alternative 3'ss
Gene
ENSG00000009709 | PAX7
Description
paired box 7 [Source:HGNC Symbol;Acc:HGNC:8621]
Coordinates
chr1:18634303-18635240:+
Coord C1 exon
chr1:18634303-18634538
Coord A exon
chr1:18635111-18635113
Coord C2 exon
chr1:18635114-18635240
Length
3 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
TCCCACCTCCACCTCTGAAGCAG
3' ss Score
2.9
Exon sequences
Seq C1 exon
TGTCCACCCCGCTTGGCCAAGGCCGGGTCAATCAGCTGGGAGGGGTCTTCATCAATGGGCGACCCCTGCCTAACCACATCCGCCACAAGATAGTGGAGATGGCCCACCATGGCATCCGGCCCTGTGTCATCTCCCGACAGCTGCGTGTCTCCCACGGCTGCGTCTCCAAGATTCTTTGCCGCTACCAGGAGACCGGGTCCATCCGGCCTGGGGCCATCGGCGGCAGCAAGCCCAGA
Seq A exon
CAG
Seq C2 exon
GTGGCGACTCCGGATGTAGAGAAAAAGATTGAGGAGTACAAGAGGGAAAACCCAGGCATGTTCAGCTGGGAGATCCGGGACAGGCTGCTGAAGGATGGGCACTGTGACCGAAGCACTGTGCCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000009709-1-2,1-1-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (disopred):
C1=0.198 A=NA C2=0.061
Domain overlap (PFAM):
C1:
PF0029213=PAX=PU(57.0=92.4)
A:
NA
C2:
PF0029213=PAX=FE(33.6=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:
GGCTGCGTCTCCAAGATTCTT
R:
TTCTCTACATCCGGAGTCGCC
Band lengths:
104-107
Functional annotations
There are 1 annotated functions for this event
PMID: 15688409
This event
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
- Autistic and control brains