MmuALTA1018787-2/2 @ mm10
Alternative 3'ss
Gene
ENSMUSG00000028736 | Pax7
Description
paired box 7 [Source:MGI Symbol;Acc:MGI:97491]
Coordinates
chr4:139828576-139829626:-
Coord C1 exon
chr4:139829497-139829626
Coord A exon
chr4:139828705-139828710
Coord C2 exon
chr4:139828576-139828704
Length
6 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
TTTTGCCTTTCATTTCTGAGGTT
3' ss Score
4.44
Exon sequences
Seq C1 exon
CAGGTGGCGACTCCGGATGTGGAGAAAAAGATTGAGGAGTATAAGAGAGAGAACCCCGGGATGTTCAGCTGGGAAATCCGGGACCGGCTGCTGAAGGACGGTCACTGCGACCGAAGCACGGTGCCCTCAG
Seq A exon
GTTTAG
Seq C2 exon
TGAGTTCGATTAGCCGAGTGCTCAGAATCAAGTTCGGGAAGAAAGAGGACGACGAGGAAGGAGACAAGAAAGAAGAAGATGGCGAGAAGAAAGCCAAACACAGCATCGATGGCATCCTGGGCGACAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028736-2-4,2-3-2/2
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=0.722
Domain overlap (PFAM):
C1:
PF0029213=PAX=FE(34.1=100)
A:
NA
C2:
PF0029213=PAX=PD(6.3=18.2)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGTTCAGCTGGGAAATCCGG
R:
ACTTGATTCTGAGCACTCGGC
Band lengths:
103-109
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]
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