BtaALTA0021269-2/2 @ bosTau6
Alternative 3'ss
Gene
ENSBTAG00000014967 | PAX7
Description
Uncharacterized protein [Source:UniProtKB/TrEMBL;Acc:E1BKL5]
Coordinates
chr2:134612666-134613594:-
Coord C1 exon
chr2:134613359-134613594
Coord A exon
chr2:134612793-134612795
Coord C2 exon
chr2:134612666-134612792
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
TGTCCACCCCGCTTGGCCAAGGCCGGGTTAATCAGCTGGGTGGGGTCTTCATCAACGGGCGACCCCTGCCTAACCACATCCGCCACAAGATCGTGGAGATGGCCCACCATGGCATCCGGCCCTGCGTCATCTCTCGCCAGCTGCGGGTCTCCCACGGCTGCGTCTCCAAGATCCTCTGCCGCTACCAGGAGACCGGGTCCATCCGGCCTGGGGCTATCGGCGGCAGCAAGCCCAGA
Seq A exon
CAG
Seq C2 exon
GTGGCGACTCCGGACGTGGAGAAAAAGATCGAGGAGTACAAGAGGGAAAACCCGGGCATGTTTAGCTGGGAGATCCGAGACCGACTGCTGAAGGACGGGCACTGCGACCGCAGCACCGTGCCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014967-1-2,1-1-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (disopred):
C1=0.203 A=NA C2=0.000
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 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:
CTCCAAGATCCTCTGCCGCTA
R:
TCGATCTTTTTCTCCACGTCCG
Band lengths:
105-108
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
- Pre-implantation embryo development