BtaALTD0022668-2/4 @ bosTau6
Alternative 5'ss
Gene
ENSBTAG00000012622 | TRA2A
Description
Bos taurus transformer 2 alpha homolog (Drosophila) (TRA2A), mRNA. [Source:RefSeq mRNA;Acc:NM_001046380]
Coordinates
chr4:32259420-32260142:-
Coord C1 exon
chr4:32260064-32260142
Coord A exon
chr4:32259845-32260063
Coord C2 exon
chr4:32259420-32259553
Length
219 bp
Sequences
Splice sites
5' ss Seq
TAGGTTAAG
5' ss Score
-0.45
3' ss Seq
AATACTGTCTTCTTTGTTAGGAG
3' ss Score
6.9
Exon sequences
Seq C1 exon
GTTAATGTTCGTGAAGAAATTGAAGAGTTTTTTCCAAGAATGTGGAAGATAAATCAAGATAAAAGAAGGCTAATGAAAA
Seq A exon
GTATTAAAGATCAGAAAATTAAAATTGAATGGGGGAAAAAATTGAACAGAAGATTGGTCAGATAGAAGCACTTGAATATTTTTTTTAAGGCTATTTTGAATTGTTTTGGGGAAGAATACACGAAGTATGAAAAATGAAAAACTCAATGAAGAATGAAGAGAAGTAGAAAGCAAGAGTGAAGTAGAATTAAAAGAATCTGGAAGAATGAATGGGTCCTAG
Seq C2 exon
GAGTCTCGCTCTCAGTCAAAATCTCCAACGGGAACTCCTGCTCGTGTAAAATCGGAGAGCAGGTCAGGATCTCGTAGTCCATCAAGGGTTTCCAAACACTCTGAATCCCATTCTCGATCAAGATCAAAATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012622-3-3,4-3,5-3,6-3-2/4
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF104084=Ufd2P_core=PD(76.0=79.2)
A:
NA
C2:
PF086487=DUF1777=FE(33.8=100)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTTCGTGAAGAAATTGAAGAGTT
R:
GGATTTTGATCTTGATCGAGAATGGG
Band lengths:
206-425
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development