BtaALTD0015683-2/3 @ bosTau6
Alternative 5'ss
Gene
ENSBTAG00000009975 | PBX4
Description
pre-B-cell leukemia homeobox 4 [Source:HGNC Symbol;Acc:HGNC:13403]
Coordinates
chr7:3682694-3683304:+
Coord C1 exon
chr7:3682694-3682850
Coord A exon
chr7:3682851-3682860
Coord C2 exon
chr7:3683198-3683304
Length
10 bp
Sequences
Splice sites
5' ss Seq
AGGGTCAGT
5' ss Score
5.85
3' ss Seq
TGACCCTCCGACCCCTGCAGGCT
3' ss Score
8.76
Exon sequences
Seq C1 exon
GTCTCCAACTGGTTCGGCAACAAAAGAATTCGGTATAAAAAGAACATGAGGAAGTTTCAAGAAGAGGCTACCATCTACACAGCCAAGACGGCAGTGGACGCCACCGAAGTCAGGGGCTCAGGGCGCCAGGCCAGCCCCCCATCGATGTCCCACTCCA
Seq A exon
GTGAGTGAGG
Seq C2 exon
GCTCCTCTGGCCCATTTCCGCTGACTGGCCCCGGAGACGCACTTATCCGCCTGCAGACGCTGGCCTGCGTCCAGCCCAGCCCCCGGGGAGGAGGCCTTCTGGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000009975-11-9,12-9,13-9-2/3
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=0.453 A=NA C2=0.667
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(21.7=24.5)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCATCTACACAGCCAAGACGG
R:
GGAAATGGGCCAGAGGAGC
Band lengths:
106-116
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development