BtaINT0108060 @ bosTau6
Intron Retention
Gene
ENSBTAG00000009975 | PBX4
Description
pre-B-cell leukemia homeobox 4 [Source:HGNC Symbol;Acc:HGNC:13403]
Coordinates
chr7:3678159-3678846:+
Coord C1 exon
chr7:3678159-3678403
Coord A exon
chr7:3678404-3678655
Coord C2 exon
chr7:3678656-3678846
Length
252 bp
Sequences
Splice sites
5' ss Seq
CAGGTGATC
5' ss Score
4.28
3' ss Seq
GGCATGTGTCCCCACCCCAGGCC
3' ss Score
6.52
Exon sequences
Seq C1 exon
TGTCGAGCATCCATGGCATTCAGGAAGTGGGCCCCCCTGATGCTCAGCTCCTGAGGCTGGATAACATGCTGCTGGCCGAGGGCGTGTCCAGGCCTGAGAAGCAAGGGAGGGGAGCATCGGCAGCAGCCAACGCAGCAATGCCAGGTGGCCGTCCAAACGACAGTGGCCTTGAGCACTCTGACTACAGGGCCAAGCTGTCCCAGATCCGACAGATGTACCACTCCGAGCTAGAGAAATATGAACAG
Seq A exon
GTGATCTTTCATGGGAATGCACGTTTGTCAAAGGAAAACATGGAGTACAAACTGCCTTCCCTTGGCAGCATCGAGCAGAGAGCCCACGAGCTTGGTCTCATAGCAGGGGTGGCTGATTTGCCCCCAGCCCCTTGCCATCATTTCTCAGTAGCCAGCCTGCATGAGAGGCTCGGGGGGCAGGTGGCTGGTCCCACCCGGGGCCCCGGGCCAGCCTGCTAGGTGGTCACCAGCTGGCATGTGTCCCCACCCCAG
Seq C2 exon
GCCTGCCGTGAGTTCACCATGCACGTCACCAACCTTCTCCAGGAGCAGAGCAGGATCAGGCCCGTCTCGCCCGCGGAGATAGAGCACATGGTGGGGGTCATCCACGGCAAGTTCCAGAGCATCCAGATGCAGCTGAAGCAGAGCACCTGTGAGGCTGTGATGGCCCTGCGCGCGAGGTTCCTCGACGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000009975:ENSBTAT00000013152:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.707 A=NA C2=0.031
Domain overlap (PFAM):
C1:
PF037928=PBC=FE(41.5=100),PF070286=DUF1319=PU(34.9=36.6)
A:
NA
C2:
PF037928=PBC=PD(31.3=95.3),PF070286=DUF1319=PD(62.8=84.4),PF0004624=Homeobox=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCTCCTGAGGCTGGATAACA
R:
CACCATGTGCTCTATCTCCGC
Band lengths:
293-545
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]