BtaINT0108045 @ bosTau6
Intron Retention
Gene
ENSBTAG00000014421 | PBX2
Description
Bos taurus pre-B-cell leukemia homeobox 2 (PBX2), mRNA. [Source:RefSeq mRNA;Acc:NM_001256883]
Coordinates
chr23:27003269-27004486:+
Coord C1 exon
chr23:27003269-27003489
Coord A exon
chr23:27003490-27004412
Coord C2 exon
chr23:27004413-27004486
Length
923 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGT
5' ss Score
9.1
3' ss Seq
TTTCTCTCCCGTTCCCCAAGGAA
3' ss Score
8.82
Exon sequences
Seq C1 exon
ATGGACGAGCGGCTGCTGGGGCCGCCCCCTCCAGGCGGGGGCCGGGGGGCCCTTGGATTGGTGGGTGGGGAGCCTGGGGGCCCTGGCGAACCTCCCGGTGGCGGAGACCCCGGTGGGGGTAGCGGGGGGGTCCCGGGAGGCCGAGGGAAGCAAGACATCGGGGACATTCTGCAGCAGATAATGACCATCACCGACCAGAGCCTGGATGAGGCCCAGGCCAA
Seq A exon
GTGAGTGCCCCCAACCCGGGACCCCACACAGACCCAGCAGAAGCCCGGTTCACAAGCTCTGAACCTTCTGGGAGCCCCCAACTCAGGACCCTCCCCAGGATACTACAGCTCTCCTCTCCTTACTCCCGGGAGCCCCAAGATAAGTGATCCCTCTCAAACCTCCCTTCACCCCCCAGTCCCTGAAACCTTAGAAAAGCGGAACCCTAGGTGGTCTTACCCCCCCACCTCTCCCTAACCACCCCACATCCTTCCATCTCCAGAGACCCCTTCTGACTCCCAGACTGAAAACCTGCTGTGCTGTCTGCTCCCCTAACTCTCCAGCCCACCCTCTTCCTAGGGCTCTCCAGACCCCTCCCCAGGGCTCCGACCATTTCTCTCCACCCAGGGCCTAGCCTCCTAGGTCCTCGGGCACCCTTCGCCCCTGCTCAGTGGAGCCCTGCTCAGTCCCAGGACCCTTCACACATCTCTATACTGAACTCCCCACTTCAGCTCAGCACCCCTCACCCCCTCGGGCACCTCAAACTCTGATCTCCTCCTCCTTCTCCTCGGCCTCCTCCTGTCTTCCTCTGAAATCTACCTAGTCACTCTTATTTCTGCAGTCATTCCCACATCCTCTTCTGTACCTTTCTAGACCGTCTCCCACAGTCCCCACCTGGCCATGGTGCCTTTAGCTCGCGGCACCTTCCCTCCTTCCAGCCAAAGCCGGGCAGCTTCACCTTGTCTCTGCATGGAAGCTGAACTCTTCCTAAGAACCCCCCAGACTTCATTCGGCCCCCAGCCTTGCTTTTTCTTGCCACAGATTGACCCACCACCTCCCTATTCCCAAGCTCCCCTCTCTTACCCTTGTGGGTGTGTCGTCCTGTGGTTGTTTTTCCCCCTTGGCAATTCCATAGCCTCTCAACTTTTCTCTCCCGTTCCCCAAG
Seq C2 exon
GAAACACGCCCTAAACTGCCACCGCATGAAGCCTGCTCTCTTTAGCGTCCTGTGTGAAATCAAGGAGAAAACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014421:ENSBTAT00000061322:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.231
Domain overlap (PFAM):
C1:
PF037928=PBC=PU(14.1=37.8)
A:
NA
C2:
PF037928=PBC=FE(12.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGGGCCCTTGGATTGGT
R:
TTCTCCTTGATTTCACACAGGACG
Band lengths:
246-1169
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]