BtaINT0108050 @ bosTau6
Intron Retention
Gene
ENSBTAG00000014421 | PBX2
Description
Bos taurus pre-B-cell leukemia homeobox 2 (PBX2), mRNA. [Source:RefSeq mRNA;Acc:NM_001256883]
Coordinates
chr23:27005671-27006301:+
Coord C1 exon
chr23:27005671-27005824
Coord A exon
chr23:27005825-27006212
Coord C2 exon
chr23:27006213-27006301
Length
388 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGAT
5' ss Score
3.56
3' ss Seq
TCCCCCTCTGCTCCCCCAAGGCT
3' ss Score
6.69
Exon sequences
Seq C1 exon
GTCTCCAACTGGTTTGGCAACAAGCGGATTCGCTATAAGAAAAACATAGGAAAGTTCCAGGAGGAGGCAAACATTTATGCCGTCAAGACCGCCGTGTCGGTCACCCAGGGAGGTCACAGCCGCACCAGCTCCCCGACACCCCCTTCCTCCGCAG
Seq A exon
GTGGATCCCACTGCCACCCTGGCTGACTGTTCTGCACGCTTCCTGCTTTTGTCCCACTTCTTGTCTAGGCAGGATCAGAGTAGAAAGAGGGGGCCTTCTGGGGTGAGAGGAACCAAGCTGGTCAGATGGGTGGGGATATCGGGGGGCTGAGGCCACTCCAGTGAAGTTATTTCTGCCTTTCTTCCAGTAAGTGGCCAGGGGAGGCTCAGAAACAGCCCGCTCCTTCTGAGTGTTGCCATGTTGTCTTGTGGATAATTTGGGTATGGTGGTACGCCTCCACCAAGCTAGTCCAGGGCACTTCCTGAAAACTGAGAGCTGTGGGGAGTCTCCCATCTGCCATCACAGGCTCTGTTACACTCTTCCCTACTTCCCCCTCTGCTCCCCCAAG
Seq C2 exon
GCTCTGGTGGCTCTTTCAATCTCTCAGGATCCGGTGACATGTTTCTGGGGATGCCCGGGCTCAACGGAGATTCCTACTCTGCCTCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014421:ENSBTAT00000061322:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.327 A=NA C2=0.467
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(21.7=25.0)
A:
NA
C2:
NO
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:
CGGATTCGCTATAAGAAAAACATAGG
R:
AGGCAGAGTAGGAATCTCCGT
Band lengths:
214-602
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]