BtaINT0108046 @ bosTau6
Intron Retention
Gene
ENSBTAG00000014421 | PBX2
Description
Bos taurus pre-B-cell leukemia homeobox 2 (PBX2), mRNA. [Source:RefSeq mRNA;Acc:NM_001256883]
Coordinates
chr23:27004413-27004956:+
Coord C1 exon
chr23:27004413-27004486
Coord A exon
chr23:27004487-27004708
Coord C2 exon
chr23:27004709-27004956
Length
222 bp
Sequences
Splice sites
5' ss Seq
CTGGTACGT
5' ss Score
9.57
3' ss Seq
TCCACTCGCCTGCACGCTAGGCC
3' ss Score
5.71
Exon sequences
Seq C1 exon
GAAACACGCCCTAAACTGCCACCGCATGAAGCCTGCTCTCTTTAGCGTCCTGTGTGAAATCAAGGAGAAAACTG
Seq A exon
GTACGTGAGTTCCCTCCTCCGATTCCTCAACTCTGGGGACAGAACCCTGGTTCCCTGTGGAACTTAGGCTAAGAGTTTGACAACTTGGGGCCCTGAGGAAAGTGTGGGTCAGGAAGATTGCTAAGGGGGGCTTGGGTGGGAACCCACACCTGGAGACTTGGGTCTCCAGGAGGGCTGAGAGCTGGGGTGTGGGGTCCCTAAGTCCACTCGCCTGCACGCTAG
Seq C2 exon
GCCTCAGCATTCGAAGCTCCCAAGAGGAGGAGCCTGTGGATCCACAGCTGATGCGCTTGGACAACATGCTTCTGGCAGAGGGTGTGGCTGGGCCTGAGAAAGGGGGTGGCTCAGCGGCTGCAGCGGCAGCAGCTGCAGCCTCCGGGGGCGGAGTGTCCCCTGACAACTCCATCGAACACTCGGACTATCGCAGCAAACTTGCCCAGATCCGCCACATTTACCACTCGGAGCTGGAGAAATATGAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014421:ENSBTAT00000061322:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.231 A=NA C2=0.651
Domain overlap (PFAM):
C1:
PF037928=PBC=FE(12.6=100)
A:
NA
C2:
PF037928=PBC=FE(41.4=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:
CCTAAACTGCCACCGCATGAA
R:
ATTTCTCCAGCTCCGAGTGGT
Band lengths:
305-527
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]