BtaINT0108056 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013314 | PBX3
Description
Bos taurus pre-B-cell leukemia homeobox 3 (PBX3), mRNA. [Source:RefSeq mRNA;Acc:NM_001046453]
Coordinates
chr11:96766772-96768453:+
Coord C1 exon
chr11:96766772-96766937
Coord A exon
chr11:96766938-96768340
Coord C2 exon
chr11:96768341-96768453
Length
1403 bp
Sequences
Splice sites
5' ss Seq
CTGGTGCGT
5' ss Score
8.29
3' ss Seq
CTTAACTCTTTCCTTTCCAGGTT
3' ss Score
11.89
Exon sequences
Seq C1 exon
GTGTCCAACTGGTTTGGCAACAAACGAATCAGGTACAAGAAGAATATTGGCAAGTTTCAGGAAGAAGCCAACCTCTATGCTGCAAAGACAGCCGTGACAGCCGCGCACGCAGTGGCCGCAGCCGTGCAGAACAACCAGACCAACTCGCCCACCACGCCGAATTCTG
Seq A exon
GTGCGTATGGGTGCTCACTCCCTCCTCGGCTCAGGAAGCCCGAGGCCACACATCCCCACCTCATGGGCCAGGACACAAGAACCATACTGAGAATACAGTGGACTCATAAAGATTTCTATTAAAATGCAGGCTTCTTCCTCGAATCAGTGAATGAGTGGTTGACCAGAGGGCCTGTAAACCCACTGTTCATAGTGAGCGCCACTCACTACCAGGAGAACCTGGAACTTACACACTTAGAAGTGGTTTTTAATTCAGCAGTGAGGCCCAGTGCTATCCCTAATGAACTATATTGTTCCATGTGCCATTTTAAAATCCGTAGTGGTCTGTCAAAGAACGAGTGAAATAGCAGAAGTGGGAGATTGACCTATTGCTGTGAGTAATGAGACTGGAATGCTGGGGTTAGTACCACAGTGCTTTCTCCCTGATGTGGCTGCAGACTCGAGTCTGCGGTCCTTCCTCAGTACCTGTGCTGACTTGGTAGGCTCAGCACGTGGTTAGCTGATCAGGACATGGTTAGCTGTGAGAGATATGGTAGTTAGTACATGGATGCAGTATCTTGGCTCCTTATACAATACATTTTGGCCAAATTTTTTGTGGCATGTTTGATGGAATTGGAAACGTTAAAATTATAGGGAACTTGAGTAGCAACGAAAGATGTGCAGCTAGCCCAAACAGATGGGCTTGAGAAGCAATTCAAGGGGCTTTTCTAAGGAGATAATTTAAATATAATCTTTAAAAATTCAGAAAGGGAGGGTTTTTTGTTTGTTTTGATGTCTTCTTTTTCCCTCCATCCCACCCCAACCCCCCCCAGGTTCTTTTTAATGGAACGTGGAAACTGATGAAAGTTAGGCAGAGTGAATGGCTAAGAAAGAGCTTCAGGGACTTTCTGGAGGGCTAGTGGTTAAGACTAAGGGGCATGGGTCAATCCCTGGTTGGGGAACTAAGATCCCACATGCTGCTTGGCATGGTCAAGTAAATAATAAATACCTTTTTAAAATAAAAATAAATAATAAAAAGTCTGGAGGAATTTTTTTTTAAAGCTTCAGAAAAATGTTTCTTCTCTGGGTAATTGTCCACCATGACAGCTAATGATGGTGAAGAGCTCACTTAATGACAAGTCCTGGAGATAAATGAAAACAAGGGGATAGTTCCAAGCCAGCTGCTGGGTGTTTCTCTGTTTTGATTCTTCCTTTGTTTCATAGTTGGGTTTCCCCATCACTAAGACTTTTCTAGATGCAAAATTCACTTCTTGCAGTTATTCTCCATCCTCTTAGATCTAGAAATGCTTTATGTTGTACACAACCTTTCCCTTCTTTACCTCTTCTCCTTTCCCTGCCTCTGGGTCTTTGAGGATTATGTGTGTAGCTCTCTGTTATTCAGCTACTTAACTCTTTCCTTTCCAG
Seq C2 exon
GTTCTTCTGGTTCTTTTAACCTCCCAAATTCTGGGGACATGTTCATGAACATGCAGAGTCTGAATGGGGATTCTTACCAAGGGTCCCAAGTCGGAGCCAATGTGCAATCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013314:ENSBTAT00000017706:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.330 A=NA C2=0.842
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(21.7=23.2)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCAACAAACGAATCAGGTACA
R:
GTGATTGCACATTGGCTCCGA
Band lengths:
262-1665
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development