BtaINT0108043 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013801 | PBX1
Description
pre-B-cell leukemia homeobox 1 [Source:HGNC Symbol;Acc:HGNC:8632]
Coordinates
chr3:4264597-4266118:-
Coord C1 exon
chr3:4266006-4266118
Coord A exon
chr3:4264687-4266005
Coord C2 exon
chr3:4264597-4264686
Length
1319 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
GTTGTTGTTCATCCGTTTAGGTG
3' ss Score
7.64
Exon sequences
Seq C1 exon
GTTCTTCCAGTTCTTTTAACATGTCAAACTCTGGAGATTTGTTCATGAGCGTGCAGTCACTCAATGGGGATTCTTACCAAGGGGCCCAGGTTGGAGCCAACGTGCAATCACAG
Seq A exon
GTAGGGACCCAGCCAATGTGCCGCCAGGTGAATGCCTTAGAGTCCAGGAGCCGTCAGTCGGACTGGCACTTCCTGCTTCTGTCCAGACAGAAAGAGACAGAGAGAGATGTAGAGACCAAACCTTACCAACAACCAAACCAAAACAAAGACAACCACTGTCGTGGGGAATCTTGTCCACACTTTGTGAATGCATTTGGCTCTGGCTTGTCAGTCATACGAGGAAGGCAGGAAAGGAGCAAGTGCAGGGTGAGGTGACTGAGGCAAGTGGACCCAGTGTATTCTTTGCTCACAAAAGGGAAAGGAAGGAGTTCACTCTGTCGGCTTGCTTTCCAGGTTTCTTTCTGGTTTGTTGGTTTTTCCACACTCAACGTTTGCCCAATATGGAGGTCATTAATGACTAGGCGCATACCTAAGTATTTCAGGGTTTCATTTTAACCTTTAAAGATACCCAGTCAGGTTGACTAAACTCATCTTTGTAGTCATCCTTGAGGTCAAGGGACTTGAGTTTCTGGTGACAAGTCTGGTCCATGCTGGGAAACAAAACTCAAGTCGTGTGGCGTAAGCCCTCAGCACGCCTTAGTCAGCAGCTTGCCTTCATGACAACTCAGAAGCCATCCTTCTGTGTGAGCACACAGCCTGACGTGACGGGGTGAAGTTGTGTGCTCTGGGTCAGGGTCGCTAGGACGATTCTGAGCCACGCCCACCCAGGGTCCCACCTGCGTGAGGAACAAGAAGCATTATGTGCCTGGAATACACCAGCTGGCTGGCGATTCAGCCCCTTGCTTTGGAAACATTGCCTGGCACCAAGTTTGAAGATACATAGTCAGGCTTTGTCCAAAAGACTAGACAACCGGCCATTATTTAAGTCCTCAAAAAGACAGCATTAGTCACACACTCTTCTCTCTGTGAGGCGGCTGGCTGGCCCTTCTAAACAGAACCTTGACTTTTATAAGCTCCTGAGCAAAGAAGTTGTATAGGACGATCTGGAAGGAAGGGAAAAATCTTTCAGCCTCCCCACTCACCCACTCCATCACCCAATCCCTGATGTCTTATGCAACAGTAGTTTCATTGTTGGGAAACCCAGCTTTCTTTGACCGTTTTTCTGTCTTGCTTACTAAGCTCAGAAAGGATAATGGATTTGGCAGAGAGTGGAGGCCCAGCCTCCTAATGGTTCCTTTCCCAGGAAGAATATCTCCAATGGTTGCAATCATTTGCAATTAATTTGGTGTGCCCAAACGGTAGCCTGTGTGCTGATGACCTGTGTCACTTACCTGCATCTCTCTGACTAATCTCCTCTCTGTTGTTGTTCATCCGTTTAG
Seq C2 exon
GTGGATACCCTTCGCCATGTTATCAGCCAGACAGGAGGATACAGTGACGGACTCGCAGCCAGTCAGATGTACAGTCCGCAGGGCATCAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013801:ENSBTAT00000018349:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.500 A=NA C2=0.733
Domain overlap (PFAM):
C1:
NO
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:
GTTCTTCCAGTTCTTTTAACATGTCA
R:
ATGCCCTGCGGACTGTACATC
Band lengths:
199-1518
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]