DreINT0110762 @ danRer10
Intron Retention
Gene
ENSDARG00000013615 | pbx3b
Description
pre-B-cell leukemia homeobox 3b [Source:ZFIN;Acc:ZDB-GENE-000405-3]
Coordinates
chr8:33942284-33943676:-
Coord C1 exon
chr8:33943486-33943676
Coord A exon
chr8:33942420-33943485
Coord C2 exon
chr8:33942284-33942419
Length
1066 bp
Sequences
Splice sites
5' ss Seq
CAGGTTGGT
5' ss Score
8.08
3' ss Seq
TCCAACTTGTCCAACGGCAGACG
3' ss Score
4.58
Exon sequences
Seq C1 exon
GCATGTAATGAGTTCACTACCCACGTAATGAACCTGTTGAGGGAACAGTCTCGCACACGGCCCATCTCGCCCAAAGAGATTGAACGCATGGTCAGCATCATTCATCGCAAATTCAGCTCCATCCAAATGCAGCTTAAACAGAGCACCTGTGAGGCTGTCATGATCTTGAGGTCCCGCTTCCTTGACGCCAG
Seq A exon
GTTGGTGTCCTCAATTTTATTTGATTTTTTTTAGAATGTGCATGTACAAATTATTCTCACTTGTGTTTGAAAGAATATATCTTCTACTTATCATCTGCAGATATATGTTATTCAAAATGACAACTCATAATTGCATTTATAGAAACACAGAAAGTCTTGGTACTTTGTTTCTTGAATTGTTTCTTGAAGTATGAACTTTTAACCTACATACCCAGGGTTAAGGCAATCCCACTGATGGAACGGCACCTGTTATAAGCCATGAGCAATAATGTATTCAGCATTATTCAACCACTAGCGGTTAAGATGGGGTGTTGCCAAGACAAGGGTTTTAGAGCTTAGAGGCCATCCACCGAACACAGTCATGCTAAGCACCTGAAAGCAGTTAAGAGTTTTATAGAGTGGAAATGAAGTCATTTGCGTTTGGTGGGTAGGAGGTCATCAGCAGGTGGTCCAGATTACTGTAATCACAAACAGTTGGTAGAGGAGATCTGGAGAGGCGTACAGGGGAGAGAAATGATGCAGTGAACAAGAGAAAAGAGTGGATGAGGTCTCGAGGAGAACACTCAAGTGAAGCGGAAGCACAATCGTTTGGCCGGCCACTCGTGTGAAAGGCATTAAACAAGGCGAGAGAAAGAAGCCAGCGCTTAACCGCGGTGGGGTGGGCTGCTGCAGTGAGTGGCGGTAAGTGCAACTCCATCAGGCCCTGCCCCAGTACTTGAGGAACAGTGTTCAGCTGGCCATGGCTTGATTTCCCTAATGTCCCAAGATACAGCTCTGACTGGGAATGCTTGAGCACCTCTAAACGCCCCCATCAGAATGAAAGCACAAGAGAGAGAGAGGGAACGCTTGTCGCTCTAAACACTGAACATTTCACGCTTCGCTTAAAGCTCAACTGATAACGTAACAATGTCCATTTGCGCGTCTACATATGTATTCCGATAATAGCCTTCCCGACTTCATTTCCTGCCAGCAGCTTCATTATGAGTTTGGCCATCTCACAAGGTTTTATTTGAGTCTCTAATTGCCTTCCTCCTCTTGTTTCCCTCTCCAACTTGTCCAACGGCAG
Seq C2 exon
ACGGAAACGGCGGAACTTCAGCAAGCAGGCGACCGAGATCCTGAATGAGTATTTTTACTCGCATCTTAGTAACCCTTATCCCAGCGAAGAGGCCAAAGAGGAGCTGGCTAAGAAGTGCAGCATAACAGTATCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000013615:ENSDART00000105204:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.227 A=NA C2=0.025
Domain overlap (PFAM):
C1:
PF037928=PBC=PD(31.0=95.3),PF0044324=UCH=FE(22.1=100),PF070286=DUF1319=PD(55.9=81.2),PF040917=Sec15=PD(63.4=81.2),PF0004624=Homeobox=PU(0.1=0.0)
A:
NA
C2:
PF0044324=UCH=FE(15.8=100),PF0004624=Homeobox=PU(75.0=97.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATGTAATGAGTTCACTACCCACGT
R:
CTGGGATACTGTTATGCTGCACT
Band lengths:
326-1392
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]