HsaINT0120869 @ hg19
Intron Retention
Gene
ENSG00000167081 | PBX3
Description
pre-B-cell leukemia homeobox 3 [Source:HGNC Symbol;Acc:8634]
Coordinates
chr9:128509617-128510902:+
Coord C1 exon
chr9:128509617-128509932
Coord A exon
chr9:128509933-128510828
Coord C2 exon
chr9:128510829-128510902
Length
896 bp
Sequences
Splice sites
5' ss Seq
AAAGTTGGT
5' ss Score
1.99
3' ss Seq
TTTCGTTATTTGTTTTTTAGGAA
3' ss Score
11.13
Exon sequences
Seq C1 exon
GCGGCCGCCTCCCCCTCCCCCTCCCCCTCTTTCTTCTCCTCCCTCGTCGCCGCCGCCGCCGCCGCCGCCTCAGCCTTCGCCTCAGCCGCCGCCCGCTCCCGCCCGCGCGCGGCGGGATGGACGATCAATCCAGGATGCTGCAGACTCTGGCCGGGGTGAACCTGGCTGGCCACTCGGTGCAGGGGGGCATGGCCCTGCCGCCTCCCCCGCACGGCCACGAAGGGGCGGACGGCGACGGCAGGAAGCAGGACATCGGCGACATCCTCCACCAGATCATGACCATCACCGACCAGAGCTTGGACGAGGCGCAAGCAAA
Seq A exon
GTTGGTGTCGTCTCATTAAGCATCTTTTGTGTGTGTGCGGGAGCCGGGCCCGCGGCCGAGTCGAGGCCCGGGGTGGCGCCCGGGGCTAGGGCCGCAGCCCCCGGCGGGGAACTTTCTCCGAAAGCCGGCCGCCCGCCCCGGCCTCGGGGGGACTTGCCCGCGCCCCCCGAAGCGGGCGGGAGTCGGCAAAGTTGCTCTGGGGGGCTCGGGACGGACTCGGTGCGGCGCGGATTCCGTGGCGTCCTTTCCCCCGTCCTGCCCCTCGCAGCCCGGCCCCCTCCCAGGGATTTAAACCTCCCGCCCCGACCCCGTGCGGGCCGCGCCGCCGGGAAGTGTAACTTTCTCCTCCGGCGGGGAGTCCCGGCGCCGGCTCCCGCGGCCGCGGGACGACCTCGCGATGCGGGCGGCCACCCGGGCCCGGCGCGGGGCGATGGGCGGTTCCCTGGCGGGTCCGGGTGCGGACGGCCAAGTTCTCGGAGAGGGAGGGCCGCCTTGCAAACTTTGCCGAGCTGTCACCCTCCCGCTGGCCGCAGTCGGCCGGCCTCCTCTGCACAGGAGCGGACGCGGGAGCCCCTCCGCACCCGTCCCCTCCCCCGGGTCGCCTTCGCCTGCCCCCGGGGCGAGGCTCCCCGCGCGGGTTCGCGTCGCGTCTGCAGTGGCCGAGGCTGCTGCCTGCCGGGCAGATGGGTCCGCCTTGTTCCGGCTGCAGCTTTCGCCGCCGGGGCTTGCTGGCTGTCGGGAACTAGTCAACTGGAGTTTTTGTTGACTTCCCACGGTTCAAAAGGGCCTTCCAGAATGGGGGGCTGGAATTAAATCTTGGGTCTAACTTAAAGGAAGGCGCCATATTATTCCATAGGTGATGCTAATACCTTTGTGTTTCGTTATTTGTTTTTTAG
Seq C2 exon
GAAACATGCCCTGAACTGTCACAGAATGAAACCAGCGCTCTTCAGCGTCCTGTGTGAGATCAAAGAGAAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000167081-PBX3:NR_024123:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.748 A=NA C2=0.146
Domain overlap (PFAM):
C1:
PF037928=PBC=PU(14.7=43.3)
A:
NA
C2:
PF037928=PBC=PU(10.1=94.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCCCTCTTTCTTCTCCTCCC
R:
TCTCACACAGGACGCTGAAGA
Band lengths:
353-1249
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)