HsaINT0120867 @ hg19
Intron Retention
Gene
ENSG00000167081 | PBX3
Description
pre-B-cell leukemia homeobox 3 [Source:HGNC Symbol;Acc:8634]
Coordinates
chr9:128722963-128724493:+
Coord C1 exon
chr9:128722963-128723128
Coord A exon
chr9:128723129-128724380
Coord C2 exon
chr9:128724381-128724493
Length
1252 bp
Sequences
Splice sites
5' ss Seq
CCGGTGCGT
5' ss Score
9.74
3' ss Seq
CTTAACTCTTTCCTTTCCAGGTT
3' ss Score
11.89
Exon sequences
Seq C1 exon
GTATCCAATTGGTTTGGCAACAAACGAATCAGGTACAAGAAGAACATTGGCAAGTTTCAGGAAGAAGCCAACCTCTATGCTGCAAAGACGGCCGTGACAGCTGCACACGCAGTAGCAGCAGCTGTGCAGAACAACCAGACCAATTCGCCCACCACACCAAATTCCG
Seq A exon
GTGCGTACTGGGGGCTCGCTCCCCAACTGGCCCAGGCAGCCTTATGCCACAATGCCCTGTCCCACAGGCCAGGAAACAAGAGCCATACTGAGGACAGAGTGGACTTAAAAAGGAAGATTTATGTTCAAATGCAGGCTTGTTCTTGAGATGGGTGAATGAGTGGAAGGTCAGAGCCTGTAAACCCACTCTTCACAGTGAATGCCACTCACTAGTAGATTATGGAAGTTTTACAATTAGTAGTGGCTTTCAGTTCAGTAATTAGGCAGAGTGCTATCGCTCATGACTATTTTAGCTATTTCTTTCCAGATACCACTTTAGGGTCAGTAGTGGTCTGTGGAGAGTGAAATAGCAGAAGTGGGAAATGCAGCAGTTGCTGTGTGTGAGGAAGCTGGAATGCTGGAGGGAAGTGCAGCAGTGCTTTCTGCCCAGCACCGCTGTCCTTTCTCTGCCTTTCAGCAGCACTGTCTGAGCGGGGCTGACGGCATGCTCAGCAGGTGGCTAGCTGTGAGGGTTATGGTGCTTAATACATGCATGCAAGATTCTTGGATCCTCGTCCGGTACATTTTGGCTGCATTTTATGTGACGTTTGTGAGGGGGTTAGAAATACTTTAAAATTTCAGGGAACTTGAATAACAATGAAAGATGTGCAGCTAGTCCAAACAGATGGACTTCAGTAGCAATTCCAGGGGCGTTTCTGAGAAGGTCTCTTAGCTATATCTTTAGAAGTTCAGAAAGTAGGGGGGTTTTTGTTTGTTTTGTCTTGTCTCCTCACCCCCCAGTTCTTTTTAATGGCACATAAAAACAGATGAAAGGAGAGGGAGGTATATGCATAGCGAAGAAAGAGCTCCTGGAAAAGTCTCTTCTCTGGGTGGCTGTCCACTGTGACAGCCATGTTGACAAGCTCGTGTAATGACTAAATCCTGGAGATGAGTGGAAACAAGGGGAAGGGTCCAGGCCAGCTGCTGGGTGTTTTGGTTTATTTTTTCTTTTTAATTTATTTTGATTTGTCTCTTTGTTTTTGCTTTTGTTTTTTAAGTTTGGGCTTCCCCACTGATGGGACTTCTCCTAGATGTGGAGTGACTCACAGGACCCAACTCTCTGGAGTTACTCTCCATCCTCTTAGATCTGGAAATGCTTTATGTTGTGCACAGCCTTTCCCTTCTGTACTTTTTCTCATCTCCCTGCCTCTAGGTCTTTGAGGATTATGTGTGTAGCTCTCTGTTATTCAGCTACTTAACTCTTTCCTTTCCAG
Seq C2 exon
GTTCTTCTGGTTCTTTTAACCTCCCAAATTCTGGGGACATGTTCATGAACATGCAGAGTCTGAATGGGGATTCTTACCAAGGGTCCCAAGTCGGAGCCAATGTGCAATCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000167081-PBX3:NR_024122:5
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.334 A=NA C2=0.875
Domain overlap (PFAM):
C1:
PF057036=Auxin_canalis=FE(32.2=100),PF0004624=Homeobox=PD(21.7=23.2)
A:
NA
C2:
PF057036=Auxin_canalis=PD(10.5=47.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCAACAAACGAATCAGGTACA
R:
GTGATTGCACATTGGCTCCGA
Band lengths:
262-1514
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)