HsaINT0120877 @ hg38
Intron Retention
Gene
ENSG00000105717 | PBX4
Description
PBX homeobox 4 [Source:HGNC Symbol;Acc:HGNC:13403]
Coordinates
chr19:19570109-19570833:-
Coord C1 exon
chr19:19570586-19570833
Coord A exon
chr19:19570300-19570585
Coord C2 exon
chr19:19570109-19570299
Length
286 bp
Sequences
Splice sites
5' ss Seq
CAGGTGATC
5' ss Score
4.28
3' ss Seq
TGTCTGTGCTCCCACCCCAGGCC
3' ss Score
9.31
Exon sequences
Seq C1 exon
TGGTAAGCATCCGTGGCATTCAAGACGAAGATCCCCCTGACGCCCAGCTCCTGAGGCTGGATAACATGCTGCTGGCTGAGGGCGTGTGCAGGCCCGAGAAGAGAGGAAGAGGAGGAGCGGTGGCCAGGGCCGGCACAGCAACACCAGGTGGCTGTCCAAATGACAATAGCATTGAGCACTCTGACTACAGGGCCAAGCTGTCCCAGATCCGACAGATTTACCACTCTGAGCTAGAGAAATATGAACAG
Seq A exon
GTGATCTTTCTGCATGGAAGAGTTTCTGTCATGTGAATGCGCATTTGTCAAAGCGAAACACGGAACGCTAACCACCTTTCTTTCGTGGCGCAGAACAGGGAGTCCATGCAGTTGGTCGCTGCAGAGGTGGTCCATTGTTACTGAAAGCCCTTTCCATTTACTTAACAGTCACCCGCCGGTGTGTGAACTACAGGGGGTGGCAGGCGGCTGCTCCGCTGTGGAACCTGCTGCCCTGTGCCACCCTGCTGCCTAGTCACAGGCCGGCGTGTCTGTGCTCCCACCCCAG
Seq C2 exon
GCCTGTCGTGAGTTCACCACGCACGTCACCAACCTCCTCCAGGAGCAGAGCAGGATGAGGCCTGTCTCCCCTAAGGAGATTGAGCGCATGGTCGGCGCCATTCACGGCAAGTTCAGCGCCATCCAGATGCAGTTGAAGCAGAGCACCTGTGAGGCAGTGATGACCCTGCGTTCGCGGCTGCTCGATGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000105717:ENST00000251203:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.516 A=NA C2=0.279
Domain overlap (PFAM):
C1:
PF037928=PBC=FE(41.4=100),PF070286=DUF1319=PU(35.2=37.3)
A:
NA
C2:
PF037928=PBC=PD(30.8=95.3),PF070286=DUF1319=PD(62.5=85.9),PF0004624=Homeobox=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGCTCCTGAGGCTGGATAA
R:
GACCATGCGCTCAATCTCCTT
Band lengths:
298-584
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development