HsaINT0120878 @ hg38
Intron Retention
Gene
ENSG00000105717 | PBX4
Description
PBX homeobox 4 [Source:HGNC Symbol;Acc:HGNC:13403]
Coordinates
chr19:19569449-19570299:-
Coord C1 exon
chr19:19570109-19570299
Coord A exon
chr19:19569585-19570108
Coord C2 exon
chr19:19569449-19569584
Length
524 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGG
5' ss Score
7.2
3' ss Seq
GAAGGCGGCTGTTTTTGCAGGCG
3' ss Score
4.94
Exon sequences
Seq C1 exon
GCCTGTCGTGAGTTCACCACGCACGTCACCAACCTCCTCCAGGAGCAGAGCAGGATGAGGCCTGTCTCCCCTAAGGAGATTGAGCGCATGGTCGGCGCCATTCACGGCAAGTTCAGCGCCATCCAGATGCAGTTGAAGCAGAGCACCTGTGAGGCAGTGATGACCCTGCGTTCGCGGCTGCTCGATGCCAG
Seq A exon
GTCAGGGCCTGTACGTACCCAAAACCTCAAGGGCCGGCTCTGAGGGACTGGAGGGAAATAGTGCTGGCTTGGGTTGAAGACAGCCCTGGAGGCTGTGTCTGCAGTCACGGTTGGAGGCCTCACAGCCTCTTGGGAAGAAGGCCTGAAGTATTGCTGTTTTCATTTTTATTTTATTTTGTATTTATTTATTTATTTATTTGAGACGGAGTCTCACTCTGGTGCCCAGGCTGGAGTGCAGTGGTGCGATCTCCACTCACCACAACCTCCGCCTCCCAGGTTCAAGCGATTCTACTGCTTCAGCCTCCCGAGTAGCTGGGATTACAGGCTCCCGCCACCATGCCCAGCTAATTTTTGTGTTTTTAGTAGAAACGGGGTTTCACTATGTTGACCACGCTGGTCTCGAACTCCTGACCTCAAGTGATTGCTGTTTTCAGAACTACTGGAAAATCATACTCAGAACTAGAGGTGGGGGTGGTACTGGAGTCCCAGCATATTAATGCCTACGAAGGCGGCTGTTTTTGCAG
Seq C2 exon
GCGCAAGCGGCGGAATTTCAGCAAGCAGGCGACGGAAGTGCTGAATGAGTATTTTTACTCCCATCTGAACAACCCTTACCCCAGCGAAGAAGCCAAAGAAGAGCTGGCCAGGAAGGGCGGCCTCACCATCTCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000105717:ENST00000251203:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.279 A=NA C2=0.239
Domain overlap (PFAM):
C1:
PF037928=PBC=PD(30.8=95.3),PF070286=DUF1319=PD(62.5=85.9),PF0004624=Homeobox=PU(0.1=0.0)
A:
NA
C2:
PF0004624=Homeobox=PU(75.0=97.8)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGTCGTGAGTTCACCACG
R:
CTGGGAGATGGTGAGGCCG
Band lengths:
326-850
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