HsaINT0120880 @ hg38
Intron Retention
Gene
ENSG00000105717 | PBX4
Description
PBX homeobox 4 [Source:HGNC Symbol;Acc:HGNC:13403]
Coordinates
chr19:19563509-19565089:-
Coord C1 exon
chr19:19564933-19565089
Coord A exon
chr19:19563616-19564932
Coord C2 exon
chr19:19563509-19563615
Length
1317 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
CCGGCTCCCATCTCTTCCAGGCT
3' ss Score
9.64
Exon sequences
Seq C1 exon
GTCTCTAACTGGTTTGGCAACAAAAGAATCCGGTATAAAAAGAACATGGGGAAGTTTCAAGAAGAGGCTACCATTTACACGGGTAAAACGGCTGTGGATACCACGGAAGTTGGGGTCCCAGGGAACCACGCCAGCTGCCTGTCAACACCTAGCTCCG
Seq A exon
GTGAGTGAGGCTGGCCCAGGGACAGTCATCTGTACCCATGTGGACGGCCACTGAGCTGCATCTGGGGAGGCCACAGTGGGACCACATCTCCCTTCCCCCAGTGGTCAACTCTGTGTAACTCTTTCTTCTGTTTCAACTGTGAGAGTTCTGTTCCTCTTGGCCATGATCCCAACCAACAGATACCTGTGCTTTGGGGACAGAATGGCGATACTAATAAGAAAAGACATGAAAGGTCTGGGTGCGGTGGCTCACACCTGTAATCCCAGCATTTTGGGAGGCCAAGATGAGTGGATCACCTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCCTGTCTCTACTGAAAATACAAAAAAAATTAGCCCGGCATGGGCTGGGTGCAGTGCCTCACACCTGTAATCCCAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATAGAGACCATCCTGGCTAACACAGTGAAACCCCATCTCCACTAAAAATACAATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTAGGGACATGGATGAAACTGGAAATCATCATTCTCAGTAAACTATCGCAAGAACAAAAAACCAAACACCGCATATTCTCACTCATAGGTGGGAATTGAACAATGAGAACACATGGACACAGGAAGGGGAATATCACACTCTGGGGACTGTTGTGGGGTGGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGACGAGTTAGTGGGTGCAGCACACCAGCATGGCACATGTATACATACGTAACAAACCTGCACATTGTGCACATGTACCCTAAAACTTAAAGTATAATAATAATAAAAAAAAAGAAAGAAAAAACAAATTATCTGGGCGTGGTGGTGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGTGTGAACCTGGGAGGCAGAGCTTGCAGTGAGCCAAGATCGTGCCACTGCACTCAAGCCTGGGTGACAGAGCGAGACTGTCTTAAAAAGAAAAAAAAAAGACAAGCCATGAGGGGACATGAGTAGTGTGGTGGGGAGGGCCCGCTGGCCTGCCTGGGTGGGGGCTGAGGAGCAGAGGCCGGATGCTGAGGAGGGGCAGGAGCCACATTCGAGGCCTCCTGCCGGCTGAGGGGCTGGGTGGGTTCCACCTGAGGAGGCGCCACGACTCTGCCCACCCCGGCTCCCATCTCTTCCAG
Seq C2 exon
GCTCCTCTGGACCCTTCCCGCTGCCCAGCGCTGGGGACGCCTTCCTCACCCTGCGGACTCTGGCCTCTCTCCAGCCTCCTCCTGGGGGAGGCTGCCTGCAGTCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000105717:ENST00000251203:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.528 A=NA C2=0.750
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(21.7=24.5)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCTCTAACTGGTTTGGCAAC
R:
TCCCCCAGGAGGAGGCTG
Band lengths:
246-1563
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