HsaINT0120880 @ hg19
Intron Retention
Gene
ENSG00000105717 | PBX4
Description
pre-B-cell leukemia homeobox 4 [Source:HGNC Symbol;Acc:13403]
Coordinates
chr19:19674318-19675898:-
Coord C1 exon
chr19:19675742-19675898
Coord A exon
chr19:19674425-19675741
Coord C2 exon
chr19:19674318-19674424
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-PBX4:NM_025245:6
Average complexity
IR-S
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:
PF0076914=ERM=PD(12.4=37.7),PF0044324=UCH=FE(21.3=100),PF0004624=Homeobox=PD(21.7=24.5)
A:
NA
C2:
PF0044324=UCH=PD(8.2=55.6)
Main Inclusion Isoform:
NA
Other Inclusion 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
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)