HsaINT0120881 @ hg19
Intron Retention
Gene
ENSG00000105717 | PBX4
Description
pre-B-cell leukemia homeobox 4 [Source:HGNC Symbol;Acc:13403]
Coordinates
chr19:19672522-19674424:-
Coord C1 exon
chr19:19674318-19674424
Coord A exon
chr19:19672927-19674317
Coord C2 exon
chr19:19672522-19672926
Length
1391 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
CTCAGTCTCTGTCGTTTCAGGCC
3' ss Score
8.42
Exon sequences
Seq C1 exon
GCTCCTCTGGACCCTTCCCGCTGCCCAGCGCTGGGGACGCCTTCCTCACCCTGCGGACTCTGGCCTCTCTCCAGCCTCCTCCTGGGGGAGGCTGCCTGCAGTCCCAG
Seq A exon
GTGAGTCTCAGGCACTGTCCCACAGCGCCCAGGTGGGTGGTAGGTTCTCAGAAAGGGTCGTCTTGTCAGCCACCCCTCGGCCTTGGGGCAGCTTCCCCAGAGGTCCCAGCAGCCACACAGGCCATGCTGCGCGGCCACCTCTGGGGCACAGCTCTGCAGGGCCCCACTCTGTAATGACTGTGCCCTCCCCCACCTCCACTTGTCACCACGGCAGCCGCTGGGAACAGTCAGTGGGGATGAACCCCAAGATGAGGGCTTTGGCTGTGGAGGGGAAGGGCACCTCCTAGAGGACTGTGGGAGGACATGGTGTCCTTCCCTCGAGAGGGAGGGGCAGGCAGCCAGCAGAGGAGGCCGGAGGAGAGATGGGGCCTTCCCTCGGGCTCAGACCTCAGTGCCGCAGCTTGGCTGGGAAGGCAGCGAGTGGGGACCGTCTTGAAGACACTGAGGAGGCCCAGGTGTCATGTGCCCAGCACAGGCACGAGGCTGTGTGTGTGGTGTGTGCCAGGGCACTGCAGAGCCGGGTGCCCCTCCCAACTCACCACTCTCTCCCAGGGGTTCAGAGAACGGATGCCTCCTGTGCTGTCTGTGGGGTCCCACCTGGTCCTGGGAAGCACACGTCCCACACTGTCCTGCTGTGGCAGCTGCCCCCCATCACCATGCAGCCCCCAGCCAGGGACACACGTGAGGGGCCTCACCTTGCCCTTTGCACCCCTGGGACCTGACTACGCGCCAGCAGCTGTGTGTCCACCCCAGTTCAGAGCAGAGTGCCCCCAGGTGGTGCACCCGTCTGAGCTGCTCCCACACTCACGGGCAGAGCAGTCCCAGCCACTTCCTTAACCTGTACCGTGCCCACCATAGTGGGGGTGGGTCCTGTGGACAAACGTCTTAGCGCCGTTGGACGTGATGCCGTCTCTGCACTGCAGACAGAGCCCCCACCCCTTATGACAAGTGGTTGCCTCCCACCCTCCTTGCTGCCCAGCCAGGCCAGTGTTGGGCCAGGTTTCAGAGCCCCTTTTTCCCACCGAGTCTCACCATGACGCTCCGGGCGTCATCATGGGCTCCAGGCCTGACCTTGCCTCCCTGCCCCTCGCCGGGCAGGAGCCCTTGTTGTACCCGATGCCAGTCAGTCCTTTGCCTAAGCCCCAGGGAAGCCACTAGAGGCCAGTTTTCCTGCCGGGGAAGCTCGTCCATGTCCCATGTCAGGTGGCAAGGCCAGCTGTGACCCAGGACCGACCCCTCCATCCCTTCCCTCCTCCACTGAGCTGGAGGTCATCTGTGGATCTTTTCCAAGCCTTCCCAGGGACCCCTGGAGGCTCCGCCTGCAGCACGTGGGCTGGGTAGTCACCAGTCTCACGGCCACCCACTCTGATGCTCAGTCTCTGTCGTTTCAG
Seq C2 exon
GCCCAGGGTAGCTGGCAGGGGGCCACCCCCCAACCTGCAACTGCCTCACCTGCTGGAGACCCTGGCAGCATCAACTCCAGTACATCTAATTAAGTTTGGGGGATAAGCAGGAAAGAGCGCTGCGTGAGCTGCCATGTATCGCCAGCCGTTGCTTTGTTACTGAACGTGCCGCCGACGACCTCAGAAAACCCAGATGGGTGGTGGTGCCCATGAGCCCCTGCTCCTCAGCCAGGCCCGTGGCGCCGGCTCATGTGTCTGCTGCGACTCGAGATGGCCTGAAACGCCACTCATTCTCCCACTTCAGTTCGTTTTTTTGACAGTAATTTTATGGTAACGCTATGAATTGAATTGTCTGTTCTAGGACTGGGCACAGATTTTCCCATTAAAATTTTTGACTTATTTTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000105717-PBX4:NM_025245:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.750 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0044324=UCH=PD(8.2=55.6)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTCTCCAGCCTCCTCCTG
R:
GAAGTGGGAGAATGAGTGGCG
Band lengths:
345-1736
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)