HsaINT0120862 @ hg19
Intron Retention
Gene
ENSG00000185630 | PBX1
Description
pre-B-cell leukemia homeobox 1 [Source:HGNC Symbol;Acc:8632]
Coordinates
chr1:164789309-164790863:+
Coord C1 exon
chr1:164789309-164789421
Coord A exon
chr1:164789422-164790773
Coord C2 exon
chr1:164790774-164790863
Length
1352 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
GTTATTGTTCATCTGTTTAGGTG
3' ss Score
7.72
Exon sequences
Seq C1 exon
GTTCTTCCAGTTCTTTTAACATGTCAAACTCTGGAGATTTGTTCATGAGCGTGCAGTCACTCAATGGGGATTCTTACCAAGGGGCCCAGGTTGGAGCCAACGTGCAATCACAG
Seq A exon
GTAGGGACCCAGCCAATATGTCACCAGGTGAATGCCTTAGAGTCCAAGAGCCCTCAGTTGTATTGGACTTCCTGCTTCTGTCCAGAGAGAGAGAGAAAAACAGATCAGAACCAAAACCTTACCAACGACCGAACCAAAATCAAGACAACCATTGTCATGGGGAATCTCGTCCACACTTTGTGAATGCATTTGGCTCTGGCTTTTCAGTTGTACTTGGAAGGCAGGAGAAGAACAGTAAGCACAGGGCAAGGTGACCGAGACACATCAGGCAGGTGGAACCAGCATATTCTTTATTCACCAAAGGGAAAAGGAGGAGGTGTTCAGGATGTTACCTCAATTTCCAGGTCTCCCTCTCATGTGTTGGTTTCTCCTGCTCAATATTTACCATATAAAGAGGCAATTAACAAGCAAGCAAATATATTACTATCGGACGTTTTCATTTTAAGCTTTAAAAACACCCAGCCAGGTTGACTAAATACATTTCTTAGTCATCCTTGAGGTCAAGGGACTTGAGTTTCTGGTGATGAGTAGAAGTCCACATTGGGAAGCAAAATCAAGCCATGTGATATCAAATTTTAGTGTTCCATAGTAAGCAGATTTCCTTCATGATACTTGAAGAAGCCATCCTACTACCTCAGCATGAAACATGTTGTGAGAGGGTAAAGTAGTATGCTGTGGGTCAGAATTACTAGGGAAGTTCTGAGCCATGTCAGCCTAGTTTCCCACCCTCCATGTGGAACAAGAAGCATTACAAGCCCGGAACAGACCAACTGGTCAGCGATTCACCCCTTTCTTGAGAAACATTGCCTGGAAACCAGTTTGAAGTGATATGGTCAGGCTTTGGTCAAGTGACTAAACAACTGGCCATCACTTAAGTCCTCAAAAAATACAAGGTCTCAATCAAGTACTGCTCTCTCTGTGAGATGGCTGCCCAAACCTCCTCTAAACAGAACCTTTGTTTTTATAGGATACCCAGCAAAGGAACAGCTGTATAGGATGACCTGTAGGGAAGAAAAATGGGGAGAAAAGAAAATTCCTTCATGCTTTCCCCTCCAGCTCCCTCTATCATCCTAATCCTTACCATCTCATGCAGACTTGTTGAACTAGTTTCAATGTGGAGATCCCAGTTTTCTTTTACCATTTTACGTCTTGCTTACTGAACTCAGAATTCTTTATGGATTGGCATACGGAGGAAGCTAGCCTCCTCCTAATGGACTCTCCCAGGACAACTGTCTCCAAAATGATTGCATTAATATGGCATGCCCAAATGGTGGCCTGCCTGATGATGATCTGCCTCCCTTTTCCTACACCTCTCTGACTAATTTTCTCTCTGTTATTGTTCATCTGTTTAG
Seq C2 exon
GTGGATACCCTTCGCCATGTTATCAGCCAGACAGGAGGATACAGTGATGGACTCGCAGCCAGTCAGATGTACAGTCCGCAGGGCATCAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000185630-PBX1:NM_002585:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.500 A=NA C2=0.783
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0157913=DUF19=FE(17.6=100),PF0004624=Homeobox=PD(4.1=6.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTCTTCCAGTTCTTTTAACATGTCA
R:
ATGCCCTGCGGACTGTACATC
Band lengths:
199-1551
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)