HsaINT0120862 @ hg38
Intron Retention
Gene
ENSG00000185630 | PBX1
Description
PBX homeobox 1 [Source:HGNC Symbol;Acc:HGNC:8632]
Coordinates
chr1:164820072-164821626:+
Coord C1 exon
chr1:164820072-164820184
Coord A exon
chr1:164820185-164821536
Coord C2 exon
chr1:164821537-164821626
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:ENST00000420696:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.468 A=NA C2=0.624
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=PD(4.1=6.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
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