HsaINT0143234 @ hg19
Intron Retention
Gene
ENSG00000007376 | RPUSD1
Description
RNA pseudouridylate synthase domain containing 1 [Source:HGNC Symbol;Acc:14173]
Coordinates
chr16:837354-837744:-
Coord C1 exon
chr16:837556-837744
Coord A exon
chr16:837478-837555
Coord C2 exon
chr16:837354-837477
Length
78 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
TGGACTCTGTCCCACTCCAGGTT
3' ss Score
8.64
Exon sequences
Seq C1 exon
GCCGGCCATGGAGCCAGGCAGCGTGGAGAACCTGTCCATCGTGTACCGGAGCCGCGACTTCCTGGTGGTCAACAAGCACTGGGACGTTCGCATTGACAGCAAGGCGTGGCGGGAGACTCTGACCCTGCAGAAGCAGCTGCGGTACCGCTTTCCCGAGCTGGCCGACCCTGACACCTGCTACGGGTTCAG
Seq A exon
GTAGGGGGGGCGGCCGGAGCCCCACGGTGGCGTCTGTGGAGGAAAGTGGCTCAGACTCTGGACTCTGTCCCACTCCAG
Seq C2 exon
GTTCTGCCACCAGCTGGATTTCTCCACCAGCGGGGCGCTGTGCGTGGCCCTAAACAAGGCAGCCGCCGGCAGCGCGTACAGGTGCTTCAAGGAGCGGCGCGTGACCAAGGCTTACCTGGCATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000007376-RPUSD1:NM_058192:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0160011=Corona_S1=PU(45.5=98.4),PF0084917=PseudoU_synth_2=PU(26.5=72.1)
A:
NA
C2:
PF0160011=Corona_S1=FE(31.1=100),PF0084917=PseudoU_synth_2=FE(24.7=100)
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:
GGAGACTCTGACCCTGCAGAA
R:
CTCCTTGAAGCACCTGTACGC
Band lengths:
172-250
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)