HsaINT0143237 @ hg19
Intron Retention
Gene
ENSG00000007376 | RPUSD1
Description
RNA pseudouridylate synthase domain containing 1 [Source:HGNC Symbol;Acc:14173]
Coordinates
chr16:834974-836928:-
Coord C1 exon
chr16:836827-836928
Coord A exon
chr16:836378-836826
Coord C2 exon
chr16:834974-836377
Length
449 bp
Sequences
Splice sites
5' ss Seq
CGGGTGTGT
5' ss Score
5.31
3' ss Seq
GCACCGCCCTCATCCCGCAGGCC
3' ss Score
11.03
Exon sequences
Seq C1 exon
GTTGTGAGAACCCAAAGCCAAGCCTCACAGATCTCGTGGTTCTGGAACACGGGCTGTACGCAGGCGATCCTGTCTCCAAAGTGCTGCTGAAGCCGCTCACGG
Seq A exon
GTGTGTCTGGGGTGGGCGGTGTCCTGGTGGTGACAGAAGGGAAACTGAGGCACAGGGCCACGAAGCTTATGTTGGGCCACCCTGAGCATCAGGGCAGAGCTGGCAACAAGCACTCCTGCGTTCTTAACTCCACGCCCTGCAGCCTCTCAGCTTCTCACCTGACACAGGGTCCCTGCTGGCTCCTGACTGATTCCTTGGGGGTCTGGCTGGCCTAGATTCTCCAGGACCGAGCACCACCCTGGCCCTGTCCTCACCAGTGGTGACCTGAACACAATCTTCTGTCCTAAATACTGTCATCCTCACTCATGGCAGGGGACAGGGAGAGTTCCACCCCAAGAGGCTGCTTCAAGACTGCAGCGGGGTCATGACGGGAGGTGGGTCCTGGTCAGGGAGATAGGTGTGGATCGGCCCCGCTCCCAGCTTGATCCGGCACCGCCCTCATCCCGCAG
Seq C2 exon
GCCGGACACACCAGCTGCGCGTGCACTGCAGTGCCCTGGGCCACCCCGTGGTGGGCGACCTGACCTACGGAGAAGTCTCGGGCCGGGAGGACCGGCCGTTCAGAATGATGCTGCACGCTTTCTACCTGCGCATCCCCACGGACACCGAGTGTGTGGAGGTCTGCACGCCTGACCCCTTCCTGCCCTCCCTGGATGCCTGCTGGAGCCCCCACACACTGCTGCAGTCGCTGGACCAGCTCGTGCAGGCCTTACGGGCCACCCCCGACCCTGACCCCGAGGATAGGGGCCCCAGGCCAGGCAGCCCCTCCGCACTCCTGCCTGGGCCCGGCCGGCCTCCTCCACCCCCAACCAAGCCCCCTGAGACTGAGGCACAGCGGGGCCCCTGCCTGCAGTGGCTGTCGGAGTGGACGCTGGAACCGGACAGCTGAGAGCCGTGGGGCTGGGGCAGGGGGTGTCAGCTGCACAGCGGGACTCTAGGGAGATGGGCGAGCGAGCGTCTGCTCACTGGCTCTGGGGCCTCGAGGTGCCAGGCAGCATCAGGCCCACTGGGTTGCCCCGGCCAGGCCTGCGAGGAAGGGCTGAGGTGGGGCCGGCAGGGGGCGCCAGGCAGCCGTGATCACAGGTGACGACCGCACCGCGGCCGTGGGACTGATGCGGGATCCCGAGGGCCTTCCTGCCCACATGCCCCGGGAGAAACCGAGGCCCCTCCCTCCTCCTGGAACAGCTTCCGGCTCTCAAGCGTCACCCCAGGGGCGTCAGTTTTACGGACTCAAGGTCACCTCAGGAAGAGGCAGGGCCAGGTTTTGGGATAGGCTTTGCCTCCAGGATGGGCTGCTCCTGGGCCTGGTGAGCTACTGCCCCCAACCTACCCTCTAGAGGGGCTGGGAAGGGCCGTTCTGGGCTCACCTGGCCTGGGAGACCCATCTGGTCCCTGCGTCCTCTGCCCCTCACTGCTCTGTGCAGATCCTGTCGCCCTCAGCTGCCTCCTCCCGAGACCTAATGGTCCCTGCTGGGCTCGAGTCTGCAGGCCCGGCTGCGTGTGCCTTGGCCTCACTGTACCAGTGGTTCCCTCTCTGCCCGGATTCTGAGCTCAGTGTGGTGTTTGGTGCACAGGGGTTGGTCAGGGGCCATGGCCAAGGCCCTGCCACGCACGCCCATCCCTCAGATCCACTGTGAGCACCAACCTGCTGCAGTCTCTTGGGCCCCTGCTGGCAGCTCTGCCACGTCACCGCCTGCCTGGCTCCCACACAGCCATGCATTGTCACTCTGCCTCCGGGACCCCAGCTTGGGAGCTGTGGGTCTGCCAGGTCCCACCTCCTCTGTCCCCCATGCCACAACCTGGGCTCCTGGCTACAGCAGGGCTCCAGGGACTCCAAATAAATGTTCAGTGACTGGCTCCAAGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000007376-RPUSD1:NM_058192:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.437
Domain overlap (PFAM):
C1:
PF0160011=Corona_S1=PD(13.4=53.3),PF0084917=PseudoU_synth_2=PD(16.3=56.7)
A:
NA
C2:
PF0084917=PseudoU_synth_2=PD(6.6=7.7)
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:
GTTCTGGAACACGGGCTGTAC
R:
CTATCCTCGGGGTCAGGGTC
Band lengths:
347-796
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)