HsaINT0132660 @ hg19
Intron Retention
Gene
ENSG00000110844 | PRPF40B
Description
PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:25031]
Coordinates
chr12:50026379-50026663:+
Coord C1 exon
chr12:50026379-50026406
Coord A exon
chr12:50026407-50026637
Coord C2 exon
chr12:50026638-50026663
Length
231 bp
Sequences
Splice sites
5' ss Seq
GCTGTGAGT
5' ss Score
7.39
3' ss Seq
ATCCTTTGGCTTTTTTCTAGCTG
3' ss Score
7.23
Exon sequences
Seq C1 exon
ACGGCTCCGGGTGCGGACACCGCCAGCT
Seq A exon
GTGAGTCTTCTGGGGGCCTGCTCCCCCCAGGCTCGGAGGTTGGGGGGCATAGGGGAGAGGGGACCGTGGACTGGAGCCCACCCTGGATCATGCCTGTTGGGATGCCAAGGAGTCTGGGATATTGATGGGACCAGGGGACTATTTACTGGGGCTGGAATACGGGAGGCATAGGTGGGAATAAGATGGAGGTCGGAGCAAGGACTTAGTATGTATCCTTTGGCTTTTTTCTAG
Seq C2 exon
CTGCTGTGGCTGGGACAGGCCCTCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000110844-PRPF40B:NM_001031698:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0039721=WW=PU(3.2=11.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)