HsaINT0132651 @ hg19
Intron Retention
Gene
ENSG00000110844 | PRPF40B
Description
PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:25031]
Coordinates
chr12:50031253-50031607:+
Coord C1 exon
chr12:50031253-50031367
Coord A exon
chr12:50031368-50031515
Coord C2 exon
chr12:50031516-50031607
Length
148 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGG
5' ss Score
10.17
3' ss Seq
CCCTCCCTCCCTCCTTACAGGCT
3' ss Score
12.45
Exon sequences
Seq C1 exon
ACCTTCCTGGACGAGCTGCATGAGACAGGGCAGCTGCACTCTATGTCCACCTGGATGGAGCTATATCCAGCAGTCAGCACTGATGTCCGCTTTGCCAACATGCTGGGCCAGCCGG
Seq A exon
GTAAGGCAGCCAGGCTCCCCCTTCTCTGGCCTGGCTTCCTGCCCTGCCAGCCTCTCTGCACCCCCTACTACCGGCTCCTGTCCTCGGCCCAGCCCCCAGGCCTTGGGAAGCTGCCGCCCGCCAGGCCCCCCTCCCTCCCTCCTTACAG
Seq C2 exon
GCTCCACCCCTCTGGACTTATTCAAGTTCTATGTGGAGGAGTTGAAGGCACGATTCCATGATGAAAAGAAGATCATTAAGGACATCCTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000110844-PRPF40B:NM_001031698:16
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF091066=SelB-wing_2=PD(48.8=51.3),PF0184614=FF=FE(67.9=100)
A:
NA
C2:
PF0184614=FF=PD(17.9=32.3)
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:
CCTTCCTGGACGAGCTGCAT
R:
AGGATGTCCTTAATGATCTTCTTTTC
Band lengths:
202-350
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)