HsaINT0132652 @ hg19
Intron Retention
Gene
ENSG00000110844 | PRPF40B
Description
PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:25031]
Coordinates
chr12:50036018-50036458:+
Coord C1 exon
chr12:50036018-50036155
Coord A exon
chr12:50036156-50036362
Coord C2 exon
chr12:50036363-50036458
Length
207 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGG
5' ss Score
4.94
3' ss Seq
CAGTGCTCTCCTCGTTCAAGGTC
3' ss Score
6.59
Exon sequences
Seq C1 exon
CTGCTGGAGAAAGCAGAGGCACGGGAGAGGGAGCGGGAGAAGGAGGAGGCACGCAGGATGCGGCGCAGGGAAGCTGCCTTTCGAAGCATGCTGAGGCAGGCTGTGCCTGCTCTGGAGCTAGGCACTGCCTGGGAAGAG
Seq A exon
GTCAGGAGCGTAGCCTGGCCCCAAGCACCCCTCAAGCCTGAGGGCAGCGGTGCTTCACCACTGAGGGCCCACCCCAGTCACGTCACAGCCCTGGGCCAGCTCCAGTTCCCTTCCTTTCTCTGCCCCAGCCCTGCCCTGTGCTCATGGCGGTGTCCAGGCCAGGCTGAGTGGGGCCTAGTCTGATCAGCAGTGCTCTCCTCGTTCAAG
Seq C2 exon
GTCCGTGAGCGTTTTGTGTGTGACTCAGCCTTTGAGCAGATCACCCTGGAGTCGGAGCGGATCCGGCTCTTCCGGGAGTTCCTACAGGTGCTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000110844-PRPF40B:NM_001031698:19
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.322 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0184614=FF=PU(46.2=52.2)
A:
NA
C2:
PF0184614=FF=PD(50.0=81.2)
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:
CTGGAGAAAGCAGAGGCACG
R:
TCCAGCACCTGTAGGAACTCC
Band lengths:
230-437
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)