HsaINT0132655 @ hg19
Intron Retention
Gene
ENSG00000110844 | PRPF40B
Description
PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:25031]
Coordinates
chr12:50036710-50037180:+
Coord C1 exon
chr12:50036710-50036799
Coord A exon
chr12:50036800-50037005
Coord C2 exon
chr12:50037006-50037180
Length
206 bp
Sequences
Splice sites
5' ss Seq
TCAGTGAGT
5' ss Score
7.68
3' ss Seq
GTATCTGCTGATCTGCCCAGGGC
3' ss Score
5.38
Exon sequences
Seq C1 exon
CAGACTGAATGCCAGCACCTCCACACCAAAGGCCGAAAGCATGGCAGGAAAGGCAAGAAGCACCATCACAAGCGTTCCCACTCACCCTCA
Seq A exon
GTGAGTAAGCGTGTAGAAGGGACATGGGGTGAAGCTGGGTTGTTTTGGGGAAATAAACACTTTGTTTTCCCCTTACAATATCTCCCTTGGAGGGAAGTTTGAGGATTCCTTTGGCCCTGGGTCCTCCTCCTCTCTCGAATTCCCAGACGAGGGCTTCTGGAGGGCAGAGAACCTCTGCACTGACATGTATCTGCTGATCTGCCCAG
Seq C2 exon
GGCTCTGAGTCAGAAGAAGAGGAGCTGCCCCCACCATCTCTCCGGCCCCCCAAGCGGAGGAGGCGGAACCCCTCAGAGTCAGGCTCTGAGCCCTCTTCCTCACTTGATTCAGTTGAAAGTGGGGGTGCTGCCCTTGGAGGACGGGGCTCCCCTTCCTCCCATCTTCTTGGAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000110844-PRPF40B:NM_001031698:21
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.933 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
CAGACTGAATGCCAGCACCTC
R:
TGCTCCAAGAAGATGGGAGGA
Band lengths:
264-470
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)