HsaINT0132662 @ hg19
Intron Retention
Gene
ENSG00000110844 | PRPF40B
Description
PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:25031]
Coordinates
chr12:50026797-50027330:+
Coord C1 exon
chr12:50026797-50026907
Coord A exon
chr12:50026908-50027209
Coord C2 exon
chr12:50027210-50027330
Length
302 bp
Sequences
Splice sites
5' ss Seq
GAGGTCCTG
5' ss Score
-2.13
3' ss Seq
CCTATCCCATCCACTTGCAGCTG
3' ss Score
10.68
Exon sequences
Seq C1 exon
AGGGCCCTATGGAGTGAGCATGTGGCCCCAGATGGGCGCATCTACTACTACAATGCTGACGACAAGCAGTCCGTGTGGGAGAAGCCCAGCGTGCTCAAGTCCAAGGCAGAG
Seq A exon
GTCCTGAGCTGGGCTTTCTGGCCCTTCCTTTCAGCTGCCCTGACCCTTCCAAGTCCTTGGCCTTCCCTTAGTCTCTAACCATATTCATGATGGTTCCTCTGATCCCAAGGTCCCTGACCATTCCTCACCCTCCCTGGAAATGCCTCCATAGGATCTCAAGAAGTCCACCTTCCCCAGTTTGAACCAGGCCAGGTGGTAGCTAAAGGTTCCTGTGTCCTCTACTCACTAGGTCCCCTTAGCTCCCCTGACTGGCTGGAGAACTTGCCCATCCCACTGATGGCTCCTATCCCATCCACTTGCAG
Seq C2 exon
CTGCTCCTGTCCCAATGTCCCTGGAAAGAGTACAAGTCGGACACAGGCAAACCTTATTACTATAACAACCAGAGTAAAGAGTCCCGCTGGACCCGGCCCAAGGATCTGGATGACCTAGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000110844-PRPF40B:NM_001031698:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.378 A=NA C2=0.683
Domain overlap (PFAM):
C1:
PF0039721=WW=PD(90.3=75.7)
A:
NA
C2:
PF0039721=WW=WD(100=73.2)
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:
AGGGCCCTATGGAGTGAGCAT
R:
TCTAGGTCATCCAGATCCTTGGG
Band lengths:
230-532
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)