HsaINT0132665 @ hg19
Intron Retention
Gene
ENSG00000110844 | PRPF40B
Description
PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:25031]
Coordinates
chr12:50027669-50028238:+
Coord C1 exon
chr12:50027669-50027875
Coord A exon
chr12:50027876-50028114
Coord C2 exon
chr12:50028115-50028238
Length
239 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
GAGTCCCCTGTGCCCTCCAGTTC
3' ss Score
4.77
Exon sequences
Seq C1 exon
GAAACAGCAGCAGCAGCTGCCACAGACACTTCAGCCACAGCCACCTCAGCCACAGCCTGACCCCCCACCTGTGCCTCCTGGCCCCACCCCAGTGCCCACAGGCCTCCTGGAACCTGAGCCAGGTGGGAGTGAAGATTGTGATGTGTTGGAGGCCACCCAGCCCCTGGAACAGGGGTTCCTGCAGCAGCTGGAGGAGGGCCCCAGCAG
Seq A exon
GTGAGGGCTGCCCCCCATGGCATTCCCAATGTTGGCCTCAGACTCCCAGCCTGGTTCAACCCTTGTCCTCTGCTGGGCCTCTCTCTCAGGAGGGGTTTGAAGATCTGGGTGTGACCTCTGAAGGGCAGAAAAAGGCTGCCCTGGGGAACAAGGAGGGGGTGATATGTTGCCAGGAGTTCAGGGCACTGAAAGCTGTGAGAGCTGGGGGACCCTGTGGCTGAGTCCCCTGTGCCCTCCAG
Seq C2 exon
TTCTGGACAGCATCAGCCACAGCAGGAGGAGGAGGAATCAAAGCCAGAACCAGAGAGGTCTGGCCTCAGTTGGAGCAACCGGGAGAAGGCAAAGCAGGCATTCAAGGAACTGCTGAGGGACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000110844-PRPF40B:NM_001031698:9
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:
PF0394210=DTW=PU(1.7=2.9)
A:
NA
C2:
PF0184614=FF=PU(24.0=28.6),PF0394210=DTW=FE(35.7=100)
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:
CCACAGACACTTCAGCCACAG
R:
TGAATGCCTGCTTTGCCTTCT
Band lengths:
292-531
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)