HsaINT0132658 @ hg19
Intron Retention
Gene
ENSG00000110844 | PRPF40B
Description
PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:25031]
Coordinates
chr12:50037644-50038449:+
Coord C1 exon
chr12:50037644-50037787
Coord A exon
chr12:50037788-50037882
Coord C2 exon
chr12:50037883-50038449
Length
95 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
CTGTGCCTTTGCTCCAACAGACA
3' ss Score
10.05
Exon sequences
Seq C1 exon
AATAGTCCTGAGAGTGAGACAGACCCTGAGGAGAAAGCTGGCAAGGAGAGCGATGAGAAAGAACAAGAACAGGACAAGGACAGGGAGCTCCAACAGGCAGAGCTCCCTAACCGTTCCCCAGGCTTTGGAATCAAGAAGGAGAAG
Seq A exon
GTGAGGGGCAGGGGCCCTAGGCCAGTCAGCACGCTGGTCAAGCTTCCACGGCCCTTAGTGCAGGCTAAGGGTGAACTGTGCCTTTGCTCCAACAG
Seq C2 exon
ACAGGCTGGGACACGTCAGAAAGTGAGCTGAGTGAGGGTGAGCTGGAGAGGCGGCGGCGGACACTCCTACAGCAGCTGGATGATCACCAGTGACCCAATGAGCTGTTCTCTGCCTCGGGTCTGTGTGAGGCCATGGCTCCTGGGCCACCCTCACCGTCTGCCTCAGACTTCTTCCTTAGTCTGGTCTGTGTCCACTTTTTCTAAAGTAACCCCACCCCCAGCACACCATTGTTGGCACCTCTCAAGGTTGCTCTTGGTGTTCAAGGGTCCCCTACTCCCTGGACTAGTGCAGTCCTTGCCCTCAGCCCCAGACCAGAGATGGGTGGTATATGCCATGTGGGGTGGGTGATGCCAGTAGATAAAAGTGTGAGAGAAGGGGTCTCCAGGGAAGAGTCACAGGCTGTTGGACGCAGCCTGGGTGGCAGAGGGCAGGGTCATCACCCTCTAGCATCAGTGCCTGCTCCTGCCTGCCCTGGCCCTGAGGCTCCACCACTTCTTCCTCCACCCAGGACCTAATGTACGTGTGTTTTGTTTTTTGTTTTTTAAATAACAATATTTATAACATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000110844-PRPF40B:NM_001031698:24
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 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:
CAACAGGCAGAGCTCCCTAAC
R:
GGCAGAGAACAGCTCATTGGG
Band lengths:
168-263
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)