HsaINT0132627 @ hg19
Intron Retention
Gene
ENSG00000196504 | PRPF40A
Description
PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:16463]
Coordinates
chr2:153520390-153520766:-
Coord C1 exon
chr2:153520652-153520766
Coord A exon
chr2:153520482-153520651
Coord C2 exon
chr2:153520390-153520481
Length
170 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
TTCTTTAGTTTTTTCATTAGGAT
3' ss Score
6.29
Exon sequences
Seq C1 exon
ATATTTTTAGATGAATTACATGAACATGGACAACTGCATTCTATGTCATCTTGGATGGAATTGTATCCAACTATTAGTTCTGATATTAGATTCACTAATATGCTTGGTCAGCCTG
Seq A exon
GTAAGATTATTTTCTTTCCTAATTTACCGTTATGGTAGTAGTTGAAATGGGCCAAATGCAAAGGTGATTGTGTTGGGGGAAAGGGTGCTTTATTTTTGTTTTTTAAACAACAAAGTAATTGCAGCTCTTTGGTTAGAGCTAGCTTTTGACTTCTTTAGTTTTTTCATTAG
Seq C2 exon
GATCAACTGCACTTGATCTTTTCAAGTTTTATGTTGAGGATCTTAAAGCACGTTATCATGACGAGAAGAAGATAATAAAAGACATTCTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196504-PRPF40A:NM_017892:17
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0184614=FF=FE(67.9=100)
A:
NA
C2:
PF0184614=FF=PD(17.9=32.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGATGAATTACATGAACATGGACAAC
R:
CTTCTTCTCGTCATGATAACGTGC
Band lengths:
178-348
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)