HsaINT0132622 @ hg19
Intron Retention
Gene
ENSG00000196504 | PRPF40A
Description
PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:16463]
Coordinates
chr2:153528973-153529556:-
Coord C1 exon
chr2:153529492-153529556
Coord A exon
chr2:153529138-153529491
Coord C2 exon
chr2:153528973-153529137
Length
354 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGTA
5' ss Score
5.89
3' ss Seq
ACATGGTATTTTTATATTAGTGC
3' ss Score
4.29
Exon sequences
Seq C1 exon
CGGGTACCATCGAATGCTTCATGGGAGCAGGCTATGAAAATGATTATTAATGATCCACGATACAG
Seq A exon
GTAGTACTTCAACTTTTTATTTACTTTTCACTTTGAGCATATAGCAGGCCTAGCACATTTAAAGTTGTGTAGAAAGATAAAACATTTAACTGTTGACTTCTGTTTAGGATACCAAGTATAGAGTTGTTTTATGTCTAATAACCAAAAAGTCAAAGGCTTATCAAACAATTTGAGTACTCCGCTACATATAAAATAATAATTATTTTAAAAGTAGAAATTACTTTCTACAATCATTTGTAATAAATTTTTGAAAATTTTTAAATTATATGTGTAAACAGTTTTATTTTTTTTTTCAAACCACTAATATTTGATTCTTTTGCCTGTGTTTACTCTTACATGGTATTTTTATATTAG
Seq C2 exon
TGCTTTGGCAAAGTTAAGTGAAAAAAAGCAAGCCTTTAATGCCTATAAAGTCCAGACAGAAAAAGAAGAAAAAGAAGAAGCAAGATCAAAGTACAAAGAGGCTAAGGAATCCTTTCAGCGTTTTCTTGAAAATCATGAGAAAATGACTTCTACAACCAGATACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196504-PRPF40A:NM_017892:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.227 A=NA C2=0.339
Domain overlap (PFAM):
C1:
PF0184614=FF=FE(42.0=100)
A:
NA
C2:
PF0184614=FF=PD(30.0=26.8),PF0184614=FF=PU(44.0=39.3)
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:
GTACCATCGAATGCTTCATGGGA
R:
TCTGGTTGTAGAAGTCATTTTCTCA
Band lengths:
222-576
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)