HsaINT0132628 @ hg19
Intron Retention
Gene
ENSG00000196504 | PRPF40A
Description
PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:16463]
Coordinates
chr2:153520169-153520481:-
Coord C1 exon
chr2:153520390-153520481
Coord A exon
chr2:153520286-153520389
Coord C2 exon
chr2:153520169-153520285
Length
104 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAT
5' ss Score
8.88
3' ss Seq
TTAAGATTTCTTTTTTTTAGGAT
3' ss Score
9.76
Exon sequences
Seq C1 exon
GATCAACTGCACTTGATCTTTTCAAGTTTTATGTTGAGGATCTTAAAGCACGTTATCATGACGAGAAGAAGATAATAAAAGACATTCTAAAG
Seq A exon
GTAAATATATTTATTCTTACCTTTTAACCAATAGTATATCTTAAAAGTTAGTACTGTATTCCTTTGATTTATGCATTATTAATGTTAAGATTTCTTTTTTTTAG
Seq C2 exon
GATAAAGGATTTGTAGTTGAAGTAAACACTACTTTTGAAGATTTTGTGGCGATAATCAGTTCAACTAAAAGATCAACTACATTAGATGCTGGAAATATCAAATTGGCTTTCAATAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196504-PRPF40A:NM_017892:18
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=PD(17.9=32.3)
A:
NA
C2:
NO
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:
TCAACTGCACTTGATCTTTTCAA
R:
TGAAAGCCAATTTGATATTTCCAGCA
Band lengths:
202-306
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)