HsaINT0132631 @ hg19
Intron Retention
Gene
ENSG00000196504 | PRPF40A
Description
PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:16463]
Coordinates
chr2:153519117-153519686:-
Coord C1 exon
chr2:153519549-153519686
Coord A exon
chr2:153519213-153519548
Coord C2 exon
chr2:153519117-153519212
Length
336 bp
Sequences
Splice sites
5' ss Seq
GATGTATGT
5' ss Score
6.31
3' ss Seq
TTTGTATCTGAATTTTTCAGATC
3' ss Score
9.03
Exon sequences
Seq C1 exon
TTACTAGAAAAGGCAGAAGCCCGTGAACGTGAAAGAGAAAAAGAAGAGGCTCGGAAGATGAAACGAAAAGAATCTGCATTTAAGAGTATGTTAAAACAAGCTGCTCCTCCGATAGAATTGGATGCTGTCTGGGAAGAT
Seq A exon
GTATGTATACTTGTTATTTTTTTCTAATGGAATTCTTTTCTTTACAGTTGAGAAATTTAAAATATTTTTATTTTTCATTTTATAGCCACAAAAATAAGCTAAATTTATTTGTAGAATATATTAAATATATTTAGAATATAATAAAAGCATTAAATCAGCTGTTGACTCTGTTTAGGAATATTTGTAAAGAATGGTTTGGACTTTTGAAGGGAGGAAATAATGGACTTTAAGGGGACTGATTCATCACAGTTTTCACTTGCTGTTATGATTTATTTTAGATGTATCGTTGTACTTTTCTTGGTATTCATATATTTATTTTGTATCTGAATTTTTCAG
Seq C2 exon
ATCCGTGAGAGATTTGTAAAAGAGCCAGCATTTGAGGACATAACTCTAGAATCTGAAAGAAAACGAATATTTAAAGATTTTATGCATGTGCTTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196504-PRPF40A:NM_017892:20
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.489 A=NA C2=0.188
Domain overlap (PFAM):
C1:
PF0184614=FF=PU(46.2=52.2)
A:
NA
C2:
PF0184614=FF=PD(50.0=81.2)
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:
GCAGAAGCCCGTGAACGTG
R:
CTCAAGCACATGCATAAAATCTTTAA
Band lengths:
222-558
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)