HsaINT0132619 @ hg19
Intron Retention
Gene
ENSG00000196504 | PRPF40A
Description
PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:16463]
Coordinates
chr2:153572509-153573975:-
Coord C1 exon
chr2:153573870-153573975
Coord A exon
chr2:153572641-153573869
Coord C2 exon
chr2:153572509-153572640
Length
1229 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
AAATGTTCACTGTTTTTCAGATG
3' ss Score
8.18
Exon sequences
Seq C1 exon
ACTCAGATCGCTTCTTGTTGGTATGTGTAGCGGCAGTGGCCGCCGGCGGAGCAGTCTGAGCCCGACGATGAGGCCGGGGACGGGAGCTGAGCGTGGAGGCCTCATG
Seq A exon
GTGAGTGAAATGGAGAGCCATCCTCCCTCGCAGGGTCCTGGGGACGGGGAGCGGAGATTGTCCGGCTCAAGCCTCTGCTCCGGCTCTTGGGTCTCTGCTGACGGCTTCCTGAGGAGACGGCCCTCGGTAAGGGATCAGTGGGGCAGGGGGAAGGCGGCACAATGAAAAACGGAGTGAGAAACAGGAAGCTTTCTCCGAAAGGAGAAGAAGATAAGAGTGGACGAAGGAAGAACTCGAGATGGTGGGATATGTTCTGAGGGAGAGAAGTGGAGGGTGGAAATGCACAAAGAGAAGGATGTGAGACCCTGGAAGTTCCCCGTGGGCTTGGCCTAGACAGATGCGTGGTGAAGGTGCTGGCTCTTGGGCGGGGTGAGCGTCTTGGAGCTTTAGGCCCGATTTTAGCTGGGAGGGGGAGGCAGGGGCTTGATACTGTAAGACTTTAACAGCGGCTGCCAAAATTTGTTTTCATTAGTCGTCGGGGTGGTCTGCAGGGGGAACTGTTGGGACAATTGGCAGGAGATAATTAGGTGGTTTTAATTTAAAACATAGAACAATGGACTCATCGGTAAAGAAAGTAGTTGTCTTTTTAAACTGCGTTAAAAAGGATGAATTAGTTGTTTGCATTTAGTGTCCGTGAGTGACAGAACCTCAGTCTTTGAAAATGTATTTTTGGCAGAAGGAATTTTACCTGTCTTAAAGGTTATGTTAGGAAATAAGTTTGTTAGGAGTGAATTGTGCCTGGGTAGCCATACTGTTTGTGTTTTGTAAGACCGACTCTCACCTGAGTTAATTGGATAGAGCATTTTAAAGTTTAAAATCAGTAGTGTTATAAAATAACAATAGCTGGCTATCTTTTATATCTGCATGAAATAGGAGAGTTGTTGTTTTCACCATAACAGTTTTAAAATTAGTATTCAATGTGTATCCTCCAAGCTTAGCAAGCCAATTAGTAGCTGGTTAAGTCAGTGCTTAAAAAAAAGAGAGAGAAAACCTATGATCCAGCGGTCCAGGATTCATCTTAACTTTTCCCATTTTTTTACGGAATTTGCAAGCTCGTTTTAAATACTAGCAGAATGCGTTTTGTTTGAAACAAGGTATAGACTAATCCAATGATGTTATTACACATAAGCTTAATATTATGTCGCTTCAGATAACTGATCTGTTGAAATGAGATTTTTGAGAAGCATTTAGTATTATTTGCTCATTTAAAAATGTTCACTGTTTTTCAG
Seq C2 exon
ATGGGGCACCCTGGCATGCATTATGCCCCAATGGGAATGCACCCTATGGGTCAGAGAGCGAATATGCCTCCTGTACCTCATGGAATGATGCCGCAGATGATGCCCCCTATGGGAGGGCCACCAATGGGACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196504-PRPF40A:NM_017892:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.931 A=NA C2=0.937
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTCAGATCGCTTCTTGTTGGT
R:
TTGTCCCATTGGTGGCCCTC
Band lengths:
238-1467
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)