HsaALTD0005075-2/2 @ hg19
Alternative 5'ss
Gene
ENSG00000196504 | PRPF40A
Description
PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae) [Source:HGNC Symbol;Acc:16463]
Coordinates
chr2:153572509-153573908:-
Coord C1 exon
chr2:153573870-153573908
Coord A exon
chr2:153573744-153573869
Coord C2 exon
chr2:153572509-153572640
Length
126 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGG
5' ss Score
10.48
3' ss Seq
AAATGTTCACTGTTTTTCAGATG
3' ss Score
8.18
Exon sequences
Seq C1 exon
ATGAGGCCGGGGACGGGAGCTGAGCGTGGAGGCCTCATG
Seq A exon
GTGAGTGAAATGGAGAGCCATCCTCCCTCGCAGGGTCCTGGGGACGGGGAGCGGAGATTGTCCGGCTCAAGCCTCTGCTCCGGCTCTTGGGTCTCTGCTGACGGCTTCCTGAGGAGACGGCCCTCG
Seq C2 exon
ATGGGGCACCCTGGCATGCATTATGCCCCAATGGGAATGCACCCTATGGGTCAGAGAGCGAATATGCCTCCTGTACCTCATGGAATGATGCCGCAGATGATGCCCCCTATGGGAGGGCCACCAATGGGACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196504-1-7,2-7-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.936 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
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGAGCTGAGCGTGGAGG
R:
TTGTCCCATTGGTGGCCCTC
Band lengths:
157-283
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)