HsaALTA0006021-1/2 @ hg19
Alternative 3'ss
Gene
ENSG00000070756 | PABPC1
Description
poly(A) binding protein, cytoplasmic 1 [Source:HGNC Symbol;Acc:8554]
Coordinates
chr8:101721774-101724685:-
Coord C1 exon
chr8:101724590-101724685
Coord A exon
NA
Coord C2 exon
chr8:101721774-101721898
Length
0 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
ATGTTTCTCCTCCCCAGAAGAAG
3' ss Score
0.69
Exon sequences
Seq C1 exon
GGTGTTAATCTTTATGTGAAAAATCTTGATGATGGTATTGATGATGAACGTCTCCGGAAAGAGTTTTCTCCATTTGGTACAATCACTAGTGCAAAG
Seq A exon
NA
Seq C2 exon
AAGCCACTAAAGCAGTTACAGAAATGAACGGTAGAATTGTGGCCACAAAGCCATTGTATGTAGCTTTAGCTCAGCGCAAAGAAGAGCGCCAGGCTCACCTCACTAACCAGTATATGCAGAGAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000070756-23-23,23-22-1/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.004 A=NA C2=0.800
Domain overlap (PFAM):
C1:
PF073187=DUF1464=PD(13.8=39.4),PF0007617=RRM_1=PU(77.8=84.8)
A:
NA
C2:
PF0007617=RRM_1=PD(19.4=63.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAACGTCTCCGGAAAGAGTT
R:
TGTGGCCACAATTCTACCGTT
Band lengths:
99-102
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)