HsaALTA0006025-2/2 @ hg19
Alternative 3'ss
Gene
ENSG00000101104 | PABPC1L
Description
poly(A) binding protein, cytoplasmic 1-like [Source:HGNC Symbol;Acc:15797]
Coordinates
chr20:43560203-43561826:+
Coord C1 exon
chr20:43560203-43560667
Coord A exon
chr20:43561698-43561712
Coord C2 exon
chr20:43561713-43561826
Length
15 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGA
5' ss Score
10.65
3' ss Seq
TGTGGTGTCTGCACCACAAGCTG
3' ss Score
0.73
Exon sequences
Seq C1 exon
TTGGCTCGCTGCAAACTCTTCCTCCTGGGTTCAAGTGATTCTTGTGCCTCAGCCTCCCGGGTAGCTGGGATTACAGGTGCGTGCCACCACACTCAGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCAAGTGATGTGCCCTCCTTGACCTCCTAAAGTGCTGGGATTACAGGCATGAGCCACCATGATCGGCCCTAAATTTCTTTACTATCTACACTATTCTACCCTAAGATGCCAATGTCTACTGAGACTCTCCAAAACAGGCACAGATTATCCAGCATTTCCCCAGCTTAGATGGTCATTTTTTTGTGGGATGCCTGTTAACATCTCCCCTGGATGTTAATGTTCTGAGGAGCATGGTTTGGGAAAGGACCTCGTGGGACTTACAGGAAGTAGAAAGATGTCACCCATTAAAGGCCACCACG
Seq A exon
CTGCCTACCCTCCAG
Seq C2 exon
GTGCCTCAATGGTCCGGCCACCAGTTGTGCCTCGGCGCCCCCCGGCCCACATCAGCAGTGTCAGGCAGGCCTCCACCCAGGTGCCACGCACGGTGCCTCATACCCAGAGAGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101104-13-27,13-26-2/2
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=0.946 A=NA C2=0.993
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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACCTCGTGGGACTTACAGGAA
R:
CTGACACTGCTGATGTGGGC
Band lengths:
118-133
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)