HsaALTD0004539-2/2 @ hg19
Alternative 5'ss
Gene
ENSG00000101104 | PABPC1L
Description
poly(A) binding protein, cytoplasmic 1-like [Source:HGNC Symbol;Acc:15797]
Coordinates
chr20:43560983-43561826:+
Coord C1 exon
chr20:43560983-43561073
Coord A exon
chr20:43561074-43561175
Coord C2 exon
chr20:43561698-43561826
Length
102 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
TGTGGTGTCTGCACCACAAGCTG
3' ss Score
0.73
Exon sequences
Seq C1 exon
CCTCCAGCCCAGGCTGCATACTATGGCTGTGGCCCAGTGACACCCACCCAGCCTGCCCCCAGGTGGACATCCCAGCCACCTAGACCTTCCT
Seq A exon
GTGAGTGACCCAGCCCCTTCCACTCTCAGACTGGCCTATTGGTGTGGGCCCCGTGAGGCAGTCATAACACAGGGATGAAACCTGGCTCTGCCACTTCCCAAG
Seq C2 exon
CTGCCTACCCTCCAGGTGCCTCAATGGTCCGGCCACCAGTTGTGCCTCGGCGCCCCCCGGCCCACATCAGCAGTGTCAGGCAGGCCTCCACCCAGGTGCCACGCACGGTGCCTCATACCCAGAGAGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101104-14-26,15-26-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.667 A=NA C2=0.995
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
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:
CCAGGCTGCATACTATGGCTG
R:
ACTCTCTGGGTATGAGGCACC
Band lengths:
210-312
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)