HsaALTA0006024-1/2 @ hg19
Alternative 3'ss
Gene
ENSG00000101104 | PABPC1L
Description
poly(A) binding protein, cytoplasmic 1-like [Source:HGNC Symbol;Acc:15797]
Coordinates
chr20:43552802-43559367:+
Coord C1 exon
chr20:43552802-43552897
Coord A exon
NA
Coord C2 exon
chr20:43559159-43559367
Length
0 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TGTGTGTTTTTCCTCCCCAGAAG
3' ss Score
11.13
Exon sequences
Seq C1 exon
GGTGTGAACTTGTATGTGAAGAATCTGGACGACTCCATTGATGACGACAAACTGAGGAAAGAGTTCTCTCCCTATGGAGTAATTACCAGTGCGAAG
Seq A exon
NA
Seq C2 exon
AAGAGGCGACAAAGGCCGTGACAGAGATGAACGGGCGCATCGTGGGCACCAAGCCACTCTACGTGGCACTGGCCCAGCGCAAAGAGGAGCGGAAGGCCATCTTGACCAACCAGTACATGCAGCGCCTCTCCACCATGCGGACCCTGAGCAACCCCCTCCTGGGCTCCTTTCAGCAGCCCTCCAGCTACTTCCTGCCTGCCATGCCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101104-11-16,11-15-1/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence exclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.025 A=NA C2=0.130
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PU(82.4=87.5)
A:
NA
C2:
PF0007617=RRM_1=PD(11.8=57.1)
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGACGACTCCATTGATGACG
R:
CACGTAGAGTGGCTTGGTGC
Band lengths:
136-194
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)