HsaALTD0004536-3/3 @ hg19
Alternative 5'ss
Gene
ENSG00000070756 | PABPC1
Description
poly(A) binding protein, cytoplasmic 1 [Source:HGNC Symbol;Acc:8554]
Coordinates
chr8:101733619-101734114:-
Coord C1 exon
chr8:101733962-101734114
Coord A exon
chr8:101733941-101733961
Coord C2 exon
chr8:101733619-101733847
Length
21 bp
Sequences
Splice sites
5' ss Seq
CCGGTTGAT
5' ss Score
-0.97
3' ss Seq
TCTCCTCCTCTCACGGAAAGGTC
3' ss Score
6.45
Exon sequences
Seq C1 exon
CCGAGACCGACCCGCCCGCCCGCGGCCCCGCAGCAGCTCCAAGAAGGAACCAAGAGACCGAGGCCTTCCCGCTGCCCGGACCCGACACCGCCACCCTCGCTCCCCGCCGGCAGCCGGCAGCCAGCGGCAGTGGATCGACCCCGTTCTGCGGCC
Seq A exon
GTTGAGTAGTTTTCAATTCCG
Seq C2 exon
GTCGCGGCCTGTGGCCCTGCGGGCAGCCGTGCCGAGATGAACCCCAGTGCCCCCAGCTACCCCATGGCCTCGCTCTACGTGGGGGACCTCCACCCCGACGTGACCGAGGCGATGCTCTACGAGAAGTTCAGCCCGGCCGGGCCCATCCTCTCCATCCGGGTCTGCAGGGACATGATCACCCGCCGCTCCTTGGGCTACGCGTATGTGAACTTCCAGCAGCCGGCGGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000070756-2-6,3-6,4-6-3/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.000
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0007617=RRM_1=PU(73.2=80.0)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
AGTGGATCGACCCCGTTCTG
R:
GGAGGTCCCCCACGTAGAG
Band lengths:
116-137
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- 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)