HsaINT0119403 @ hg19
Intron Retention
Gene
ENSG00000070756 | PABPC1
Description
poly(A) binding protein, cytoplasmic 1 [Source:HGNC Symbol;Acc:8554]
Coordinates
chr8:101717154-101717901:-
Coord C1 exon
chr8:101717817-101717901
Coord A exon
chr8:101717285-101717816
Coord C2 exon
chr8:101717154-101717284
Length
532 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
TTGAATGTTTCTGTTCCTAGGTG
3' ss Score
10.7
Exon sequences
Seq C1 exon
CCTGCTGTTCATGTACAAGGTCAGGAACCTTTGACTGCTTCCATGTTGGCATCTGCCCCTCCTCAAGAGCAAAAGCAAATGTTGG
Seq A exon
GTGAGTACTTCTGTCCCACCTTGTCAGTTCAGAAAGACTAGAAAATATAGGAATCACTTAGGCACTAGGTCAATCAATTGACAGCTAGGGCAGTGGAATTGATCTGAATTGGCATGAATGATTATGATAGTACAGTTGGTCTGCCTAATTAAAACCACTGGAAAGCCAATAAGAAAATGTATTGTTAGTAATAAATAGGGTAGTAGGGCATTACTCACCATGGGCCCTCACTACATTTTTGAGAGAAGGAATTTGAAGCAAATGAGAAGAAAACTTGTGACTTTGCCTGAACACCGATTTAACAACCTAATGGTAACATTGCTTAATTGGCAAGCTGATAATATCAAGAGTTAATTGCCTTGTGGCAGATTTTATTCTGTCTTCCCATGAAGACATAATGAAATTGTGGATTATGGGTTATTATATACGTGAGACAGAAGTATGGTTCTTAAACCCCAGTTTAATGTGGTAATTCAATGCAGTTAAAAACTTTTTTTTATTGAAGGGAGTTTTTGAATGTTTCTGTTCCTAG
Seq C2 exon
GTGAACGGCTGTTTCCTCTTATTCAAGCCATGCACCCTACTCTTGCTGGTAAAATCACTGGCATGTTGTTGGAGATTGATAATTCAGAACTTCTTCATATGCTCGAGTCTCCAGAGTCACTCCGTTCTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000070756-PABPC1:NM_002568:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.841 A=NA C2=0.257
Domain overlap (PFAM):
C1:
PF0065813=PABP=PU(31.7=69.0),PF085466=ApbA_C=PU(10.1=24.1)
A:
NA
C2:
PF0065813=PABP=FE(59.7=100),PF085466=ApbA_C=PU(54.1=75.0)
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:
CCTGCTGTTCATGTACAAGGTCA
R:
TAGAACGGAGTGACTCTGGAGAC
Band lengths:
214-746
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)