HsaINT0119406 @ hg19
Intron Retention
Gene
ENSG00000070756 | PABPC1
Description
poly(A) binding protein, cytoplasmic 1 [Source:HGNC Symbol;Acc:8554]
Coordinates
chr8:101730001-101730508:-
Coord C1 exon
chr8:101730315-101730508
Coord A exon
chr8:101730117-101730314
Coord C2 exon
chr8:101730001-101730116
Length
198 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
GGGTATATGTTTTTCCCTAGGTG
3' ss Score
10.19
Exon sequences
Seq C1 exon
CGGAGCGTGCTTTGGACACCATGAATTTTGATGTTATAAAGGGCAAGCCAGTACGCATCATGTGGTCTCAGCGTGATCCATCACTTCGCAAAAGTGGAGTAGGCAACATATTCATTAAAAATCTGGACAAATCCATTGATAATAAAGCACTGTATGATACATTTTCTGCTTTTGGTAACATCCTTTCATGTAAG
Seq A exon
GTAAGCCAAAAATGTCCGATACACATGTTTACATTGTTGAGCTACATTTAGTTTAGTGCTTGAAATAGGAACTGTGCAGTAATGGATATCTTTATTTCACAAATATCCAGGTTAGATGGCTAACAGATTGTCTCTCAACACTGAACAAATGTTAAATCAATAGCAAATAAAGAAAAATGGGTATATGTTTTTCCCTAG
Seq C2 exon
GTGGTTTGTGATGAAAATGGTTCCAAGGGCTATGGATTTGTACACTTTGAGACGCAGGAAGCAGCTGAAAGAGCTATTGAAAAAATGAATGGAATGCTCCTAAATGATCGCAAAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000070756-PABPC1:NM_002568:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.002 A=NA C2=0.002
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(47.4=27.7),PF150631=TC1=WD(100=87.7),PF0007617=RRM_1=PU(52.8=43.1)
A:
NA
C2:
PF0007617=RRM_1=PD(2.8=5.1),PF0007617=RRM_1=PU(92.7=97.4)
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:
GCGTGCTTTGGACACCATGAA
R:
CTGCTTCCTGCGTCTCAAAGT
Band lengths:
254-452
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)