HsaINT0119409 @ hg19
Intron Retention
Gene
ENSG00000070756 | PABPC1
Description
poly(A) binding protein, cytoplasmic 1 [Source:HGNC Symbol;Acc:8554]
Coordinates
chr8:101724880-101725409:-
Coord C1 exon
chr8:101725315-101725409
Coord A exon
chr8:101725018-101725314
Coord C2 exon
chr8:101724880-101725017
Length
297 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
TCTTTTTTTTTGGGGGGAAGGCT
3' ss Score
1.22
Exon sequences
Seq C1 exon
GGCCTGCCTTAAGTGTGAAAGTAATGACTGATGAAAGTGGAAAATCCAAAGGATTTGGATTTGTAAGCTTTGAAAGGCATGAAGATGCACAGAAA
Seq A exon
GTAAGTGGTCTGTATTCAGCAGGAAGAAGGGGGTACAAAGTTGAGTTGCTCTTGTGTTGAAGTCTATGTGCATACTAATAGCTATTTGACATGTTCTTATATTTTCAGTTATTTGCATTTTATGCATTAGGTTTGAGAGTATAAATTGGTAACCTATATTGTCCCAAAACCTTGAGATTTTGGGATGGGTTTGTCTTTAGCTTTTGTGACTTAACAAATTTGTCTTAACTGTTAAGGAAATGAACTGTAAGTTGAAAGTTTTGTGATTTTTTTTTTTTCTTTTTTTTTGGGGGGAAG
Seq C2 exon
GCTGTGGATGAGATGAACGGAAAGGAGCTCAATGGAAAACAAATTTATGTTGGTCGAGCTCAGAAAAAGGTGGAACGGCAGACGGAACTTAAGCGCAAATTTGAACAGATGAAACAAGATAGGATCACCAGATACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000070756-PABPC1:NM_002568:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.231
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=FE(53.3=100),PF073187=DUF1464=FE(34.0=100)
A:
NA
C2:
PF0007617=RRM_1=PD(26.7=34.0),PF073187=DUF1464=FE(48.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCCTGCCTTAAGTGTGAAAGT
R:
TGGTATCTGGTGATCCTATCTTGT
Band lengths:
232-529
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)