HsaINT0119402 @ hg19
Intron Retention
Gene
ENSG00000070756 | PABPC1
Description
poly(A) binding protein, cytoplasmic 1 [Source:HGNC Symbol;Acc:8554]
Coordinates
chr8:101717817-101719033:-
Coord C1 exon
chr8:101718879-101719033
Coord A exon
chr8:101717902-101718878
Coord C2 exon
chr8:101717817-101717901
Length
977 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGG
5' ss Score
9.99
3' ss Seq
AGTTCTCATTTTCTGTCTAGCCT
3' ss Score
5.19
Exon sequences
Seq C1 exon
CTAACACATCAACACAGACAATGGGTCCACGTCCTGCAGCTGCAGCCGCTGCAGCTACTCCTGCTGTCCGCACCGTTCCACAGTATAAATATGCTGCAGGAGTTCGCAATCCTCAGCAACATCTTAATGCACAGCCACAAGTTACAATGCAACAG
Seq A exon
GTATGGATTTAATGATTTCTTAATAAAAATCACATTTCTTGGGTGAAATCAAAGGTGTGAAGACAGCTGGGCACAGTGGCTCACACCTATAACCCCAGCACTTTGGGAGGTTGAGGCAGGCAGATTGCTTGAGACCAGGAGTTTGGGACCAGCCTGGGCAACATACAGGACCCTGTCTCCACAAAGAAAACTAGCTGGGTGTGGTGGCATAAGCCTGTAGTCCTAGCTGCTAGGAAGGCTGAGGCAGGAGGATTGCTCGAGCCCAGGAGTTTAAGGCTGCAGCAAGCTGTAATCCCTGCTGGGTGACAGCAAGACTCTGTCTCAAAAGAAAAAATGTGAAGACAGCTGCATGATAGATTCTTGAGAGCTTAGCCTATCTGGAACATTCTGCTAATATGATAGTATGTAAAATGTCTTACGCTTTTGGAATTGGACAAGCAGCGAGAAATTCACATCCTAAATCACCACGCCTGGTCTGAAACAACTATTACAAGTAGCTATGGGCCAGGCGTGGTGGCTCACACCTCTATGTAATCCCAGCACTTCAGGAGGCCAAGGCAGGTGGATCACTTGAGGTCAGGAGTTTGAGACCAGCCTGGTCAACAGGGTGAAACCCCAGCTCTAAAAATATAAAGATTAGCCAGGCTTGGTGGCACATGCCTGTAATCCCAGCTACTGGGGAGGCTGAGGCAGGAAAGTTGCTTGAATCCGGAGGCGGAGGTTGCAGCGAGCCAAGATTGTGCCGTTGCATTCCAGCCTGGGCGACAAAGTGAGACTCCATCTCAAAAAGAAAAAAAATGTATCTGTGATACATAGTATATAATAACTACTTTGGCTTCTTTCTAATTCGCTCACTCAACTTCTCCACCTCATGTTTCGATGGAAGTCTACCACTTCAGCAGATGTCCATTGATGACTATTTGTATTTGCCATCTTTTTCTGTGCTTTAAACTTAAGAGTTCTCATTTTCTGTCTAG
Seq C2 exon
CCTGCTGTTCATGTACAAGGTCAGGAACCTTTGACTGCTTCCATGTTGGCATCTGCCCCTCCTCAAGAGCAAAAGCAAATGTTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000070756-PABPC1:NM_002568:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.853 A=NA C2=0.841
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0065813=PABP=PU(31.7=69.0),PF085466=ApbA_C=PU(10.1=24.1)
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:
TAACACATCAACACAGACAATGGG
R:
GCTTTTGCTCTTGAGGAGGGG
Band lengths:
230-1207
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)