HsaINT0119431 @ hg19
Intron Retention
Gene
ENSG00000090621 | PABPC4
Description
poly(A) binding protein, cytoplasmic 4 (inducible form) [Source:HGNC Symbol;Acc:8557]
Coordinates
chr1:40027995-40029413:-
Coord C1 exon
chr1:40029286-40029413
Coord A exon
chr1:40028089-40029285
Coord C2 exon
chr1:40027995-40028088
Length
1197 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CTGCCTTTCCTGGTTCCCAGGCA
3' ss Score
9.5
Exon sequences
Seq C1 exon
GCGTTCCCACAGCTGTGCAGAACTTAGCGCCACGCGCTGCTGTTGCTGCTGCTGCTCCCCGGGCTGTTGCCCCCTACAAATACGCCTCCAGTGTCCGCAGCCCTCATCCTGCCATACAGCCTCTGCAG
Seq A exon
GTGAGGTTCACCAGACAGAATGCTTAAAAGGATTTCCCCCATTTCCACTTGATGTAAAAGAAGCTGTGCTTTTGATTCCTTCAACAGGTATTAAATGCCTGCTCTGTGTTATGACGCTATGTTCTGATTCACTGTCCCTGCCCTTCAGGGGCTCACTAGTGGGAAAGAAGGGGCTTAAAAGTGCTCTGCCTGATGCCAGTTCACTCAGAAATGCCTCAGAGCGGGCAGCCAGTGCTTCCTCTTCTGTTTGTACGAAATAATGTGCTCATTCAGCTGTTTGAGCCTCCAGGTCACTTCCGCATCCAATGACCTATTGGATCCTTGGCTGCTCTGCAAGATGATTGGTACATTAATGCAGGAAATAACTTCAACTTACAGATCGGATGTTCAGCTTCAAAGATGTAAAGTGTGTGTAGGAGGTGAAGGGGTTGAACCTAGAGCTTAGATTTTCTAAGCTGTAACTTGCTGTCTCTAGACCTGTGCTCTAGATGCAACTAGTTTGTTTCAGAGCCTAATAGCAATTTGCTGTGGAGGTGTCACCCTAAGCCTTCAGGCCCATAAGCTGCTTAGGAGATTACTCTTTAACTGTCCTGTCTCATACTCTCTAAGTTGGGGATTTCCTAGAACTTGATGCTATGTAAAATACCTTTTCTTTGCAAGGCTTTGACTAGCATTGACGTTGCATGTTGACCGTTTTTAAGCATTTGATACAAAAACATTTGGTAGAATTAAGGTGATGTGGAATGTAATTATAAATGTGTTGATATTTACTCCCTTTGATCCAATCTGCACTGAGATTTACCCTAAAGGAAAACTAATTTTCAGGAAAAGGTTATATACAAGTGTTTACCCTTATTTATATCAAGGCTTTTCATTCTTGAGTAACTTTGGGTGTATTAAGGAAATGTCAGAAAATGCTTGCCTAGCACTATAGGTTTGTTTTATTATTTACGTTTCACTTCGCTTTCTGATAGCATGCCATTTTCATTGTAATTGGTTGTGTTTATGTCCATACCACTCTGTTCCTCAACACACCCCTCAATCCTTCAAGGACTGAAATTAGTTCCTTTAGAGCAAGGACAGCCACCTCCTCTCCTCTTTCACATAGTCAGATGTTCAGATATTGAACAGGCACTCAACCACCATCAGGTGTTGTCCTTTCCTCAGTGCTAACCCACTGCCTTTCCTGGTTCCCAG
Seq C2 exon
GCACCCCAGCCTGCGGTCCATGTGCAGGGGCAGGAGCCACTGACTGCCTCCATGCTGGCTGCAGCACCCCCCCAGGAACAGAAGCAGATGCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000090621-PABPC4:NM_001135653:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.570 A=NA C2=0.914
Domain overlap (PFAM):
C1:
PF0065813=PABP=PU(0.1=0.0)
A:
NA
C2:
PF0065813=PABP=PU(27.8=62.5)
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:
CCCACAGCTGTGCAGAACTTA
R:
GCATCTGCTTCTGTTCCTGGG
Band lengths:
214-1411
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)