HsaINT0119439 @ hg19
Intron Retention
Gene
ENSG00000090621 | PABPC4
Description
poly(A) binding protein, cytoplasmic 4 (inducible form) [Source:HGNC Symbol;Acc:8557]
Coordinates
chr1:40033423-40034611:-
Coord C1 exon
chr1:40034474-40034611
Coord A exon
chr1:40033519-40034473
Coord C2 exon
chr1:40033423-40033518
Length
955 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
CAGTGATCTTTTTCCTTCAGGGG
3' ss Score
8.06
Exon sequences
Seq C1 exon
GCTGTGGAAGAGATGAATGGAAAAGAAATAAGTGGTAAAATCATATTTGTAGGCCGTGCACAAAAGAAAGTAGAACGGCAGGCAGAGTTAAAACGGAAATTTGAACAGTTGAAACAGGAGAGAATTAGTCGATATCAG
Seq A exon
GTAAGGTGGTCTTGGCCCAGCCTAGCAATGGGATTTGCTGTGAAATATTTGCAGAACACCCCTATGTTTAGCGGGCTTTCTTTTTGAGGACTTGGAGTGTGTTCTTCTTCCCATTTTACCTAAAAAGATGAGGTTTAAAAGGATATATACCTACTACATATGACTGATTATTATAGAACCAGAAACAAGAGATGGGTTTATTCATCAAGAAGCTCTCTATTTTGGAAGCCTCAGCCTGTTGCTTTTAGCCATGTAGGTTCCTTTTACTTAAATGAGACTCCTTTGTTTGGCATGGCTTCAAGAAGACCCCTGCTGGGGTGGGTGAGTGGTCACCAGAACAGCTGTGGGGAGAGGTGACAAAAGGTGAGTGCACTGATGATCCTGTCAGTTTCAGGGCAGTAGTTTCACAACTTTGGACTTGCATCAGATTCATCAGCAGAGCTTGTTAAAACAGATAGCTGGGCTCCAGCCCCAGAGTTTTTCTTATTCATTGGGTTTGGGGTCTGGCCTAAGAATTTCATTTCTTTCTTTTTTTTTTTTTTTTCTTGAGACAGTCTCGCTCTGTCGCCCAGGTTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAACTCCGCCTCCCGGGTTCGCACCATTCTCCTGCCTTAGCCTCCTGAGTAGCTGGGACTACAGGCACCCGCCACCATGCCTGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACTGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTTGTGATTCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGTCCGGCCGAGAATTTCATTTCTAACAAGTTCCCAAAGATGCTGGTGCTCCTGGTCTGGGGCCACCCTTGGGGAACCACTTTCTTAGGGAATATTTGTGATATAGAAGTGTAGTTAACAGTGATCTTTTTCCTTCAG
Seq C2 exon
GGGGTGAATCTCTACATTAAGAACTTGGATGACACTATTGATGATGAGAAATTAAGGAAAGAATTTTCTCCTTTTGGATCAATTACCAGTGCTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000090621-PABPC4:NM_001135653:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.087 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(21.4=32.6),PF0227010=TFIIF_beta=FE(26.8=100)
A:
NA
C2:
PF0227010=TFIIF_beta=FE(18.5=100),PF0007617=RRM_1=PU(40.6=87.5)
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:
GCTGTGGAAGAGATGAATGGA
R:
AGCACTGGTAATTGATCCAAAAGGA
Band lengths:
231-1186
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)