HsaINT0119439 @ hg38
Intron Retention
Gene
ENSG00000090621 | PABPC4
Description
poly(A) binding protein cytoplasmic 4 [Source:HGNC Symbol;Acc:HGNC:8557]
Coordinates
chr1:39567751-39568939:-
Coord C1 exon
chr1:39568802-39568939
Coord A exon
chr1:39567847-39568801
Coord C2 exon
chr1:39567751-39567846
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:ENST00000372857:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.085 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(21.4=32.6)
A:
NA
C2:
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