HsaINT0119438 @ hg38
Intron Retention
Gene
ENSG00000090621 | PABPC4
Description
poly(A) binding protein cytoplasmic 4 [Source:HGNC Symbol;Acc:HGNC:8557]
Coordinates
chr1:39568802-39569689:-
Coord C1 exon
chr1:39569595-39569689
Coord A exon
chr1:39568940-39569594
Coord C2 exon
chr1:39568802-39568939
Length
655 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
GACATATTTTTCCTCTCTAGGCT
3' ss Score
10.67
Exon sequences
Seq C1 exon
GTAAGACCCTAAGTGTCAAGGTGATGAGAGATCCCAATGGGAAATCCAAAGGCTTTGGCTTTGTGAGTTACGAAAAACACGAGGATGCCAATAAG
Seq A exon
GTGAGTATACCACAAAGATTGGGAAAAGCTTTTAAGAGGTTGCCCCAGAGTATGGGTAGGGTCTTGCTAGCACCTACCTAGAGCTGGGACGGTCTGAGTATCTGGTAGTAGATGTACCATTACTATACTCTGGGATCATCTTCCTGGGTTCCGCATGTTAACTTCATGTAGGTGTTTACAAAGCACTTGGCACATACCTGTCACCTCAGCTATCAGTTGTTGAAAGAATAGGACAGACGTTTGTTATGCTGCAAAGGTGAGAGAACTAAAGCCCAGTGAGTGCTGATTTGATAACAGCACGGCAGCTACTTGTGGGCAAAGCATTGTGCCAGACCCTCAATATTTATCACTTAAATACCCACAAAAGCACCTGCAGAATTTACTGGCAGCCGGAATATTATATCGCCCTAGGCTCATGTCAGCACACTTGTGTTTATACACCTGTACTATTTCTATATTATCTGGATCAATAACCCATTTAAATATTAACCTCACTTTACAGATGAGGAAGTTTGGATTTGTGTGACAGACTTCAGAGGTGGAGTGAATTTAGTTTTTAGTCCTATAGTAGAAAGAATATTTTTTGGGACTTAGACCTCCAGAATAAGACCCCATCGCTGCAACTTTATTTTAAAGACATATTTTTCCTCTCTAG
Seq C2 exon
GCTGTGGAAGAGATGAATGGAAAAGAAATAAGTGGTAAAATCATATTTGTAGGCCGTGCACAAAAGAAAGTAGAACGGCAGGCAGAGTTAAAACGGAAATTTGAACAGTTGAAACAGGAGAGAATTAGTCGATATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000090621:ENST00000372857:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.085
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=FE(44.3=100)
A:
NA
C2:
PF0007617=RRM_1=PD(21.4=32.6)
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:
AGACCCTAAGTGTCAAGGTGA
R:
CTGATATCGACTAATTCTCTCCTGT
Band lengths:
230-885
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