HsaINT0119437 @ hg38
Intron Retention
Gene
ENSG00000090621 | PABPC4
Description
poly(A) binding protein cytoplasmic 4 [Source:HGNC Symbol;Acc:HGNC:8557]
Coordinates
chr1:39569595-39570002:-
Coord C1 exon
chr1:39569863-39570002
Coord A exon
chr1:39569690-39569862
Coord C2 exon
chr1:39569595-39569689
Length
173 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
GTTCTGTCCTTTGGTAATAGGTA
3' ss Score
7.14
Exon sequences
Seq C1 exon
ATTTGTGGGCAGATTCAAGTCTCGCAAAGAGCGGGAAGCTGAGCTTGGAGCCAAAGCCAAGGAATTCACCAATGTTTATATCAAAAACTTTGGGGAAGAGGTGGATGATGAGAGTCTGAAAGAGCTATTCAGTCAGTTTG
Seq A exon
GTAAGTTGGGGTTCCTTGTCTCCTTTCACAGTCTACCAGACCCATCTGTTTTTTCTTAAGAGATGAGGGCACTGCTCCAGAGATTTGCTTCAAGTGAGTTTCCAGAGGGAAGCCTTCTGTTCCTGAGCTGTGCTCAAGATGGTGTTACTAATAGTTCTGTCCTTTGGTAATAG
Seq C2 exon
GTAAGACCCTAAGTGTCAAGGTGATGAGAGATCCCAATGGGAAATCCAAAGGCTTTGGCTTTGTGAGTTACGAAAAACACGAGGATGCCAATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000090621:ENST00000372857:4
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=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(1.4=2.1),PF0007617=RRM_1=PU(31.4=45.8)
A:
NA
C2:
PF0007617=RRM_1=FE(44.3=100)
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:
TTTGTGGGCAGATTCAAGTCTCG
R:
CTTATTGGCATCCTCGTGTTTTTCG
Band lengths:
234-407
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