HsaINT1026016 @ hg38
Intron Retention
Gene
ENSG00000070756 | PABPC1
Description
poly(A) binding protein cytoplasmic 1 [Source:HGNC Symbol;Acc:HGNC:8554]
Coordinates
chr8:100709133-100709731:-
Coord C1 exon
chr8:100709459-100709731
Coord A exon
chr8:100709224-100709458
Coord C2 exon
chr8:100709133-100709223
Length
235 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
TGTGCTTTTTTTCCCTGCAGACT
3' ss Score
12.79
Exon sequences
Seq C1 exon
GTTATGATGGAGGGTGGTCGCAGCAAAGGGTTTGGTTTTGTATGTTTCTCCTCCCCAGAAGAAGCCACTAAAGCAGTTACAGAAATGAACGGTAGAATTGTGGCCACAAAGCCATTGTATGTAGCTTTAGCTCAGCGCAAAGAAGAGCGCCAGGCTCACCTCACTAACCAGTATATGCAGAGAATGGCAAGTGTACGAGCTGTTCCCAACCCTGTAATCAACCCCTACCAGCCAGCACCTCCTTCAGGTTACTTCATGGCAGCTATCCCACAG
Seq A exon
GTAGGTTTTAGAAGGCAACCAGAACCATGAAGGTTTTCGTATTTGGTCATTTCTAGTGTTTTTTGTGCCCCTCGCCCCGCAAATGTGAAACATTAAGAAAGGGGAATTATGATTGAGTAGGAAAAAATGCTTGAGTGTGAAGTCCTGGTAAATGTTTTGAAAAAGTACATATAATTTATTGCATTATTTGCTTTTTTCTTCAACTGATAAACTCATGTGCTTTTTTTCCCTGCAG
Seq C2 exon
ACTCAGAACCGTGCTGCATACTATCCTCCTAGCCAAATTGCTCAACTAAGACCAAGTCCTCGCTGGACTGCTCAGGGTGCCAGACCTCATC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000070756:ENST00000318607:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.259 A=NA C2=0.645
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(56.5=42.9)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTATGATGGAGGGTGGTCGC
R:
GTATGCAGCACGGTTCTGAGT
Band lengths:
294-529
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains