HsaINT1026014 @ hg38
Intron Retention
Gene
ENSG00000070756 | PABPC1
Description
poly(A) binding protein cytoplasmic 1 [Source:HGNC Symbol;Acc:HGNC:8554]
Coordinates
chr8:100712652-100713181:-
Coord C1 exon
chr8:100713087-100713181
Coord A exon
chr8:100712790-100713086
Coord C2 exon
chr8:100712652-100712789
Length
297 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
TCTTTTTTTTTGGGGGGAAGGCT
3' ss Score
1.22
Exon sequences
Seq C1 exon
GGCCTGCCTTAAGTGTGAAAGTAATGACTGATGAAAGTGGAAAATCCAAAGGATTTGGATTTGTAAGCTTTGAAAGGCATGAAGATGCACAGAAA
Seq A exon
GTAAGTGGTCTGTATTCAGCAGGAAGAAGGGGGTACAAAGTTGAGTTGCTCTTGTGTTGAAGTCTATGTGCATACTAATAGCTATTTGACATGTTCTTATATTTTCAGTTATTTGCATTTTATGCATTAGGTTTGAGAGTATAAATTGGTAACCTATATTGTCCCAAAACCTTGAGATTTTGGGATGGGTTTGTCTTTAGCTTTTGTGACTTAACAAATTTGTCTTAACTGTTAAGGAAATGAACTGTAAGTTGAAAGTTTTGTGATTTTTTTTTTTTCTTTTTTTTTGGGGGGAAG
Seq C2 exon
GCTGTGGATGAGATGAACGGAAAGGAGCTCAATGGAAAACAAATTTATGTTGGTCGAGCTCAGAAAAAGGTGGAACGGCAGACGGAACTTAAGCGCAAATTTGAACAGATGAAACAAGATAGGATCACCAGATACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000070756:ENST00000318607:5
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=0.238
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
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCCTGCCTTAAGTGTGAAAGT
R:
TGGTATCTGGTGATCCTATCTTGT
Band lengths:
232-529
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains