HsaINT0119403 @ hg38
Intron Retention
Gene
ENSG00000070756 | PABPC1
Description
poly(A) binding protein cytoplasmic 1 [Source:HGNC Symbol;Acc:HGNC:8554]
Coordinates
chr8:100704926-100705673:-
Coord C1 exon
chr8:100705589-100705673
Coord A exon
chr8:100705057-100705588
Coord C2 exon
chr8:100704926-100705056
Length
532 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
TTGAATGTTTCTGTTCCTAGGTG
3' ss Score
10.7
Exon sequences
Seq C1 exon
CCTGCTGTTCATGTACAAGGTCAGGAACCTTTGACTGCTTCCATGTTGGCATCTGCCCCTCCTCAAGAGCAAAAGCAAATGTTGG
Seq A exon
GTGAGTACTTCTGTCCCACCTTGTCAGTTCAGAAAGACTAGAAAATATAGGAATCACTTAGGCACTAGGTCAATCAATTGACAGCTAGGGCAGTGGAATTGATCTGAATTGGCATGAATGATTATGATAGTACAGTTGGTCTGCCTAATTAAAACCACTGGAAAGCCAATAAGAAAATGTATTGTTAGTAATAAATAGGGTAGTAGGGCATTACTCACCATGGGCCCTCACTACATTTTTGAGAGAAGGAATTTGAAGCAAATGAGAAGAAAACTTGTGACTTTGCCTGAACACCGATTTAACAACCTAATGGTAACATTGCTTAATTGGCAAGCTGATAATATCAAGAGTTAATTGCCTTGTGGCAGATTTTATTCTGTCTTCCCATGAAGACATAATGAAATTGTGGATTATGGGTTATTATATACGTGAGACAGAAGTATGGTTCTTAAACCCCAGTTTAATGTGGTAATTCAATGCAGTTAAAAACTTTTTTTTATTGAAGGGAGTTTTTGAATGTTTCTGTTCCTAG
Seq C2 exon
GTGAACGGCTGTTTCCTCTTATTCAAGCCATGCACCCTACTCTTGCTGGTAAAATCACTGGCATGTTGTTGGAGATTGATAATTCAGAACTTCTTCATATGCTCGAGTCTCCAGAGTCACTCCGTTCTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000070756:ENST00000318607:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.835 A=NA C2=0.257
Domain overlap (PFAM):
C1:
PF0065813=PABP=PU(27.8=69.0)
A:
NA
C2:
PF0065813=PABP=PU(55.0=91.7)
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:
CCTGCTGTTCATGTACAAGGTCA
R:
TAGAACGGAGTGACTCTGGAGAC
Band lengths:
214-746
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