HsaINT0119426 @ hg38
Intron Retention
Gene
ENSG00000101104 | PABPC1L
Description
poly(A) binding protein cytoplasmic 1 like [Source:HGNC Symbol;Acc:HGNC:15797]
Coordinates
chr20:44930460-44932432:+
Coord C1 exon
chr20:44930460-44930726
Coord A exon
chr20:44930727-44932341
Coord C2 exon
chr20:44932342-44932432
Length
1615 bp
Sequences
Splice sites
5' ss Seq
CAGGTGACG
5' ss Score
7.66
3' ss Seq
GGTCTTCTTTTCCCATGCAGCCT
3' ss Score
8.32
Exon sequences
Seq C1 exon
GTGATGACAGAGGGTGGCCACAGCAAGGGGTTTGGCTTTGTGTGTTTTTCCTCCCCAGAAGAGGCGACAAAGGCCGTGACAGAGATGAACGGGCGCATCGTGGGCACCAAGCCACTCTACGTGGCACTGGCCCAGCGCAAAGAGGAGCGGAAGGCCATCTTGACCAACCAGTACATGCAGCGCCTCTCCACCATGCGGACCCTGAGCAACCCCCTCCTGGGCTCCTTTCAGCAGCCCTCCAGCTACTTCCTGCCTGCCATGCCCCAG
Seq A exon
GTGACGGCCTGCCCGCAACTCCCACCGCAGCCTTCCCCCCTGCCCCAGCAAGGCAGAGCATGAAGACTAGAGTTCTAGGGAAATGGAGGTTTCTAACTTGCTTCTGCCGAGGACTCATTAGGAAGTCTTTGTTTCCCTCTCTATAAAAGGGAGAGATAGTGTTAGTCAAATGGCATTTCCCAGTGAGAGAAGCTCGTGAATGTTGTGCTGAAAAAGACTCTTAATGATCCAGCAAGTTTGGGAAATGCTGCGTTAAGCAAGACCTACATTTTTCCTTCCTCCCTTCCTTCCCTTCCCTCCCTTCCCTCCCTTCCCTCCCTTCCCTTCCCTTCCCTTCCCTCCCTCCCTCCCTCCCTCCCTCCCTTCCTTCCTTCCTTCCTTCGTGGGGTCTCCATGTCACCCAGGCTGGTGAGCAATGGCGTGATCATGGCTCCTTCCTTCTTCCCTCCCTTCCTCCCTTCCTCCCTTCCTTCACGGGGTCTCCATGTCACCCAGGCTGGAGAGCAATGGCATGATCATGGCTCACTGCAGCCTTGAATTCCTGGGCTTGAGTGATCCTCCCACTGTAGCCTCCTGAGTAGGTGGGACTACAGGTGTGTGCCACCATGCCCAGCTAATTTTTTTGTTTATTTTAAAGAAGGGGTCTCGCCATGTTGCCCAGGCTGGTCTCAAACTCCTGGGCTCAAGCAATTCTCCTGCCTTGGCCTCCCAAAGTGCTGGCATTACAGGAGTAAGCCACCGTCCCCCGCCCTACATTTTTTTAAAAATTAAATTTTTATTTTTTTGGAGACAGAGTCTTGCTCTGTTGCCCAGAATGGAGTGCAGTGACACCATCTTGGCTCGCTGCAAACTCTTCCTCCTGGGTTCAAGTGATTCTTGTGCCTCAGCCTCCCGGGTAGCTGGGATTACAGGTGCGTGCCACCACACTCAGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCATGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCAAGTGATGTGCCCTCCTTGACCTCCTAAAGTGCTGGGATTACAGGCATGAGCCACCATGATCGGCCCTAAATTTCTTTACTATCTACACTATTCTACCCTAAGATGCCAATGTCTACTGAGACTCTCCAAAACAGGCACAGATTATCCAGCATTTCCCCAGCTTAGATGGTCATTTTTTTGTGGGATGCCTGTTAACATCTCCCCTGGATGTTAATGTTCTGAGGAGCATGGTTTGGGAAAGGACCTCGTGGGACTTACAGGAAGTAGAAAGATGTCACCCATTAAAGGCCACCACGGTAAGAACATTCCTCTCCTTTTAGCAGTTGCTTAAGCTGCACAAGTTGGAGTAAGATGTCACCCTTTTTATCCAGGTCATTGGGTTAGCTGACAGGGAGCCAAGATTGAAATCTAAGATCTTTGCCCTGCAGGATTCAGGGCTAATGGACATCCTGAGATGGGAGGAAGGAGCTTTCATTACAGCCTTGTGGGTCTTGACTCACCAGTCCCTGCAGGAGCCAGTGGAGTTCCTGCCATGGTGTCCCTGAGGAGGTGTAGCTTCTCACCTACCCTGCCGCCAAGCCCCTCAGTCTGGGTCTTCTTTTCCCATGCAG
Seq C2 exon
CCTCCAGCCCAGGCTGCATACTATGGCTGTGGCCCAGTGACACCCACCCAGCCTGCCCCCAGGTGGACATCCCAGCCACCTAGACCTTCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101104:ENST00000217073:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.162 A=NA C2=0.677
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(56.5=43.8)
A:
NA
C2:
NO
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATGACAGAGGGTGGCCACAG
R:
GAAGGTCTAGGTGGCTGGGAT
Band lengths:
354-1969
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