HsaINT0119426 @ hg19
Intron Retention
Gene
ENSG00000101104 | PABPC1L
Description
poly(A) binding protein, cytoplasmic 1-like [Source:HGNC Symbol;Acc:15797]
Coordinates
chr20:43559101-43561073:+
Coord C1 exon
chr20:43559101-43559367
Coord A exon
chr20:43559368-43560982
Coord C2 exon
chr20:43560983-43561073
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-PABPC1L:NM_001124756:8
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.120 A=NA C2=0.667
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(56.5=43.8)
A:
NA
C2:
NO
Other Skipping Isoforms:
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)