HsaINT0119417 @ hg19
Intron Retention
Gene
ENSG00000101104 | PABPC1L
Description
poly(A) binding protein, cytoplasmic 1-like [Source:HGNC Symbol;Acc:15797]
Coordinates
chr20:43565278-43566832:+
Coord C1 exon
chr20:43565278-43565371
Coord A exon
chr20:43565372-43566701
Coord C2 exon
chr20:43566702-43566832
Length
1330 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGT
5' ss Score
9.27
3' ss Seq
TTAGAAGGTGTTCCACACAGGGG
3' ss Score
2.14
Exon sequences
Seq C1 exon
GTCCAGGAGCCGGCTGTGCACATCCCAGGACAGGAGCCCCTGACCGCGTCCATGCTGGCTGCGGCGCCCCTGCATGAGCAAAAGCAGATGATTG
Seq A exon
GTGAGTGGCTGGTTCTCCTACTGTGGAGCAAGAAGAGGAGGGCTGCGAGCTGGCTAGCCTGCTGGGAAACACCTCACCTGGTGGTCCAACGTGAGGTCAAATTCCAGCTTTGTCACCGACCCCCCTACTGGGTGACCGTGGCCAAGCTGGCTCTATTCTCTAGGCACCTGTTATCTTGTCTTAAAACGCTGGTCAGACTGGATGGTCCTGAGCTTTCTTCCACTGCTGCTGTCCTGTGACTTTGAGGTTGGGAGACAGTCCAGATGTGGGGAGATCAGGGGACAAAGGGAGGAGTAGGGGTATGGTCTTGGGTTTCTGCTGAGAAATGGCTTGTAGGTGGGGGGTTAAAGTTCCTCACACCTCTCCTGAACGGGAGGAAGCTGCTGTTCACCAGTTTCCAGTGCTCAATGCGGGCAGGTGGGGCATCTGTGCGTTTGGTAAATACATGATGTTTCCCATAGATTCTGGATTCCTTGTGCAATTCATCTTCACCCCTAGTGTCCATGGCAGGCCCTGATAAAAATGCCACTAAGTGAACACAAGCTTGTTCCTGGTTGGCAGGTTCTTTACTGCATGGCCCCCGAGACCTCCAGACCCTTTACTGAAGGCCCCCATTACCACTGCCCCATTGTTTCCTCAGCTTACTTAGGGTTTTGCCACATTACCCCTTCCCCTCACCCCGAAATTTTTTTTTTTTTCCCTGAGATGGAGTCTTGCTCTGCTGCCCCGGCTGGAGTGCAGTGGCACGATTTTGGCTCACTGCAACCTCCACCTCCCGGGTTCAAGTGATTCTCCTGCCTCAGCCTTCTGAGTAGCTGGGCTTACAGGCACATGCCACCATGACCAGCTAAGTTTTGTATTTTTATTAGAGATGGGGTTTCACCATGTTGGCCAGGCTGGTTTCAAACTCCTGATCTCAGGTGATCCACCCACCTCAGCCTCCCAAAGTACTGTGATTACAGGTGTGAGCCACCATGCCTGGCCTCACCCAGAAACATTTTGAATGAGCTTAATGGAAGTAGAAGTCTTTGTTAGTAGTTCTCTGTAAACATTTTCACTTTCTTCATGGGACGATCCTTTCCGCCCCCACTTAAGGCACCCAGTCCTGGCTGGGCCCTGGACACATTGCTGAGATGGGCTGACCACCAATACCAGGCCCAGTCATTAAAAGTACCTGATGTTAGAAGATCAAGTGTTAAATGTCATAGCCTAGAAGGAGCAGTTCTGGGAGAAGAACCCAGATGTCCTCAGTGCTCCACTCCATACGAGCCCTGGGATGCTGGGGTGTGAGCTAGGCCGTGCACAAGCCATTAGAAGGTGTTCCACACAG
Seq C2 exon
GGGAGCGTCTCTACCCCCTTATCCATGATGTCCACACCCAGCTGGCTGGCAAGATCACGGGCATGCTGCTGGAGATTGACAACTCAGAGCTGTTGCTCATGCTGGAGTCTCCAGAATCCCTCCATGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101104-PABPC1L:NM_001124756:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.391 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0065813=PABP=PU(29.0=62.5)
A:
NA
C2:
PF0065813=PABP=FE(62.3=100)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCAGGAGCCGGCTGTG
R:
TTGGCATGGAGGGATTCTGGA
Band lengths:
224-1554
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)