HsaINT0119427 @ hg19
Intron Retention
Gene
ENSG00000101104 | PABPC1L
Description
poly(A) binding protein, cytoplasmic 1-like [Source:HGNC Symbol;Acc:15797]
Coordinates
chr20:43560983-43561826:+
Coord C1 exon
chr20:43560983-43561073
Coord A exon
chr20:43561074-43561712
Coord C2 exon
chr20:43561713-43561826
Length
639 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
ACAAGCTGCCTACCCTCCAGGTG
3' ss Score
6.46
Exon sequences
Seq C1 exon
CCTCCAGCCCAGGCTGCATACTATGGCTGTGGCCCAGTGACACCCACCCAGCCTGCCCCCAGGTGGACATCCCAGCCACCTAGACCTTCCT
Seq A exon
GTGAGTGACCCAGCCCCTTCCACTCTCAGACTGGCCTATTGGTGTGGGCCCCGTGAGGCAGTCATAACACAGGGATGAAACCTGGCTCTGCCACTTCCCAAGGTGGGTGACTTCACTTCTCTGAGCCTCAGTTTCCTCTTCTGAGCATGGGCCTGAATGAGACGTGTGTAAAGTACCAAGCACAGTGGTGAGCCAATGGAAGACACGCAGCTAGCCACCAGCAGTCATCACCAAAGATGCCTCTGATTTGTGACTCTGAAAATTCTTGCAAAGCTGAGAAGGTGAAATTCCTCTGGCTATATTGTTGACCAAAGGCCCTCCTCTGTAAGAGTGAATTGCACGCTCACTTGAAACTATCTTGAGGGACTAAGGTGTACAATCCTGGTGCTTATGCAGTTTGGGGCTCTAGGTAGACACGAGCTGGCTTTGAAATTGTAGATTCCTACACTCCCCCTTTCTGGAGTTCTGGGTCTAAGTGAATTGACTCCTATTTCTGTTGTGAATGTTGTAGTTTCCCTTCCCATTCTCTTGGTGGCCCTGGAAGCTTCTAGGCACAGTGTGCCACCCTGATTATTCCCACCACTCCATCCAACTTTTCTCTCTCTGTGGTGTCTGCACCACAAGCTGCCTACCCTCCAG
Seq C2 exon
GTGCCTCAATGGTCCGGCCACCAGTTGTGCCTCGGCGCCCCCCGGCCCACATCAGCAGTGTCAGGCAGGCCTCCACCCAGGTGCCACGCACGGTGCCTCATACCCAGAGAGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000101104-PABPC1L:NM_001124756:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.667 A=NA C2=0.994
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCCAGGCTGCATACTATGG
R:
TACTCTCTGGGTATGAGGCACC
Band lengths:
198-837
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)