MmuINT0114458 @ mm10
Intron Retention
Gene
ENSMUSG00000054582 | Pabpc1l
Description
poly(A) binding protein, cytoplasmic 1-like [Source:MGI Symbol;Acc:MGI:1922908]
Coordinates
chr2:164042317-164043640:+
Coord C1 exon
chr2:164042317-164042565
Coord A exon
chr2:164042566-164043549
Coord C2 exon
chr2:164043550-164043640
Length
984 bp
Sequences
Splice sites
5' ss Seq
CAGGTGACA
5' ss Score
5.49
3' ss Seq
CAGATCGTCTTCTTCCACAGTCT
3' ss Score
7.42
Exon sequences
Seq C1 exon
GTGATGACAGAAAGTAGCCACAGCAAGGGCTTTGGCTTTGTGTGCTTTTCCTCTCCAGAAGAGGCAACGAAGGCCGTGACGGAGATGAACGGGCGCATCGTGGGCACGAAACCGCTCTATGTGGCCCTGGCACAGCGCAAGGAGGAGCGGAAGGCCATCTTGACCAACCAGTATAGGCGACGCCCCTCTCACCCTGTCTTGAGCTCCTTCCAGCAGCCTACCAGCTACCTGCTCCCTGCTGTACCCCAG
Seq A exon
GTGACAGTGTGTCTACAGCTCCAGCTGGGGGACAGAACTTCACAGACAAATAGAGATTCTGTTGAAAAGACCTCGGACAAGCTGCTTCAACCCTTAGAGCCTCACTTGCTCCATCTTTAAAGGGGCCTCCATGCTATCTTGTCTTCCAGTCTCTGTGAGATTCCTGAATGTTGTCTGGCAGGAACTCTGGTTAAATGGATTTTGGAGGTCTTGAATTAAGTATCAAAGCCTAAATTTTTCTTTCTTTCTCCATTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTGATTTAATTATTTACTTCATGTATGTGAGTACACTGTCACTGTCTTCAGACACACCAGAAGAGGGCATCAGATCCCATCACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGAAGAGCAGATGGTGCTCTTAACCACTGAGCCATCTCTCCAGCCCCAGAATTTCTTTATCGTATCCATTATCTTCCCCAGTTATGTCAGCATCCATCGCCCCCTCCACCTCCCCACCTCCCCCCAAGCAGCCACAGTGCCTTTGGCGTTTTCCCCAACTCAGATGGTCACACAGCTGCCCTGGCTGTTTGTGTTCTGAGGTCCATGGCTAGGGAAATGACTTCATAGAACTCAGAGCAATAGAAAGATATGTGTGTTTGAAGACCAATTGCTGACATTCTTTAGCAATTGCTTGAGCTGGAACACATTGGAGTGACATACTCTATCACTGGGCCAGAGTGAGAAACACTGGTTGACATAAATCTGAGATCTTGTTCTGAGGGGCTTAGGGATAAGGGGAGATGGGAAGGGAGGGCGAATCCTTCATGGAGGCCAGAGATGTTTCCTGCAGGGGATAGTGTGGTTCCTCACATTGGTGTCCTTGAGAAGATGCGAAGCCCCTCACTTCAGATCGTCTTCTTCCACAG
Seq C2 exon
TCTACAGCCCAGGCTGTGTACTACAGTTCTGGCTCCATAACTCCAATGCAACCTGACCCCAGGTGGACAGCCCAGCCACATGGACCTCCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054582:ENSMUST00000067715:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.217 A=NA C2=0.613
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(56.5=47.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGACAGAAAGTAGCCACAGCA
R:
TGGAGGTCCATGTGGCTGG
Band lengths:
335-1319
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types