MmuINT0114448 @ mm10
Intron Retention
Gene
ENSMUSG00000054582 | Pabpc1l
Description
poly(A) binding protein, cytoplasmic 1-like [Source:MGI Symbol;Acc:MGI:1922908]
Coordinates
chr2:164044264-164045969:+
Coord C1 exon
chr2:164044264-164044380
Coord A exon
chr2:164044381-164045862
Coord C2 exon
chr2:164045863-164045969
Length
1482 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGT
5' ss Score
8.83
3' ss Seq
TTTTCCTTTCTTTTTTACAGTCA
3' ss Score
10.71
Exon sequences
Seq C1 exon
CTACCTGCCCTCCAGCTGCCTCTGTGGTCCAGCCTCTAAGCACGACGCAGCATCCCTGTATCCACCTGAGGGGTGCCAGCCAGGTCTCCAGCCAGGTGCCTCACACGCAGAGAGTAG
Seq A exon
GTGAGTGTGTGTGAGTGTTGCCAGGATTCGGAATGGAAGGGTGTCAAAGAGTGAGAGACCTGGGGGTTGGCAGTGAAGGTAAGTTTTGACCAGGCTCCATAGTGACCTTGCTTTCGTGGTGAGCCAGCCCGGCTTTGGAGGATGTCCGTTAACATAAACGTTAGCATGGCATCCAGCCCTTGGGAGTCACTTTGGGACCCTTGCTGATGGCTGTCTCTGCCGACTTAGTCTTTAAAATAGGGATAAAAATAGCGTGCCCATTTTGTTGGGAGGATTGGTGAGTCCACAAATGGAAGGACTTGCATCTTAGCAAGTACGGAAGGGGCTATGACTTGGAGACAGGTTGTCTCTTGCTAATATCCTCATATCTCTGTGCTGACCCTGTGCTCAGCACTGCGGTGGGGTGTTCTTCAGGGATTCTGCATAATGAGTCAGATGAACCCTCTGGTCTTCTGTTGCTGCCAGGTTTCAACTTATATAACATTTAGCTCTGTTGCTGCCGGGTTTCAACACCCATGGTCATTGTTATAGTCTTCAACTGTGGGAAAATCTGCACAACATATAATTGGCTGCTTCACTATTTTTAAAGGTTTATTTATTCTCATTTTATGTGCATGAGTGTTAGCCTCCACGTATGTGTGTGTAGTGCCCATGGAGGTCAGAGGAGGGTGTTGGATTCCCTGGAACTAGAGTTAGAGACAGTTGTGCATTGCTGTATGGGTGCTGGGAAGTGAACCGTGGTACTCTGCAAGAGCAGTGAGGACCTGATTGTTTTTAAGCCTGTTGTTTAGAGGCCTCCAGTACGTTCACAGTGCTGAGTACGAACTGCAGCCATTGCCACCACTGTCTCGAAAACAAAACTTTCCACCAGCCACAATTCCTCATTCATAATTCTTTCTAGCCTCTGAAAAACAAACCTATCCTTTTTTTTTTTTTTTTTGCCCCTTTGAATTTGCACTTGATCTTAGCCAGGAGGCTGACAAGCAGTCGTCCCTCTGATGCTGACTGAGTGTGGTTACTTCATGCAAATGGCGTGGGACTCTCAATGCTTTGTTATTTAGCATGGCGTCCTCAAGATTCAGCAATGTTCCGGCAAGATGCGATGTCTTGCATATGTAGATTCTGTGTCTTTTGGCTATGCATTCACGTGTTGAACACATGGACTGCTCTCACCCGTGGGTTCTTGTACACAGAAATTGCTACTATGAGCATGGGTTTTCAGATATCTCTTTGAGACTTTGCTTGCAACTCTTTTGAGTGCACATTCAGAACCTAGATTGCTAGATGTGTTGACCCTATGTTTAATTCTTTGAGGAATCGCCCCCCCCAATTGTATTTCCACAGTTGCTGTATCCCCAACATTCCTGCCAGCATTGCCCACATGTCCCAACTTCTTTACTGATTCACCAAAATTTGCCATGTATTTTTTTCTAAGTGGCCATTTGAAATCTGCTTTTTTCGTTTTTCCTTTCTTTTTTACAG
Seq C2 exon
TCAACATTGGTACCCAGACTACAGGACCAGGTGGGGAGGGATCCTCTATCCCAGGCCAGCTTCTCGTGCCACATAGAGGAACCTCAGCTGTACACAGTGCCCATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054582:ENSMUST00000067715:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.833 A=NA C2=0.926
Domain overlap (PFAM):
C1:
NO
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:
CTACCTGCCCTCCAGCTGC
R:
CCCATGGGCACTGTGTACA
Band lengths:
224-1706
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