MmuINT0114455 @ mm10
Intron Retention
Gene
ENSMUSG00000054582 | Pabpc1l
Description
poly(A) binding protein, cytoplasmic 1-like [Source:MGI Symbol;Acc:MGI:1922908]
Coordinates
chr2:164032488-164035382:+
Coord C1 exon
chr2:164032488-164032582
Coord A exon
chr2:164032583-164035244
Coord C2 exon
chr2:164035245-164035382
Length
2662 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
TTCCTCCTCTTCCTCTCCAGGCC
3' ss Score
12.24
Exon sequences
Seq C1 exon
GAAATATGCAGAGTGTGAAGGTGATGAGAGACAGCAATGGGCAATCCCGGGGCTTCGGCTTTGTCAACTTTGAGAAGCATGAGGAAGCCCAGAAG
Seq A exon
GTAGGTGTCTCCATGGTTCTGCTCCAGAAAGGAGCCGCAAAGCCAGGCTTGGGAAGCCAGAAGATCAGGGGCAGGCCTGCCAGCAGAGGGTGAGAAAGCCCCGCCCTCCCCCTGCCCCGCCCCCTGCCCGGAATGGTAGGATTTGGCCTTATCCTTCCTTGTTGGTTTCTAAATCTAGAAGTTCAAAGAATTGAACATTTAGGCATGGAAGCATTCCTCACTGTGTGCAAACACTAATAACTGACTTCTTGGGAAGCCAGAGTTCCCCCTCAAATATTTCTCCCCACGCCAGTAAAAAGTCCTAACCACCGAGTCAGTGTGCACTAGGGTCTGTCTGACTACCATGGCTTTCTGTGGATAAACCGATGGGAAATCAATTCTTCAAGTGGATGTCCTCAGGCAGAAGGTGCAGGATCGTATGCCATGTAACAGGGTCAGGCTTGTTAAGAAGAGAAAACTCTCAGGGCTGGAGAGATGGCTCAGCAGTTAAGAATACTTGCTGCTCTTCCAGAGGCCACTGAGTGCAGTTTCCAGCACCAACATCAGTGGGCTCACAACGGGCTGTAACTCCAGCTCAGGGATCTGCTGCCCTCTTCTGGCCCCTTGAGCACCTGCCCACAGGCAGCACACTCACACACAGATAGACACCATACATTACATCTTTTTCTTATATGCTTTGTAATGTAATGTAAAATATTGAGGTGGCCGGGAGATGGCAGAGTGGTTAACAGCACTGGCTGCTCTTACAGAGGACCTGGGTTCAATTCCCAGCTCTCCCATGGTAGCTCACAACCATCCATAACTCCATGTCCAGGGAATCTGACTCCCTCTTTTGGCCTCCATGGGCACCAGGAACAGACATAGTACACAGACACAATTCAAACTGTTATACACATAAAATAATAAAATAACTTTATTTTTATTTTATTTTTTTATTTATTTATTTTTAGTTTTTTGAGACAGGGTTTCTCTGTGTAGCCTGAATGTCCTGGACCTCACTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATTCGCCTGCCTCTGCCTCCCAAGTGTTGGGATTAAAGGCATGCGCCACCATGCCCAGCTAACTTTAAATTTTTTAAAAAAATATTTTTTTTAAAAAGAAGATAAAGCTGGGTGGTGATGGCACTCTCGGGAGGCAGAGGCGGGCAGATTGCACGAGAGTTCCCAGATAGCCAAGGCTACACAGAGAAACCCTGTCTCAGAGAGAGAGAGAGAGAGAAGAAAAGAGAAAGAGAGGGAGGAAGAAGAGGGGGAAAGTGAGAGGAAAGAGGAAGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGAAGAAAAATCAGGATTGAAGTGCAATGTTTCTTGAACTTATGAAAGCCCTCATGGTTAGCAAAAGGCATTGTTCTGCATTGTAAACTGTACCACGAAGGATTGTGATTTAGACACCAAGCCATCTTGGAAGAACAATGCTTGCTTTGTTCTAATGAGCCCTGTGTGGGGGCGACAGAATACAAGTTTAACTTATTTTCTAATAGACCTTCTAGAGCAGTGTAAAGTTCCTGGCAAAACTGGGTAGATGGCGTAGATGTCCCCCATACCTCTGCCATGCACAGCTTCCCCCACCCTCAGCATTCCCAGCAGGGAGGTACATTTGTCACACTGGCGAATCTACTTCCGCGATGTACCATCATCAACTGGGGGGGGGTGTCTCTGGTTTACTCTGGGATTCATTCTTGGTGTTGTTCACTCTCTGGCTTTGGACCAATATCGAAGTGTATGCATCCACCGTTACCATAGTTTTAGCTCTCTAAAGCCTGTATTCCACTAGTCCTTTACAATCTGCTAGCCTCCTGACCTGCACTGAGTTTCTTACTGGCCTCGAAGTTCTGCCTTTTCCAGACTGTCACCTGGAGAGAGTTAGATGTTCATTAGAGTGAGAGTTAGTTGCATCCTTTACGGATTGGCTTCTTTCAGTGGAATGTGCATTTAAATATTTGGGGCTAGAGAGCTGGCTCAGCAGTTAAGAGTTCCTGCAGAGAATCCAAGTTCAGTTCCCCTGGACTCTACAGTGCAGTAGGAGGCTCACAACCCTCTGTAGCTCTGGGGATCTGATGTCCTCTTCTGGCCTCACTGGGCACTGGCATACAAGCATTCATACCAATGCATACCAATACAATGTACCTACACACGCATTAAACGTCTTTAAATTTAAATATGGAAAACTTAACATTAATTTGAGTTTTGTTTTTCTTTTCGTTTGAGACAGGTTCTTAGCTTGTAGCCACAACTGGCCTGGTCAAAGAGGAAACCAAGTTAGCCCTATACTTACCACAGTTCTCTGTCCCATCTCCTGGATGCCAGGGTTCACAGCCACATTGTCACCACTCAGGCTTCTGTTTATTAAAATAAAGCCTAAATCAAAAATATTAAATCCATCACTTACTCTAGAATCTTGGCCATTTCTTTTAAAATGTGGTTGTCCTGTAAGAGACTTTTCCATGGTATCAATTATTCTCAGCTAAGAAGGCCAGCCTAGTTATAGGTGGTCTCAGCTGGCCCAGGAGTCAGGATTGGAGACAGGGCCACGTGTAGATGGTTCACCAGGGGCTTTCCTCCTCTTCCTCTCCAG
Seq C2 exon
GCCGTGGACCACATGAATGGGAAGGAGGTGAGCGGGCAGCTGCTCTATGTGGGTCGGGCCCAGAAGCGGGCAGAACGGCAGAGCGAGCTGAAGCGCAGGTTTGAACAAATGAAGCAGGAGAGGCAGAACCGCTACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054582:ENSMUST00000067715:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.062 A=NA C2=0.391
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=FE(44.3=100)
A:
NA
C2:
PF0007617=RRM_1=PD(21.4=32.6)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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