MmuINT0114449 @ mm9
Intron Retention
Gene
ENSMUSG00000054582 | Pabpc1l
Description
poly(A) binding protein, cytoplasmic 1-like [Source:MGI Symbol;Acc:MGI:1922908]
Coordinates
chr2:163871599-163873310:+
Coord C1 exon
chr2:163871599-163871705
Coord A exon
chr2:163871706-163873216
Coord C2 exon
chr2:163873217-163873310
Length
1511 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGG
5' ss Score
8.05
3' ss Seq
GTTCCTGGCACCATGTGCAGGTC
3' ss Score
5.98
Exon sequences
Seq C1 exon
TCAACATTGGTACCCAGACTACAGGACCAGGTGGGGAGGGATCCTCTATCCCAGGCCAGCTTCTCGTGCCACATAGAGGAACCTCAGCTGTACACAGTGCCCATGGG
Seq A exon
GTAAGGTGGTCTGCTCACTGTGGGCTCTGGGTATCATAAGTTTGGCTAAGGTGTTTTTCCTCTGGTCCTTGCTTTGCTTTCTTTTTCTTTCTTTCTTTCTTTTTTTTTTTTTTTTTTGGTTTTTTGAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTCTGTAGACCAGGGTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGCGTGCGCCACCATGCCCGGCTGGTCCTTGCTTTTCTTCACTTACAAAATTTCATTTACTAATGTTCGCAAATCAGTCAAAGATCACTCCTGCTAACAGAGGGGAGAGAGAACTGTGGTCACGTTCTGTTTACTGGTTACAAACCTTTTGTTTAAGTCATTACCAAAATGAACTTGAACTTGTGTTTGAGTGCAGGAGACAGATTCTAAGACCGTGCTGAGCGTGGAAGGGCTGAGAGGAACCTTCAAAACAGGACTAAAACTGTTTATTATAATTAAAAGGCTATGTATCTCCTATCCCCACAAAGGTTTTAAATTCAGTATTACTGAAACATGTCTAGAATTTCAATGTTTTCTTTGGATGACTTCTTGTAAAAAGAACAATTGTCTTTTAATCGCAACAGCACTTTTAAAGTTAGCGCAATATAAGAGGGCTATGGAGGAGCTGGAGAAATGGCTCAGTGGTTAAAAGCACTGGCTGCTCTTCCAGAGGTCCTGAGTTCAATTCTCAGCAACCACATGGTGGCTCACAACCATATGTAATAGGATCTGATGCTCTCTCCTGGCACACAGGTATACATAGCACTCGTATACATAAAATAAATACATAAATCTTTTCTTTTAAAAAGCAAGCATAAGCCGGGCAGTGGTGGCGCACTCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGCGGATTTCTGAGTTCATGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGATAGCCAGGGCTACACAGAAGAAACCCTGTCTCGAAAAACAAAACACAAAACAAAAACAAAAAACAAACAAAAAAATTTAAAAAACTAAAAAAATAAATAAGCAAGCGTAAAATTCAAGGAAAATCAAGAATAACACACACAACACATGCATGTACCCCAATAAGATGTATGTTGCTGTTGCTGTGTTCATAAAGCTTGCTGAGAAAAGTGCTCTATCGGATGCACAGTGATTATTATTAAGTGTGCCTTTCAGGTGACAATGGATTTTCATTGGTTCACAGCATCTCTGTGCATAACTTTGTTTTCCAGTCCACGCCCTTGTGAGGGACTCTCTGCGCCCCGCCTCCTGCCCCGCCCCACCCCGCCACCACCACCCCCCCCCCCCGCCCCGCCCCGCCCCTGACTGTGTAGACCTTGCTTCCTTCCCTCTTCCAGAGCCTTTCCTGGATGCTTGTGTTCACCCGCTAGGGTAAGTGTATGAGGCCTTTCCTATCCGTGTGGTTAAGGGATGTGTTCCTGGCACCATGTGCAG
Seq C2 exon
GTCCAGGAGTCGGCCGTGTATGTCCCTGGCCATCAGCCTCTGACTGTGTCCATGCTGGCCGCTGCACCCCTACACGAGCAAAAGCAGATGATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054582-Pabpc1l:NM_001114079:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.986 A=NA C2=0.328
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0065813=PABP=PU(27.8=62.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACATTGGTACCCAGACTACAGGA
R:
GCTTTTGCTCGTGTAGGGGTG
Band lengths:
190-1701
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: