MmuINT1026147 @ mm10
Intron Retention
Gene
ENSMUSG00000022283 | Pabpc1
Description
poly(A) binding protein, cytoplasmic 1 [Source:MGI Symbol;Acc:MGI:1349722]
Coordinates
chr15:36595661-36596655:-
Coord C1 exon
chr15:36596563-36596655
Coord A exon
chr15:36596100-36596562
Coord C2 exon
chr15:36595661-36596099
Length
463 bp
Sequences
Splice sites
5' ss Seq
TAAGTGAGT
5' ss Score
6.43
3' ss Seq
TCTTTTTTTAACATTTACAGATT
3' ss Score
9.04
Exon sequences
Seq C1 exon
GTTGATGAAGCTGTAGCTGTACTACAAGCCCACCAAGCGAAAGAGGCTGCCCAGAAAGCAGTGAACAGTGCCACTGGTGTTCCAACTGTCTAA
Seq A exon
GTGAGTTCTCCCTCGCCCGCTTGTTCCAGACATAAGGACATTAGGTCAGCTTTCCAGAGGGGTATATACATAACGAAATCTTTTTCACCTTAAATACTGATCAGCAATTTTAAGTCAATACTTGGAAACAGATTTTGCATAGTAAATTGTATGCAATGCCCTGTAACGGAAGTTGGCTTTCATAATCGGTACTTTTTAAAAAATTGGGTGATGGCTTTAAGCAGTTTCTTGGACCTCTCTCTGTCCCACTACCAGGAAACTGTTAGTGCTTGGTTGAGTATATATAGTAAGGTCAGTAGTAAAAAGATACTAGAATCCTGTTTTTTGTGGGCCATGTTGTATGTGATGTGATAGCTGTGAGTATTAAAGGAGTGGGTGTGGCTGTGCCAGTACAAACAGGCAGCAGACTGACCCACTGAATTCAGGCAGGGGCTTTAATTATGTCTTTTTTTAACATTTACAG
Seq C2 exon
ATTGATCAGGGACCACGAACAGAAACTCGTGCTTCACCGAAGAAAAATATCTTAAACATCGAAAAATTTAAATATTATGAAAAAAAACATTGCAAAATATAAAATAAATAAAAAAAGGAAAGGAAACTTTGAACCTTATGTACCGAGCAAATGCCAGGTCTAGCAAACAGTGCTAGTCCTAGATTACTTGATTTAAAACAACAAAAAAATACAAAAAAATAGTAAAATATAAAAACAAATTAATGTTTTATAGACCCTGGGAAAAGAATTTTCAGCAAAGTACAAAAATTTAAAGCATTCCTTTCTTTAATTTTGTAATTCTTTACTGTGGAATAGCTTGGGACATCAGCTCTGTTTTAAGGAGCAGAACTGATGACTGAGCAAGGAAACGTAATTTGGATTATAAAATTCTTGCTTTAATAAAAATTCCTTAAACAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022283:ENSMUST00000001809:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=0.669 A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0065813=PABP=PD(9.7=22.6)
A:
NA
C2:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCTGTACTACAAGCCCACCA
R:
TCTTTTCCCAGGGTCTATAAAACA
Band lengths:
346-809
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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