MmuINT0114438 @ mm9
Intron Retention
Gene
ENSMUSG00000022283 | Pabpc1
Description
poly(A) binding protein, cytoplasmic 1 [Source:MGI Symbol;Acc:MGI:1349722]
Coordinates
chr15:36525413-36526410:-
Coord C1 exon
chr15:36526318-36526410
Coord A exon
chr15:36525855-36526317
Coord C2 exon
chr15:36525413-36525854
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
ATTGATCAGGGACCACGAACAGAAACTCGTGCTTCACCGAAGAAAAATATCTTAAACATCGAAAAATTTAAATATTATGAAAAAAAACATTGCAAAATATAAAATAAATAAAAAAAGGAAAGGAAACTTTGAACCTTATGTACCGAGCAAATGCCAGGTCTAGCAAACAGTGCTAGTCCTAGATTACTTGATTTAAAACAACAAAAAAATACAAAAAAATAGTAAAATATAAAAACAAATTAATGTTTTATAGACCCTGGGAAAAGAATTTTCAGCAAAGTACAAAAATTTAAAGCATTCCTTTCTTTAATTTTGTAATTCTTTACTGTGGAATAGCTTGGGACATCAGCTCTGTTTTAAGGAGCAGAACTGATGACTGAGCAAGGAAACGTAATTTGGATTATAAAATTCTTGCTTTAATAAAAATTCCTTAAACAGTAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022283-Pabpc1:NM_008774:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
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
Rat
(rn6)
No conservation detected
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: