MmuINT0114439 @ mm9
Intron Retention
Gene
ENSMUSG00000022283 | Pabpc1
Description
poly(A) binding protein, cytoplasmic 1 [Source:MGI Symbol;Acc:MGI:1349722]
Coordinates
chr15:36535197-36535692:-
Coord C1 exon
chr15:36535499-36535692
Coord A exon
chr15:36535313-36535498
Coord C2 exon
chr15:36535197-36535312
Length
186 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
AGTGTTCTGTTTCACCCTAGGTG
3' ss Score
10.96
Exon sequences
Seq C1 exon
CGGAACGTGCTTTGGACACCATGAATTTTGATGTTATAAAGGGCAAGCCAGTACGCATCATGTGGTCTCAGCGTGATCCATCACTTCGCAAAAGTGGAGTAGGCAACATATTCATTAAAAATTTGGACAAATCCATCGACAATAAAGCACTATATGATACGTTTTCTGCGTTTGGTAACATCCTTTCATGTAAG
Seq A exon
GTAAGCTGAGCTATAACAGGTTAGTATTTGCAGCGTTGTGCTACTTTTAGATTTGGAAGAGATCTTTGTGCTGTCTGTTAAATACTGTCATTATTTCTGAAGTTCCTGGGATTGGGTGGCTAACATTTCTACAGAGTAGGAAAGCAATAGCAAGTAGTGAAAAGTGAGTGTTCTGTTTCACCCTAG
Seq C2 exon
GTGGTTTGTGATGAAAATGGCTCCAAGGGCTATGGATTTGTACACTTTGAAACACAGGAAGCAGCTGAAAGAGCTATTGAAAAAATGAATGGGATGCTTCTAAATGATCGTAAAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022283-Pabpc1:NM_008774:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(25.4=27.7),PF0007617=RRM_1=PU(40.6=43.1)
A:
NA
C2:
PF0007617=RRM_1=FE(55.1=100)
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:
ACGTGCTTTGGACACCATGAA
R:
TCAGCTGCTTCCTGTGTTTCA
Band lengths:
258-444
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: