MmuINT1026151 @ mm10
Intron Retention
Gene
ENSMUSG00000022283 | Pabpc1
Description
poly(A) binding protein, cytoplasmic 1 [Source:MGI Symbol;Acc:MGI:1349722]
Coordinates
chr15:36598952-36599477:-
Coord C1 exon
chr15:36599205-36599477
Coord A exon
chr15:36599043-36599204
Coord C2 exon
chr15:36598952-36599042
Length
162 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
GACTTATTTTCTTTACCCAGACT
3' ss Score
6.47
Exon sequences
Seq C1 exon
GTAATGATGGAGGGTGGGCGCAGCAAAGGGTTTGGTTTTGTATGTTTCTCATCCCCTGAAGAAGCCACTAAAGCAGTTACAGAGATGAATGGTAGAATTGTGGCCACGAAGCCACTGTATGTAGCTTTAGCTCAGCGCAAAGAAGAGCGCCAGGCTCACCTCACTAACCAGTATATGCAGAGGATGGCAAGTGTACGAGCTGTGCCCAACCCCGTGATCAACCCCTACCAGCCAGCACCTCCTTCAGGTTACTTCATGGCAGCTATCCCACAG
Seq A exon
GTGAGTGTGAAGAAGAAACTAAGTCAGGTTGGCTTCATAAGCTCTCCACGATAAAGCACTAAGTTATTCGATTGGGAAGACAAATGACAAGGGTGGTAGAGTCAGTTGTTTTGAGAGCATGTAATGATAGTTGTGTTTTGTGGACTTATTTTCTTTACCCAG
Seq C2 exon
ACTCAGAACCGTGCTGCATACTATCCTCCTAGCCAAATTGCTCAACTAAGACCAAGTCCTCGCTGGACTGCTCAGGGTGCCAGACCTCATC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022283:ENSMUST00000001809:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.308 A=NA C2=0.742
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(56.5=42.9)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCATCCCCTGAAGAAGCCACT
R:
GTATGCAGCACGGTTCTGAGT
Band lengths:
246-408
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