MmuINT1026144 @ mm10
Intron Retention
Gene
ENSMUSG00000022283 | Pabpc1
Description
poly(A) binding protein, cytoplasmic 1 [Source:MGI Symbol;Acc:MGI:1349722]
Coordinates
chr15:36597457-36598127:-
Coord C1 exon
chr15:36597973-36598127
Coord A exon
chr15:36597542-36597972
Coord C2 exon
chr15:36597457-36597541
Length
431 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAG
5' ss Score
8.68
3' ss Seq
GTTTTCTGTTTTATGTGTAGCCT
3' ss Score
7.78
Exon sequences
Seq C1 exon
CTAACACATCAACACAGACAATGGGTCCACGTCCTGCAGCTGCTGCTGCTGCAGCCACTCCTGCTGTCCGCACCGTTCCCCAGTATAAATATGCTGCGGGAGTCCGCAATCCCCAGCAACATCTTAATGCACAGCCACAAGTTACCATGCAACAG
Seq A exon
GTACAGTTTAATCATTTATTTGCAAGGGTCATAATGTTCAGCTGAAATCCAAGGTCTGATGGTAACTGCACAAGCTATGAGCATAGACTTACCTGGGCCATCTTATTAAGGTTCTATGTGAAGAAAGTTGACGGGCAGCCAGCAGTCTCCCTATGTGGTGTCTTGTTTAGGATGGGTGTATTAGACTTAATCTTTTTCCTAGTCCTGGAACCAAAAACTATAAAGAAGACTAAAATGTAATTGCATCTCAAGCACAGATGTGCCACATGGGGTTGGTTATCTGTACTTGCTGACCTTTAGTCAGTATTTCTCTCAGCTTCTCTAGATCAAATTCAGGTAGCACTCTGTCCTTCCTATGACTATCCGTTGAGAGATGGCTGGTTTATGTCTCATTACTTCAATATTAAGAGGGTTTTCTGTTTTATGTGTAG
Seq C2 exon
CCTGCTGTTCATGTGCAAGGTCAAGAACCTTTAACTGCTTCCATGTTGGCATCTGCGCCCCCGCAAGAGCAGAAGCAAATGTTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022283:ENSMUST00000001809:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.860 A=NA C2=0.966
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0065813=PABP=PU(27.8=69.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACACATCAACACAGACAATGGG
R:
CCAACATTTGCTTCTGCTCTTGC
Band lengths:
238-669
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