MmuINT1026145 @ mm10
Intron Retention
Gene
ENSMUSG00000022283 | Pabpc1
Description
poly(A) binding protein, cytoplasmic 1 [Source:MGI Symbol;Acc:MGI:1349722]
Coordinates
chr15:36596964-36597541:-
Coord C1 exon
chr15:36597457-36597541
Coord A exon
chr15:36597095-36597456
Coord C2 exon
chr15:36596964-36597094
Length
362 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
TAGAGTGTCTGTTGTTCTAGGTG
3' ss Score
6.86
Exon sequences
Seq C1 exon
CCTGCTGTTCATGTGCAAGGTCAAGAACCTTTAACTGCTTCCATGTTGGCATCTGCGCCCCCGCAAGAGCAGAAGCAAATGTTGG
Seq A exon
GTAAGTAACTTTGTTGTCTTGGTCTGTCAGTTAGAGTTGACGAAAATAACAAGGACCACTTAGACACTTTGCACCTAAAATGAGATGGCTTAGGATGGTATGTGAAGGAATACTAGAAAACATGGTGGGCTACTGTTTGCCATTGACATTCCACTCTAGCCTTGAAACAAAGAAGCATTGTCTATGTTAATACCAAACACTTGAGGAACTGATACCACCAGAGAAGTGACTGCCTTGTGACAGATTGTGCTATACATACGGGTGTGGTAGCTAGTACATACTCTATATTAAATAAGGTAGGTTCCTAAACCCCTGGTTGATAATAGCCATTGCCACTCTGATTAGAGTGTCTGTTGTTCTAG
Seq C2 exon
GTGAACGGCTGTTTCCTCTTATCCAAGCCATGCACCCTTCTCTTGCTGGTAAAATCACTGGCATGCTGTTGGAGATTGATAACTCAGAATTACTTCACATGCTCGAGTCTCCAGAGTCTCTCCGCTCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022283:ENSMUST00000001809:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.966 A=NA C2=0.284
Domain overlap (PFAM):
C1:
PF0065813=PABP=PU(27.8=69.0)
A:
NA
C2:
PF0065813=PABP=FE(59.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGCTGTTCATGTGCAAGGT
R:
TTGAGCGGAGAGACTCTGGAG
Band lengths:
214-576
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