MmuINT0117567 @ mm9
Intron Retention
Gene
ENSMUSG00000026784 | Pdss1
Description
prenyl (solanesyl) diphosphate synthase, subunit 1 [Source:MGI Symbol;Acc:MGI:1889278]
Coordinates
chr2:22785060-22785377:+
Coord C1 exon
chr2:22785060-22785140
Coord A exon
chr2:22785141-22785263
Coord C2 exon
chr2:22785264-22785377
Length
123 bp
Sequences
Splice sites
5' ss Seq
CAGGTTGGT
5' ss Score
8.08
3' ss Seq
CTCATCTTTCCTTTTGCCAGCTC
3' ss Score
7.82
Exon sequences
Seq C1 exon
GTCTCTGTCCTGGGTTGCCCTGACCCAGTGGTGCATGAGATAGCCTATCAGTATGGGAAAAATGTTGGAATAGCTTTTCAG
Seq A exon
GTTGGTATACTTGTTTGTGGGAATGGTGACATACAGGCACAGCCTGCATTTTTCTCAGTGTAGTGTGCTAAGCAGTGGAGACAGTGGCAGCTCAGTGGGTGTACTCATCTTTCCTTTTGCCAG
Seq C2 exon
CTCATAGATGATGTATTGGATTTCACCTCATGTTCTGACCAGATGGGCAAGCCAACATCTGCAGACCTGAAGCTAGGCATAGCCACTGGCCCTGTCTTGTTTGCTTGCCAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026784-Pdss1:NM_019501:8
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:
PF0034812=polyprenyl_synt=FE(9.9=100),PF073076=HEPPP_synt_1=PD(3.0=14.8)
A:
NA
C2:
PF0034812=polyprenyl_synt=FE(14.1=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:
TCTCTGTCCTGGGTTGCCC
R:
AAGCAAACAAGACAGGGCCAG
Band lengths:
186-309
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: