MmuINT1026433 @ mm10
Intron Retention
Gene
ENSMUSG00000024992 | Pde6c
Description
phosphodiesterase 6C, cGMP specific, cone, alpha prime [Source:MGI Symbol;Acc:MGI:105956]
Coordinates
chr19:38180006-38180254:+
Coord C1 exon
chr19:38180006-38180080
Coord A exon
chr19:38180081-38180170
Coord C2 exon
chr19:38180171-38180254
Length
90 bp
Sequences
Splice sites
5' ss Seq
ATTGTAAAG
5' ss Score
-3.19
3' ss Seq
GGATTCACTTCTCTTTCTAGCCT
3' ss Score
6.82
Exon sequences
Seq C1 exon
GTAGCACTTCTGGTTGCAAATGAATTTTGGGAACAAGGAGATCTGGAAAGAACAGTGCTGCAGCAGCAACCAATT
Seq A exon
GTAAAGACCCCTTCATCACTGTGTTACCTATTAGAAACCACCCCCGAAACTCTTAGAAAATACCTTAAAAGGATTCACTTCTCTTTCTAG
Seq C2 exon
CCTATGATGGACAGAAGCAAAAAGGATGAACTCCCGAAACTTCAAGTGGGATTTATTGATTTTGTTTGTACTTTCGTATATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024992:ENSMUST00000025956:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.160 A=NA C2=0.196
Domain overlap (PFAM):
C1:
PF0023314=PDEase_I=FE(9.6=100)
A:
NA
C2:
PF0023314=PDEase_I=FE(10.8=100)
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:
GTAGCACTTCTGGTTGCAAATGA
R:
ATCAATAAATCCCACTTGAAGTTTCG
Band lengths:
135-225
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