MmuINT0117081 @ mm10
Intron Retention
Gene
ENSMUSG00000024992 | Pde6c
Description
phosphodiesterase 6C, cGMP specific, cone, alpha prime [Source:MGI Symbol;Acc:MGI:105956]
Coordinates
chr19:38180171-38180932:+
Coord C1 exon
chr19:38180171-38180254
Coord A exon
chr19:38180255-38180775
Coord C2 exon
chr19:38180776-38180932
Length
521 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGT
5' ss Score
9.79
3' ss Seq
CCACCTCAACTTCTCTGCAGGAG
3' ss Score
8.24
Exon sequences
Seq C1 exon
CCTATGATGGACAGAAGCAAAAAGGATGAACTCCCGAAACTTCAAGTGGGATTTATTGATTTTGTTTGTACTTTCGTATATAAG
Seq A exon
GTATGTAAACAAACTATTTGAATGAACTGTAGAATCATTTCATTGAGAAGTTTCCTTTCAAACTAAAATTAGAGTGAGCTGGGTGTGGTGGTATATACCTGCAATCCCAGCTCTCAGGAGGCTGGGGGTCAAGATTTCAAAGTCACCTTGGACTACATGCTAAGTTTCAGGCCAGCCTGGGATATATCACAATACCTTATCTAATAAATTAATTAAAACTAACCCAAGTAAAAAAGTTACCAATGAAGAAAGCCATTAGGTCATCCCACTCCCTGAGTAGTCTGAGCACTCACATTTATTTATTCAGAGTGGAATAAAATGTACAAGAACTCACATGTGAGCCATGCACAGACCTACTTGACAGACGGCAAAGAGCACCCACGTTTCCCAAGCTTCAGAAGCAGACAGGCTCACCCCAGCAGCTCCCAACACTGCCCAGCTCACAGCTTCCCTTCTACACCAGATCACGACTGAAAGTCAACTACCTGATTAATCAGACTCCCACCTCAACTTCTCTGCAG
Seq C2 exon
GAGTTCTCTCGGTTTCATGGAGAGATCACACCCATGCTGAACGGCCTTCAGAATAACAGGGTGGAATGGAAATCCCTGGCGGAGGAGTACGAGGCGAAGGTGAAGGTGACTGAAGAAGAGGCGGGAAAGCAGGAAGAAGAAGCCTCAGATGGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024992:ENSMUST00000025956:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.196 A=NA C2=0.349
Domain overlap (PFAM):
C1:
PF0023314=PDEase_I=FE(10.8=100)
A:
NA
C2:
PF0023314=PDEase_I=PD(7.6=35.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTATGATGGACAGAAGCAAAAAGG
R:
TTCCATCTGAGGCTTCTTCTTCC
Band lengths:
238-759
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- 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