MmuINT0117090 @ mm9
Intron Retention
Gene
ENSMUSG00000024992 | Pde6c
Description
phosphodiesterase 6C, cGMP specific, cone, alpha prime [Source:MGI Symbol;Acc:MGI:105956]
Coordinates
chr19:38231875-38233048:+
Coord C1 exon
chr19:38231875-38232024
Coord A exon
chr19:38232025-38232904
Coord C2 exon
chr19:38232905-38233048
Length
880 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGC
5' ss Score
9.85
3' ss Seq
TCACTGTTCTTCCACTTCAGACT
3' ss Score
9.15
Exon sequences
Seq C1 exon
AAAGGACCGGTAGATGAGACTGGCTGGGTCATTAAAAATGTCTTGTCCCTGCCTATTGTCAACAAGAAAGAAGACATCGTGGGTGTAGCTACGTTTTACAACCGGAAGGATGGGAAACCCTTTGATGAGCATGATGAACATATCACTGAG
Seq A exon
GTAAGCGTGGGAAAGAACGGCAGGTGTGTCTGAGCATATCGCGGAACGACTGAGTCTGCAGTGATACTGTGAGGAACGGTTAAGACGAAGAGTCTCATCGTTGTCATCAGGGCATTGTTAACTGTGTCATTTCGGTTTCTGGGTTGCTATATATTGCATCATCTTCTGTACAAGTATAAAGTCTGACTTCGCCCATATTCTCTCCAATCCTATAAAAACATTGAAAAGTATTTTTTTTATATTCCTCCTTTTCTTTTTATAATCTCTCTCATTCTCAGCCTCAAACGTCTGTCTAATTTTTAGCTCCTGCTTTATTTTATCCTGTTTGTAATTCCTTTCCTGCGGTAGACCGTTCTTGAGACTTGGCACTTTGAAAAGCAAAGCTTAGTTCATTTTACTGTCTGGGCAATAAATTCTGATTTTATTTTTTTTCTCATGCTAATACAAAGAACTGGGTTGGCAGCGTAGGTCGGGGAGGGCTCATGACATCCCACCCCTAGCCACTGTTAATTGGTGGCTGATGGAGAAGGGTCAGTTTTCCTCAGGAAGGAGCCCCCGAGAAGCTATTTGTGCTCAGTAGCTGGTTCCACACCCACGCACATACAGTCAGCCCTGAGTGGATCTGGTGGGTTTGAACCCAGAGGACATGAAGTTGGGAAGTAGGAGTGATAGCAGAAGAACTAGAAGGAACAGAACAGAGGTGTGAATTTGATTAAAGAGATTATATGCACAGATGATTTCTCAAGCAATAATATTTTTTTTTTAAGAAAAGAACTGGGTCGGTGGTGGTGGGAGATCAGTATAGGAAAGTATGTGGGTTTTCCACAAAGCAATTTTAATTTAACATTAGAGGATCTGAGTCACTGTTCTTCCACTTCAG
Seq C2 exon
ACTTTAACCCAGTTTCTTGGATGGTCTCTTTTAAACACCGATACCTATGAGCGAGTGAACAAGCTGGAAAGCAGAAAGGACATTGCTCAGGAAATGGTTATGAACCTCACAAAAGCCACCCCGGATGAAATCAGCTCTATTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024992-Pde6c:NM_001170959:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.040 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0159021=GAF=FE(27.5=100)
A:
NA
C2:
PF0159021=GAF=PD(5.1=18.8)
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:
AAAGGACCGGTAGATGAGACTG
R:
CAGAATAGAGCTGATTTCATCCGGG
Band lengths:
294-1174
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: