MmuINT0117088 @ mm9
Intron Retention
Gene
ENSMUSG00000024992 | Pde6c
Description
phosphodiesterase 6C, cGMP specific, cone, alpha prime [Source:MGI Symbol;Acc:MGI:105956]
Coordinates
chr19:38226187-38228231:+
Coord C1 exon
chr19:38226187-38226253
Coord A exon
chr19:38226254-38228183
Coord C2 exon
chr19:38228184-38228231
Length
1930 bp
Sequences
Splice sites
5' ss Seq
TTTGTAAGT
5' ss Score
7.4
3' ss Seq
CTCTGTCTATTGCTTCACAGATC
3' ss Score
10.48
Exon sequences
Seq C1 exon
GTCACCTCCAGCAGACCACTGGACGCTTGTTAGTGGATTGCCAACATACGTTGCAGAAAATGGATTT
Seq A exon
GTAAGTCATTAGACAAACTTAAATGCTAAGTAACCATGTGTGAGACCCTTACTAGATAAATACAACTGTTGACCCAAGAATAACTGAAACAAGGGTAGATGGTCACTTTCTTGGCATAGGAGAAAGGAAAGAGGAATCTAGGGAGGGAAATGTGGGTTAATCAGGATGCTGATATTGTGTCAGAATATTCAGTTAACTTGAGAAAGATTCATTCATTTCTCCACCTTTTACTCTGAAGCCACACACTTTTCAGACATCTGCTTTAAAGCCAGGAATATTAAAAGTCAGTGGCTGTGGCTTACGATAGGTTCAATTCCATTTCAAATGCTCACTCAATGGTCTTAATATGATCACAAGTGTTTTCTGTGAGACCTCAAAGTAAAGGCTGGAAAACACATGTCCATGACAGAAAGGCGGGGGGGGGGGGGGGCAAGGGGAATTGATTGGTTTGCATCTTTAAACCACATTTGGGAGACCCACAGTCCAGGAAATAATGTTGAATATTCAAGTTAGATCATGAAATTAAGAATGGAAGGTTAAGAATCCTCAGGTTCTTAAACTATGAGTACTCATGGAAACAGCAGGATTCTATAATCCCAGCAGCGAGGAGGCTGCTGAGCAGCAAGATTGCTAATGCTATGCCATGCAAAGCTACATAGAGAAGTCCAGACAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAACAAGTAAGCAAAAACAAAAAACAAAAAACAAAAAAACACCCAAAAGTAAATATGCATAAATCAATCAATCAATCGATCGATCGATCAATAAGCCAAAGCTTCAGAAGAGTTCCACATTTTCTTTGTAAGGCTAGTGGAGAAAGAGTAGATATGTTTTATTTACTGTTAGAAGGCACTTAACAGGGCTGGAGGGATGGCTCAGAGGTTAAGAACACTGACTGCCCTTCCAGAGGTCCTGAGTTCAAATCCCAGCAACCACAGATGGCTTACAACCATCTGCAGTGAGATCTGATGCCCTCTTCTTGTGTGTCTGAAGACAGCTACAGTGTACTTACATATAATAAATAAATAAATCCTTTTTTTTTAAAGGCACTTAATATTGGCAGCCCCCTTGTCTCACAGAGCTTGAAATTTGTGAGTGGGTAAATGTTAGTAGAAGTATTCTCCATGGTAGGAGTATTGCACCAGGATTTTCCCCAACCCTTAGCCAGGAGAGTCCATCCCATCAGTCCATCCCATCGCCCCTCTTTGGAGTTTCAAATTACAATTCAAGTTTCACCCAGTGAATCTGAACAGAGCCCTAAACCTTTTGGGACTTCAATGTCCTCATCTTTCAAAGGAGAAGATGACTCAGCCATTACCACCCAAGCCTGAAATGCTATCATTTTAAGTGGAACTCTGGAAGAAGTGAAAATAGAGACTTGTATTAAGACCCTCGTGTGCTTATGACTCTAAAAACTAAAAATGGGTATAAGAAACTACCTCTGAATTCTGACAGTAAGCGCAGTATTTCATAAGGAATCCTTACGTTGGAGCAAGTGAAACATTGCTTAGCCTTTTCCTTTTACCAACCCCCCAAGCAACCCTACTTTGTAAAAGAATAAAGGGAGATCAGCACCCAGGCTCAAACCTGCCTCAGCAGAGCAGTCTTTCTCTTTTGCTTGGGTTGAGGAGTTGGGAAGTCGAAAGACATCACTTGGAAGTTGAAGAGTGGGGAGGAGCAAAGAGCAGGAAATGTCAATCAACGGCATAGCAGAAGAGGAGGTAACTTCAGAAGCAAATATGGCCTGACGTAGTGAGTGTGTCTTCATGTGTTTACCGAACAGCCAAGAGCTGTGTGGGAAACTCACTCCCAACATGCCTTCTCACTCTCCTCCATGGACTTACATGGTCCTAACCTCACCATGTTTCAGAATGACTCTGTCTATTGCTTCACAG
Seq C2 exon
ATCTGTAACATGCTGAATGCCCCTGCAGATGAGTACTTCACATTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024992-Pde6c:NM_001170959:7
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:
PF0159021=GAF=FE(12.4=100)
A:
NA
C2:
PF0159021=GAF=FE(8.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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: