MmuINT0117080 @ mm9
Intron Retention
Gene
ENSMUSG00000024992 | Pde6c
Description
phosphodiesterase 6C, cGMP specific, cone, alpha prime [Source:MGI Symbol;Acc:MGI:105956]
Coordinates
chr19:38252748-38254744:+
Coord C1 exon
chr19:38252748-38252811
Coord A exon
chr19:38252812-38254660
Coord C2 exon
chr19:38254661-38254744
Length
1849 bp
Sequences
Splice sites
5' ss Seq
CAGGCAAGT
5' ss Score
3.1
3' ss Seq
GGATTCACTTCTCTTTCTAGCCT
3' ss Score
6.82
Exon sequences
Seq C1 exon
GGCCATGATGATGACTGCCTGTGACCTGTCTGCCATCACCAAGCCCTGGGAGGTGCAGAGTCAG
Seq A exon
GCAAGTCCCACAGCATTTCCTTCCCTGTCACACACCTGTGACCTGTCAGTCACACACCTTTATAACCTGTGACCTGTTACCTGTCACACACCTGTCAGTTACACACCTGTGACCTGTCAGTTACACCCCCTGTGACCTGCCACACACCTGTGACCTTTCATTCACACACCTGTGACCTGTCTGCCATCACCAAGCCCTGGGAAGTACAGAGTCAGGTTAAGTTTTGGGACATTTCTCTTCCTGTCACACATCAGGAGCTGCCTAAGTCCTGAAAGGCCACACAGTGATCTCTGACAACTACAGACTCCTCTTTTATGTTTACACACAGCAGCAGGCCAGTGGGTCACTGGATAATGTCCCAGAACAAGGAAAAACATAGAAGACTTTGGGAATAAAATGTGAGGTTGAAAGTGGGGTCTTCCTTATTATTAGACAAGCTATTTTTATGTAGAATTCTCCAGACATGATGGCTCAGTCCTATAATCTCATGAGGGGTCCAAGGCAGGATACAGGATTCAGTGATAACCTGGGCTACATAATAAGACCTATTAAATGAATCCAACATGTGATCTTCTCAGTATGGGAGGTGAGTCAGAACAGGCCTCAGTGGGATGGATGGTTCGTTCTATTTAGCTGGCCTTGCTCCCGAGGTCTCTTCTACAATGCACTCTCACTTCCTGGAAGGTACTGACTGGGGGTCCACACTCAGGGCTGTTCTTCATCTGTTTTGGGGGGAAGGTGATGAGGGGGTGCTTAGCTACCTGTCCTCTCATTAACTAGATGGAAGCAGCTGCCCTTTTTCAGTGACATCTAGGTGAAACTTTCGGCAGTAGAGCCAGAATTACTTCGGTTTAACTGACCATCCTGATTACATTTAGAAAGAAAAAGTCACTAGACTGCACTGTGGGAGAGGGCAGACACCTTGTTTTCAGCCATCTCTGGTTTGTGGCTGTGGATCCTGAGGAAAAGATAGTTTGCAAAGAGAAAAGTGTATACGCTTATGTAAGTTTTACATGGCCCAGGGCCTTCATAAGTAAACTCAAGCAAGTTACCATTGTGTATTTAAAAAACATATAAATTGTATATGTATATATATGTGTGTGTATATATGTATGTATATACACATATATATGTATATATGTATTATGTATGTATGTGTGTATACATATATAATACATGCATATATATATACATATATATGTGTGTGTGTGTGTGTGTGTTTGTATACACACGTACATACATGATGGAGCGATGGCTCAGTGGGTAAACACAACCCTGCAACACAATCCTGTGGTGTATTAGATACGTGTATAGCCCCTCTTCTGTGTGTTGTGGTGTGTGTGTATATGTGGTGTGTTCACCATATGCAGACCTATGCAAGGTGATCACAGCAGATTAAAACAGGTTCGGAAACCATGAGGGCCTAAGGCAGTTTGGTTTGAGAAACTCAAACATCCTCCCATCCCCCTTTTCACTGAGAAGCGATGGAAACAACTTCAAGACACTGTGCTCAGAGTTGGTCCAGAGCCTTCCCGTAGGCGTCGTTTTGTAACTCCAGAACAGATAACTTGGCAGCAGCTCAAGCTTCGGCTGGAGATCCAATGCTCAGACATCGCTCATGCTAACATGTCGAGAGTTCTCGGCTAGCAGAGGGTATCACAAACCATGCCTCTGTGTTTTGCAGGTAGCACTTCTGGTTGCAAATGAATTTTGGGAACAAGGAGATCTGGAAAGAACAGTGCTGCAGCAGCAACCAATTGTAAAGACCCCTTCATCACTGTGTTACCTATTAGAAACCACCCCCGAAACTCTTAGAAAATACCTTAAAAGGATTCACTTCTCTTTCTAG
Seq C2 exon
CCTATGATGGACAGAAGCAAAAAGGATGAACTCCCGAAACTTCAAGTGGGATTTATTGATTTTGTTTGTACTTTCGTATATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024992-Pde6c:NM_001170959:18
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.045 A=NA C2=0.196
Domain overlap (PFAM):
C1:
PF0023314=PDEase_I=FE(11.8=100)
A:
NA
C2:
PF0023314=PDEase_I=FE(10.8=100)
Main Inclusion Isoform:
NA
Other Skipping 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: