MmuINT0117078 @ mm9
Intron Retention
Gene
ENSMUSG00000024992 | Pde6c
Description
phosphodiesterase 6C, cGMP specific, cone, alpha prime [Source:MGI Symbol;Acc:MGI:105956]
Coordinates
chr19:38250125-38252645:+
Coord C1 exon
chr19:38250125-38250225
Coord A exon
chr19:38250226-38252537
Coord C2 exon
chr19:38252538-38252645
Length
2312 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
CACAGCTGTATCTTTTCCAGGAA
3' ss Score
9.05
Exon sequences
Seq C1 exon
AGTTTAAACATCTTCCAGAATCTAAACAAGCGGCAGTTTGAAACGGTGATCCATTTGTTCGAGGTTGCAATAATAGCAACTGACCTGGCACTCTATTTCAA
Seq A exon
GTAAGTACGAGACTGGGTGTCAGGATGTCCTTGGGCCCTGTGTCCTGCCTGCCATGAACTGCACTGACGTCAAAAGACATGGAGAGATGGCTCATTACTTAAGAGCATTTGATGTTCTTGCAAAGGGCTAGGGTTGGATACTAGGACCCACGCTGGGTGGCTCACAGTGGCCTGTCCTGTAACTTCAGCTTGAGGGATATGATGTCCCCATCTGGCCTCCGTAGTCATTCACACACATAGATAAAATGTTTTAGAACAGGCTCACAAATCTGTTTTCTTTTTAGAATGCCAGTTTTTCTCAAGATAGTTGACTGACAGTGAACTTACTCTATTTTGGAGATGTAGTTTTGAAAACACGAGCCTCTCCTGTGAAATAACCTATGACCTAAAGGAGCTCAAACAGAAGGAAACAGAGCACACTGCTTAAATAATGTCACAAAACTGCACAGGAGGCTTTGCGTCCTGGTGACTCACAGTGGTTCAGAATCTAGTGTTTAATTGGATTTGTTTAGTGGTAGAATCCGTGCCAGAATCTGGTATATGGTATTTCAGGCTCAGAAATTTGATTGTGAGAGTTTTGGGCTGAACAATCTTGATGATTCTAACACAAAAACTAAATTCACAAAACTTGAGCTTTACACAGCAGAGGGCCAAGGAGACCAGATGTGCCAAGTGTATGCACAGTTTCTTCTCAATAAAATATAAGGTTTCATGGGGGAATATTGATTAGAAAGAGGTGGTATATTTATCGGATCCAGATAAAAGGTGATGTTTTTGCACAGTCAAAAATTACCTTGCGAATCCTCCTTTAAAAATCTAACTATTGAACAGTTCAGCTGTGACAAGTGCTTAGAATAGCATGGTTTCCAGATACCCAGGGCTCACATCCCTGTGATAACCCATCGTGTTATCCCATGTGTAACCCATCGTGTCTCATGTGCTTGGGAGTTTCATTTTTAAGGATAGAAATGAAAGTCATGATGCAGTTGGGCGCTCCATCCCCGTTTCATCATGAAAAGTTCTCTTACCTTCCAAAGAGAGACTCTGATACCAACACGTTTCACCCTTTCTGATCCTGTCCCTCTGCGGTCCTGTTGAGTGTGTGCGATTTTTTTCCCCACATATGACACCAGGGTGTTTGCAAATATATTTCTGCAACTTGCTTTTCCCACATAGCGTTGTGTAAGGATTTGCCTTTGTTGATGAGTCTTCTAGGTGGTTTAAAATATTCCTGTTGAGGCACTACAACTGGATTGATTATAAGGCCTTCACTAATGCGTCAGATTCAAGATATGACCCTGATGCAACCAAACAACGATGCAATTAAGAGCTAATAAAAGGGCTGGCCAGAGGCTCAGTAAATGCCATATAAGCATGAAGTTCTGAGTTTGGATTCCCTAGCATCCATACACAAAGCTGAGTGTGTCAGGAAGCTCTGGTAACTCTAGCATGCAGAGGGGATGGTAGAGAAGGTGGCTGGGTAGTGACCCATCAAGCAAAGACATCTAATGTCCAGCTTGGCTTTTACACACAGAAGTGCACTCACCTGCCTTCCATCCTTACACACACACACACACATAGACAGATGAATAAATAATAATAATAATAATAATAGAGTTTCAAGTCACTTGCTTCAGTTGTACAGTGCTCAACTGTTAGATAATTCCCTTCCACTTCTCCACATATATAAATTCAGATTCTATCTTATTTCCATGATTGCCCATGATGCTACGTTGCAGATCCTTGTGCACTCGATATGTGAGTTCCTATACCTGGGAGTGGGCGTATGCGGTGTGTGCATGTGTGTTGTATATGCTGTATATCCTGTATATGTCAGGCTCCACCACTGACACCCTACCAGCAGTATGCCAAGATTCTCTGAGGGGCACATTTGGATTTCCATTTGCTAACCTATTGAGCATGAGGTGACACCCTCTTGCTTAGATCTGTATTTTCCTAATTGCCAATGAGATCAGCCATCCGTGAATATCGGCTTCTGTGTTTCTGTTGGGCCTGTGTGCTACGCTGGTACAGCTCGCGGCCTCTGTGTCTCTTTTGCTTTTTTCTTGTTTGAACCTTTGGTTTTTACTGTACTCAAATGTTTGTGGGTTCTCCCCCACTCTGTGGTTTGTGCTTTTTCTGCTTCCAGCCCTTTCTATGCCAGGGAGAGTCAGAATTGCCTGCTCTCTATCCTGGCTCTTGGCCCCTGCTCGGCAGACAGCCTGAGACAGAGTGGGAGCATAGAATATGAAAGGCAAGCATTTAAGATCATTCTCTGTGGAAAAATCGTTGCACAGCTGTATCTTTTCCAG
Seq C2 exon
GAAGAGAACCATGTTTCAAAAGATCGTTGATACCTGCGAGCAGATGCAAAGTGAAGAAGAAACCATCAAATACGTAACCTCCGACCCGACCAAAAAGGAAGTCATCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024992-Pde6c:NM_001170959:16
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=0.108
Domain overlap (PFAM):
C1:
PF0023314=PDEase_I=FE(13.3=100)
A:
NA
C2:
PF0023314=PDEase_I=FE(14.5=100)
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:
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: