MmuINT0117049 @ mm9
Intron Retention
Gene
ENSMUSG00000024575 | Pde6a
Description
phosphodiesterase 6A, cGMP-specific, rod, alpha [Source:MGI Symbol;Acc:MGI:97524]
Coordinates
chr18:61413321-61414100:+
Coord C1 exon
chr18:61413321-61413470
Coord A exon
chr18:61413471-61413956
Coord C2 exon
chr18:61413957-61414100
Length
486 bp
Sequences
Splice sites
5' ss Seq
GAGGTGTGG
5' ss Score
4.48
3' ss Seq
AACTCTTTCTTTCTCTACAGTCT
3' ss Score
9.91
Exon sequences
Seq C1 exon
AAAGAGCCTCTGGATGAGTCTGGGTGGATGATTAAAAATGTACTCTCCATGCCCATCGTCAACAAGAAGGAAGAGATCGTCGGCGTGGCCACATTTTACAACCGCAAAGATGGGAAGCCCTTCGACGATATGGACGAGACCCTCATGGAG
Seq A exon
GTGTGGGATGCTGGGTAGCCCTTGGCTGGTGGGGCTTGGTGACCACCAGTTTCAGAGTTGCCCTTCAGAGCTGCATGGTGTTTCCCAGTGTGTAGCTGCCTGACCGTGGGGGTGGGGTGGGGGATGGGAGGCCATAGCCCTGAGGAGCCATGAGAGCCACTCTCTCCACGCTCCTTCCTCACTGCCCCTCACTTCCACACTTTACTATTGGGAGCAGTTTGAAGATCACTTGAGAACTGATGAAAAAGCACAGAGCTCCTACATACATCCATCCTCCTTGCGCCATACATTTCTATTTGTGACATTATTACTTATAAATCTTCACTTAAAATACATTTACACCCATTGTTTTATCACAGCCTACCTGCCCTGCACAGCTTTGCAAACCCACTTTATAGCTGAGAACATTGAGGTCTCAGCAGTCTTGTCCTCAGCTAGCATCAGGATGCAGGCTCCCGCCTCCTCTAACTCTTTCTTTCTCTACAG
Seq C2 exon
TCTTTGACTCAGTTTCTGGGATGGTCAGTCTTAAACCCTGACACCTACGAGTCCATGAACAAGCTCGAGAACAGGAAGGATATCTTCCAGGACATCGTGAAATATCACGTGAAGTGTGATAACGAAGAAATCCAGAAGATCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024575-Pde6a:NM_146086:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.020 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:
AAAGAGCCTCTGGATGAGTCTG
R:
CAAGATCTTCTGGATTTCTTCGTT
Band lengths:
294-780
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: