MmuINT0117038 @ mm9
Intron Retention
Gene
ENSMUSG00000024575 | Pde6a
Description
phosphodiesterase 6A, cGMP-specific, rod, alpha [Source:MGI Symbol;Acc:MGI:97524]
Coordinates
chr18:61441175-61441556:+
Coord C1 exon
chr18:61441175-61441238
Coord A exon
chr18:61441239-61441481
Coord C2 exon
chr18:61441482-61441556
Length
243 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGG
5' ss Score
9.26
3' ss Seq
ATCGGGTCCATCGGTTGCAGGTG
3' ss Score
6.37
Exon sequences
Seq C1 exon
GGCCATGATGATGACCGCCTGTGATCTCTCAGCCATCACCAAACCCTGGGAGGTACAGAGCAAG
Seq A exon
GTATGGACTCTTCCTGTCCTGGCAGAGGGAGTTCAGTACTGCTGACCACAGTTACCGAGGCTGGACCCTCTCAGCCCTCCGGTTCTCCAGTGAAGAGTGGGAATACCAGGGTTTCCTCTTTGGCTGAGCTTGAAACACAAGTGAAGTGGGAGTAGGGGTAGGGTGTTGGGCTGTGCATGTGTGTGTATGTATGTATGTATGTATGTATGTATGTATGTATGTGATCGGGTCCATCGGTTGCAG
Seq C2 exon
GTGGCTCTGCTGGTGGCTGCTGAATTCTGGGAGCAAGGTGACCTGGAGCGCACAGTGCTGCAGCAGAATCCCATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024575-Pde6a:NM_146086:18
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=0.218
Domain overlap (PFAM):
C1:
PF0023314=PDEase_I=PU(20.4=95.0)
A:
NA
C2:
PF0023314=PDEase_I=FE(21.0=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:
CCATGATGATGACCGCCTGTG
R:
AATGGGATTCTGCTGCAGC
Band lengths:
137-380
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: