MmuINT0117034 @ mm10
Intron Retention
Gene
ENSMUSG00000024575 | Pde6a
Description
phosphodiesterase 6A, cGMP-specific, rod, alpha [Source:MGI Symbol;Acc:MGI:97524]
Coordinates
chr18:61262416-61264010:+
Coord C1 exon
chr18:61262416-61262525
Coord A exon
chr18:61262526-61263922
Coord C2 exon
chr18:61263923-61264010
Length
1397 bp
Sequences
Splice sites
5' ss Seq
GAAGTGAGT
5' ss Score
7.97
3' ss Seq
TGTCTGTCTGTCTCATTTAGATC
3' ss Score
11.12
Exon sequences
Seq C1 exon
ACAGGAAAGCTGAAACGGTACTTCACTGATCTAGAGGCCTTGGCCATGGTCACTGCTGCCTTCTGTCATGACATCGACCACAGAGGCACGAACAACCTCTACCAGATGAA
Seq A exon
GTGAGTCAGGCCTTACCGGGCCCTCCCCCCTCTATCTCCCCCCTCCACCCCCAGATCCATTACCCAGGTCTGCACTATCCCAGGACTAACTTACCAGAGAAAGGCCCCACTGTCCCAAGCCTCCATTTTTCTTGCTCTTCGGGTCTAGGTCCAGTCCTATAGCAAAAGAAGTGACAGTTTCCCAAAGATGTCCACATACCAAATCCAGGAGCCCACGATTGTTGACTGACGCTCAGAAGGGGACTTTTCACACTGATAGAGTTCGGAAGCTTGGGATATGAACCAGGATGATGTGCAGGGAGGGCTCCTGCCGTCCCAAGGGTCCTGGTGAGGAGGAGGCAGGCAGCTAAGAAGAGATAAGATTGTATCTGCTGTCTTTGAGGATGGCAGAAGGGCCTACCTGCAAGGGATGCGAGGGGGCTCCAGAAGAGGGAAAGGACATAGAGACAGACTCTCCCCCGGGGGCCTCGAGGAGGAGCACCCCTAGGATCCGCATTCGCTATCTGAACTCCAGAGTTAAAAGAAGATGCACTTTATGTTTTACACCACTAAGTCAGTGACGGTTGGTTATTGTAGCAATAGGATGTTCTTTCACTCTCCTCTTCCCTGTCTTAGGTATGGGACTAATTTGAGTCAAAATGTTAGTAATTCATTCACCTTTGCATCTGTAATGCTCCAGCCTGCATCCTAACCAAATTTATACTCCCGTTGACCTCTGAGGCACCGTCTTTGAAGCATGCAGTTTCATTGAAACCTTACACGATGAGGCTTTGAGCTGTGCATATGTTACCTCAGTGTCTTAGTTAGGTTTCTGGTGCCATGAAAGACATCATGACCAAAAGCAATGTAGAGGAGAGAAGGGTTCTAGTCTTGAAGACAGGGCAGGAACTTCAAGGCAGGAACCTGGAGGCAGGAACTGAAGCTGAGACCCTGGAAGGGCTCTGCTTACTGGCTTGCTTCTGAGGCTTCCAGTCAGCTACCATCCTTATAGTTCCCAGGACCACCTGCCTACAGGTGGCACTATCCCCAGTGGCTGGACCCTCCCATATTAATCAAGAAAAGGCCTCTTACAGACTTGCCTACAGGCCAATCTGATAGACATTTTTCTCAGTTAAGGTTTCCTCTTCCCAGATGACCCTGGTTTGGTGTCAAAGTGACACAACTCAAACATGTTACATGAGAGCAGTTACATGAGAGACAATCTGACATCTGCTCCTCATCTTCTGCTCCATTTTTATTTTGTGCAAGATCCTTCCTGCTCCTACCTCTTCAGTATCTGCCTACAGAATTAGGAGAAAGATGGCAGGACTAGATTAGAATGTCTTTAGTCTCTATCTTGCCTGTTCTATGTTGATATTTACATTTATTCTGTCTGTCTGTCTGTCTGTCTCATTTAG
Seq C2 exon
ATCACAGAACCCCCTGGCCAAGCTCCATGGGTCCTCCATCTTGGAAAGGCATCATTTGGAGTTTGGCAAAACACTCCTGAGAGATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024575:ENSMUST00000025468:14
Average complexity
IR
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:
PF0023314=PDEase_I=FE(14.5=100)
A:
NA
C2:
PF0023314=PDEase_I=FE(11.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAGGAAAGCTGAAACGGTACT
R:
CTCATCTCTCAGGAGTGTTTTGCC
Band lengths:
198-1595
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types