MmuINT0117041 @ mm10
Intron Retention
Gene
ENSMUSG00000024575 | Pde6a
Description
phosphodiesterase 6A, cGMP-specific, rod, alpha [Source:MGI Symbol;Acc:MGI:97524]
Coordinates
chr18:61284006-61286060:+
Coord C1 exon
chr18:61284006-61284089
Coord A exon
chr18:61284090-61285912
Coord C2 exon
chr18:61285913-61286060
Length
1823 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGC
5' ss Score
10.08
3' ss Seq
ACTTCTGCACTTCTCCCCAGGAG
3' ss Score
9.17
Exon sequences
Seq C1 exon
CCCATGATGGACAGAAACAAGGCGGATGAGCTCCCCAAGCTTCAAGTCGGCTTCATCGACTTTGTGTGCACTTTTGTCTATAAG
Seq A exon
GTAGGCTTCCTCAGAGTCCAGCAGACAGCGGGGCAATCACATGATGCTTTGCAGAACAATTTTCATCTCCAGTGGCACTTGGTTGTCGGGATTGATCTACAGAGGGGAATGACGGTACCTCTGGCTGAAGCCTGGAGTTTTTTCCTTCTCTTTGCTTAATAAATACTCCTGGGGCAAATGGCTAAGCGTGCTTTTATGGACACAATGTCATTGTGAAAAGGTAAGTCAGTTTCTCTGGGAGTTCTCGTCCAGGTTAGTCCCTTCTTGAGAGGCCCACCACCGCCTAATCCATCTCCACTATCTACCTGCTGCCTCTTCGTTTTTGAGACTTGATCTGGCTATGTTGCCCGGGCTGATCTCCAATTCGTGATCCTCCTGCCTCAGCCTCTGAGGTGCTGGTGTAGCATCACTACATCATCATGCCTGACTCCACCTCCTGTGAATTATTTTTCTTTTGGCCACACTATATATAAGGAGACAGAGGTCAGAAAGGATGTGACAGGGCCAGCATCTCTGGACCCATCTATGGGGCAGGACTGAAGCTGGCTCACCTAACACCCAGGTCAGGGCTTTCCACAAGCAACTCTGTTGTCACACAGACCAAGGGCCATCTGCTCAAAAGGACAGCATGGCTGCTGCTCACACTGCCTGCAGTAGAGTTATGAATGGGGATTCTGAGCTTCATATTTACCCACTTAATCCCAACTACTCTAGGATAGGTGCCATTACCGTCCTTCTATCTAGATGAAAGTGAGCTTTGGCAGTGACTATCCTAAACTCACACAGCTTCTGGTAGAGCCTAGACCACAACTCAGGCATCTCTGGGCACAGTAAGCCCTGCCTGGCTCCTGCTGCCATGGACCCTCCTCTCTTCAGCAAACCTTCTTCATCAATCTGCACTCCAGTCTCTCTGACTACAAGCTCAGGAGCAAAGAGACAACCCACATTGGGGGCCCGGCTCAGAAGCCCGGAGAAGATAAAATGACCCCATAGATTTCAGGGTACTGTGCTCAAGGTATTATTATTCAATCCCTAGAGTTGCCGGAGTTCATAGGAATAACCCAGTTTTATTCACTGAGTATTTATGAAGTATCTGTGGAACCAAACCAGTGCTAATTCAGAACCAACCGAGGGGGTGACCCAGTGTTCCTGCCATCTCTAGGTGTCAGCCTCTGGGAGAGGCAGCAAAGGGAGTCATTACAGGGAAGTGGGGATTGACTAGAGAGGGCTTTGGGGACATCTAGTGGGAACTCAGTTTACCTACAGGGTCAGGAAAGGTTCTGAGTGTTAGGGATATAGGGACCGCAAGGAAAGGTGGAAGGGTGGAATGCTCCATCAAAAAGAATGGCTGTAGGAAGTCCACAGATGGGAGGAAACAGTCATGAAGTGAGATTGGGGTGCCTGGGACTTCCGGATGTGAAAGAATAGAGATCAGTGAGATCAGTGGGTGACAGCTAAGGCTTACATTGCACCCTGAAGGAATGGCTATACAGGAAGGTTCCAGGCAGGGGAAGGAGGGGCTCCCTAGTGTCAGCAGACATGAGAGGCAGCTTACTCCAGTGCCAGGCAGAACGGACTCCACCTTGATCCAGGGCCCTAGGGCAGTGCCCCTGTTTCACTGCTGCTGCTGGAGACAAAGTGTTATGGCCAAGCCCCGCAGTCTGTATGTGGCAAAATCTGGTCCCTAGATAGAGGCTGCGGGATGTTCTAGGGTCCTGTAGTTGATCATAAAGTAGACTTGTTCTCTCTCCCTCGCTCCCTCTCTCCCTCCCTTCCTCCTTCCCTCTCTCTCCAGCTCATTGCACTTCTGCACTTCTCCCCAG
Seq C2 exon
GAGTTCTCCCGATTTCATGAGGAGATTACACCCATGCTGGATGGGATCACTAACAACCGCAAGGAATGGAAGGCGCTGGCTGATGAGTACGAAGCCAAGATGAAGGCCCTGGAGGAGGAGAAGCAGAAGCAGCAGGCAGCCAAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024575:ENSMUST00000025468:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.246 A=NA C2=0.310
Domain overlap (PFAM):
C1:
PF0023314=PDEase_I=FE(10.8=100)
A:
NA
C2:
PF0023314=PDEase_I=PD(16.8=40.0),PF141951=DUF4316=PU(81.1=86.0)
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:
CATGATGGACAGAAACAAGGCG
R:
CTTGCTTGGCTGCCTGCT
Band lengths:
230-2053
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