MmuINT0116761 @ mm10
Intron Retention
Gene
ENSMUSG00000023868 | Pde10a
Description
phosphodiesterase 10A [Source:MGI Symbol;Acc:MGI:1345143]
Coordinates
chr17:8941141-8943027:+
Coord C1 exon
chr17:8941141-8941281
Coord A exon
chr17:8941282-8942871
Coord C2 exon
chr17:8942872-8943027
Length
1590 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGG
5' ss Score
8.05
3' ss Seq
TTTCCTTGCTTGATTTCCAGGAT
3' ss Score
9.94
Exon sequences
Seq C1 exon
AGCCTGTGTGTGTTCATACCACCCGGGATGAAGGAAGGCCAACCCCGGCTCATCCCTGCAGGGCCCATCACCCAGGGTACCACCATCTCTGCCTACGTGGCCAAGTCTAGGAAGACGTTGTTGGTAGAGGATATCCTTGGG
Seq A exon
GTAAGGCACTTTGACCCTGGCGGTCTGAGGACTTAATTAAGAGAGATGATATACATCATTTTGGTCTTGCCATTCAAGTTGTCTCCTGATTAATTATAAAAGCATTAAATGAAGATACAGATCAATAAATGAATTGGCTTAGAGTTTAACCTTCTTATTCAGAAAAATTACACCCATGGTGCTCCCTGGGAAATGGAGCCCTTATTTCAACACCTGGTTAAACAGAAAAAAGAAGTTTCTATCCACGTAAATTAGATGGTGTGGCACCTCTTGGTAACTCACATTGGCACTGATGCAGGACTGACCGTCTCATCTGAAGGGTTCCCTGCAGTGCCCAGTTCTCAGGCATCTATTGATGGCCATTCTGCTGAGGTGGGCTGTAGGTTTCTGGGTAATAGAAGACAGATGTCAGCTGGCCATGAGCTAGGTATGGCTGGTTTCCAGTGACCCTGCTGGCATTTCTCACTCCCCACCTGTGAGGACAGCGTGGTAGGGTCTGATGAGAAGAGAAGTGGAAAGTTAAAAACCCACCGTAGACATCGAACTCACTGCCTTCCCCTTAGCCAGAATAGCAATTGTGTGAACATGCCTGAGGCCAGACTGGGTCTCCTCGGTGTCAGAGGGTACCAGAAAAGATGCAGCTGCCAAGAGGGATGGCAGACATCCTTAGCACAGTTTGTCAAGAGTGTTTAGGCAAATGTCTGATGAATGTTACTTCAGGTGGTGCTGGCTTCACAGGGGACAAATGAAGGCAATAACATATGTGGGGGGAATTTGTTTTGGGAAACTGCTGAACTGATAGAGACTTGAAATGTGGCTTCTCCTCCTCCTCTTCTTCCTCCTCCTCCAGCACCTCCTCCTTTTTCTTCTTCTGACAATGATTTACCTAGAACAAAGTTGCTATTGCTTTATTGGAGTAAAGGAAGGAAGGAAGGAAGAAAAAAGGAAGGAAAGAAAGGAGGAAGGAAAGAAAGGATCCACAGTGAGGAAAGAGAAGGAAGGAAGCAAGCAAGAGTAGATGCTCTGTGGATTCTCATTTGAAAACGTTCAGTTCTGAATGCAGGCTTTCAAAAGCTAAAAGCTACAGGAACACTTTCATATTGCCCCCCATTCAGGGAGAGTTTGACATGTCCCATTAGCTTCCTGTAGATAGTAGAATCTGAGCGTATTGAACTGCCGTCTTGATATTAATCCTTCCCATTGCTCTGTACTGGCCTGCTGGAATTTTAGCTGAGATAGAAAAATCATTCAAGCTGAATCCATCTTCATTGTGGTGCTAAGTAACTGATAATGTTTGCCTCTAGGACATGGCGTGGGCCCTTGAAGTTCAACTTAGGCAATGGTTGGCATGACTTTAAAAACAGAAGAGAAGGCGTGTTTGTGTGCACCTGTCTTCATGTGTGTGTCTGCCTGTGCTCTCTCTGCTGCGTTCACCTGGGAAGCCTGGGGCGGTTCCAGCAGAGAAGGAGGGAGCCAGTGCCAGACTTGCTGATAAGTGTTCTTCCGGTCACATGACACTGGCATCCACTGAGTATGCATGCAAACGCTGAGAGGCCCTGAAGTTCCTGGTTTTCCTTGCTTGATTTCCAG
Seq C2 exon
GATGAGCGATTTCCTCGAGGTACTGGCCTGGAATCAGGAACCCGCATCCAGTCTGTTCTTTGCTTGCCCATTGTCACTGCCATTGGAGACTTGATTGGCATCCTTGAACTGTACAGGCACTGGGGCAAAGAGGCCTTCTGCCTCAGCCATCAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023868:ENSMUST00000089085:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.083 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0159021=GAF=FE(31.9=100)
A:
NA
C2:
PF0159021=GAF=FE(35.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGTGTGTGTTCATACCACCC
R:
TCCTGATGGCTGAGGCAGAAG
Band lengths:
294-1884
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