MmuINT0119252 @ mm10
Intron Retention
Gene
ENSMUSG00000079484 | Phyhd1
Description
phytanoyl-CoA dioxygenase domain containing 1 [Source:MGI Symbol;Acc:MGI:3612860]
Coordinates
chr2:30266863-30269847:+
Coord C1 exon
chr2:30266863-30266941
Coord A exon
chr2:30266942-30269688
Coord C2 exon
chr2:30269689-30269847
Length
2747 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGG
5' ss Score
8.76
3' ss Seq
GAGTCTTGTCCCTGCTGCAGTTC
3' ss Score
4.94
Exon sequences
Seq C1 exon
CCCTGGAGCCATCGAGCTGAGCCAGCTGAGTCCTGCAGTATTCCCCATGGCCTGCCTGAGTCCCTCACAACTCAAGAAG
Seq A exon
GTAGGGGCCCGTGGTTTGGAGGGTGCAGACCTCTAGTGACCTTTGAACTACCTCTGACATTTCACAAAGGAGAGAAAGATCCCTGCATATCAACCCTAATTTCTGCGAACAAAGCCCAAGAGGGCCAGGTCACAACACCACCTCCCCAGGTGCCATCTCCCCGGTCAGATACAGTGGGGGTTGGGGCTAGGAGGTAGAGAAACCACAATTCAGATTATCTAATCCAGCTAGCCCCAGGGGCCTGTTGATGAAGGCCTGGATAGGGCAGGCCAGTAGCTAGGTCAGCTCATTATGAAAGCCTACCATACAGGGGGTGGACTACGCACACTTTAAGTTAACCACCCCCAATCTCATATGCCAGGACTGTTAATGTATTAGATCTAGCCGAGGATCTTTGTTTCAAAGTCCCTCCTGGAGCTGTGGTTGGGGCTTAGCAGTTGAGTGCTTGCTTTAGGCTCCAAGATTTGATCCCAACACTCACAACACATACAGAAACACACACCACCACCACACACACCCCACACACACACACATACCACACACACCATATGCATACCACATACACATCAAAACACATACACAAACACATCACACATATCACCACACATAAACACGGCACACTCCACAATACATAAACACACACATACAAACAGACTACACACACACCAACACACATACATATACCACTATTACCACCACCACACACACCACACATCATGCATACACAGACACTCACACCACACACACACACACCATACTCACACACACATCCCATACAAATGCACACACACATACCGCACACACTCACATACAAACACATACATATGCATGCACACACCACACACACACACTCACACACAAATGCACCCATGTGCACATACACACAGAGACACATACATAAAAGCACACACATACCACACAGACAAACACTCATCACCCAACCCACACGCACTCACACAGACCTACTCTCTTTTGACAGCTGCCACTGCTGCCACAGTTCCCAAATTTGTCTGTGACTAAATATGTAGTGGAAGTCTGTCTGTCTTTTCCTTCTGTCTCACAGGCTATCTTTTGAGGGACAAAGCCCCATGTCAGTATTTTTTTGTACAGTTTGTGCTGAACTTTTGTTCAGTTTTTATGATTTCAAGCATGGAGGGCCTCCCTGTGTTAACCCTGAGTGATGGTTTGTTGCTCTGGCCTAGAACTCAGTCTGTAGAGCAGACTGCCCTTCAGCTCACAGAGCTCTGTCTGCCTCTGCTTCCTAAGTGCTGGGGTTAAAGGCATGGGCCACCATGCCTGGCCACGCTTACATCCTTGCTTTCTGTCCCTTACTGTGTTGGTTCTGTTTGTTTTCAGTGCTGGGAACAGGAGCCAGTCCTTGTACATGCTAGCAAGCAGTCAGCTTCTGAGAGGCGACCCAGTCACACACGTAATGTGCCTCAGCACCTTAGGCTAGCCTCAGAATAAAGAGACTTGGGGCAAAGTCAGAATCAGGCATCTGTGTTCACAGCCCCTAGCCTTCCCCACACTCACTCAGGAGAAAGAAAGCCAGCAAGGTCCTGCGACTGGGGACTTTCTAGCCTTGTCCTTCCTAGTGCTGGTGCTGACTCAAGCGTCCTGGCAGTCCCCTGCCGGCCCACACTGAGTAACACAATGGAAATAAAATTTCCAATGCATGGGTTTGGGGTTACAGGACAAGCCATAGCATGGGCAAATTCACTCTCCCTTCTGTCTGCTCCCCTGGCTATCCTCCCCTCACCCTGTGCTCCAGCCCTTCCCAATTTCCCAGTCGTCCAGTGCCCACAGGCTTTGTACTTCCTGTTCTCTGTCTTTAATGCTCTTTCCTATCTCTTTGCTTCCCAATGTTCTGCTCTTCCTTTAACCCCACTTCCTCCAAGCTGCCCATTGACCCCTTCACCTCGTAGATTCTTTGCCTTTAATTCTCAAAACCCTGCCCTTGTCTCCCTGTAAGTCAGTGTGATGTGGGATGGTATGTTTGTCTGATGGTAAGGGATGCATGGGTCTCCTTCACTGGACTATAAATTGTGTGAGTGTGGAGGGTGGCTGGTTCATAATCACATGTCCATCTGCTGAAGCTGTCTCGTACTCGCAATGCTTAGTCGGGATTGGAATAGCCTCCAAAGCCAGCATTAGAAGGCTGAGGCAGGAGGATCTTGAGTTTGAGGCCTCCCTGTCTTCAAACAAATAAAAACAAAACAAGGGAGTTAGGCGGGGTCGGTGGTTAAGAGTGCTTCTGCAAGCATGAAGATCAGAGTTCAAATCTCAGCACCCACTCCATGAGCTGCACACACCTGCAGCTCAGATCGCCAGGGCTCACAGGCTGCCAGTCTAATGAAGAAAACAGCCTAGGTTCAAGGAGAGCCTCAGAAATAGAAAGTGGAAGAGGGGCACCGTATGTCCTCTCCTGATGCCCCTGCACATGCGCACCTGCAGTTCTCACACATGTTCTACACTCACACCTGCACTTTAACACACAAATGAGCAAATGTTTCCGTATGTCCCAAACCCATTGGAGGGCAAGAGCAGAGGCAGCTGCCACTTCCCCTTCCTCGATAAGATGCAAGCAGCCAGTACTGACGGCTCCTCACTAAGCACTGGATGCCCATGTCCAGGGTGGGGGGCAGAGCCATGAGCAGGACACTTGATCTTGGTTCGAGTTTGTGGTCCAACATGGATATAAGGAATGAGCGAGGGCGGAAGGAGCCTGAGTCTTGTCCCTGCTGCAG
Seq C2 exon
TTCCAGGAGGACGGGTTTCTGCTGTTGGAAGGATTCTTCACAGCGGATGAGTGTGTGGCCATGCAGCAGAGGATCGGTGAGATTGTAGCTGAGATGGATGTCCCTCTGCACTGCCGGACAGAATTTTCCACCCAGGAAGATGAGCAACTTCAAACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079484:ENSMUST00000154647:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.012 A=NA C2=0.080
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF057218=PhyH=PU(21.0=98.1)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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