MmuINT0119249 @ mm9
Intron Retention
Gene
ENSMUSG00000079484 | Phyhd1
Description
phytanoyl-CoA dioxygenase domain containing 1 [Source:MGI Symbol;Acc:MGI:3612860]
Coordinates
chr2:30122069-30122461:+
Coord C1 exon
chr2:30122069-30122145
Coord A exon
chr2:30122146-30122382
Coord C2 exon
chr2:30122383-30122461
Length
237 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAA
5' ss Score
8.59
3' ss Seq
CTGAACTTTCTCCTCTCCAGCCC
3' ss Score
8.34
Exon sequences
Seq C1 exon
TAGACACACTAGTACTGCCCGGGAGTGAATTTTAGAGAAAGACTTGAGGGATCAAGCCAGCCTATGAAAGAAAACAG
Seq A exon
GTAAAAGCTAATCCTGGATTAACTGGAGGCTGGGCCAGGGCTGAGACTGGGCCCACCTCCAAGGTCAGAAATGGGGGAGGAGCAAGGGGAGGGACTGGGCCCTGGGTGGAAGGCACAGACTGGATTTGTTTGGAAGGGTGGAGCATGGGGTTGAATATTTTCTGGGTAGGTAAGAGTTAAATCCTTCTGGGCCTCAGTCACTGGTCTTTCTCCCCTCCTGAACTTTCTCCTCTCCAG
Seq C2 exon
CCCTGGAGCCATCGAGCTGAGCCAGCTGAGTCCTGCAGTATTCCCCATGGCCTGCCTGAGTCCCTCACAACTCAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079484-Phyhd1:NM_172267:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.400 A=NA C2=0.018
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TAGACACACTAGTACTGCCCGG
R:
GCAGGCCATGGGGAATACTG
Band lengths:
132-369
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
Other AS DBs: