MmuINT0119250 @ mm9
Intron Retention
Gene
ENSMUSG00000079484 | Phyhd1
Description
phytanoyl-CoA dioxygenase domain containing 1 [Source:MGI Symbol;Acc:MGI:3612860]
Coordinates
chr2:30135691-30136656:+
Coord C1 exon
chr2:30135691-30135807
Coord A exon
chr2:30135808-30136529
Coord C2 exon
chr2:30136530-30136656
Length
722 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGT
5' ss Score
9.65
3' ss Seq
ACTGTGTGGTGTTCCCCAAGGGG
3' ss Score
6.53
Exon sequences
Seq C1 exon
GTGGGGTGTCAAGAAGGATGATTCGAGCCCCTTCAGACTCTGGGCCTGGCACCAGCTTCCTCGGGTCAGATCCAGCCTGGGCTAGCAACCTCTTTGTGCCTTTGCCAGTGAGGAGAG
Seq A exon
GTAGGTGAGGTGCAGGTGGCCATGCATAGTGTTCTATATTTGCCCCACTCCCTGCATACAAAGGCTCCCCGTGGTGCCTGCCATCTGAGGGCCTTGAAATTGGAGAATGGTTGGTGGTGGCACAGTATGGGGCTTGGATGTCAGCAGAGGTGTGCTTCCAGTAGGTTTTTTAAGGTCAGACTAAAGTTCTTGACGGACCATTTCTTGAAGTAGACGTTTGCCCCTTTGACCCTTAGTGTTCCCAGGTAGAAGGCAATCAATGCAGGTTGATTACAGGGAACGTATGAGGTGCAGTGTTCCTTGTGTGTTGGCAGGTAGTGCCTGGTTTTCCTTATGGTAAGGGGATACTTGATGCCAACTCAGTCTATCTAGGGAAGGGGAGCCCCCCACCCCCAGCTTTTGAGGCATGGTTTCCCGCCTGCCTCTGCCTTCCAAGTGCTGGGATTGATTAAGGACTTGCCCTGCCACACCTGGCCTGCAAAGGCCCTTCATAACGCTTCCCACGGCAGGTCACTGTGGAAAAGACTTGACATCACAGGAACCTCTAACAGCATGGCCTCAGCTCCGGGAGGGAGCACGAGTGACAGCCCGAGTTCCTAAGGATAGGAACGGACACTTCTCCCTTTGCGGAAGGAGGGCTATGTTCCTTATTCCCTTGGGAAGAAGACTGGTTGCTACGGGGTTGGTGGGGACTTGCTGGTAACTGTGTGGTGTTCCCCAAG
Seq C2 exon
GGGGTCTGGTTCTGATCCATGGAGAAGTGGTGCATAAGAGTGAGCAGAACCATTCCGACCACTCCCGCCAGGCCTACACTGTCCACCTCATGGAGGCTGCCGGCACTGTCTGGAGCCCAGGGAATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079484-Phyhd1:NM_172267:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.288 A=NA C2=0.223
Domain overlap (PFAM):
C1:
PF057218=PhyH=PD(10.2=80.8)
A:
NA
C2:
PF057218=PhyH=PD(10.7=55.8)
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:
GTGGGGTGTCAAGAAGGATGA
R:
TGGGCTCCAGACAGTGCC
Band lengths:
236-958
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: