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Phyhd1 phytanoyl-CoA dioxygenase domain containing 1 [ Mus musculus (house mouse) ]

Gene ID: 227696, updated on 5-Mar-2024

Summary

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Official Symbol
Phyhd1provided by MGI
Official Full Name
phytanoyl-CoA dioxygenase domain containing 1provided by MGI
Primary source
MGI:MGI:3612860
See related
Ensembl:ENSMUSG00000079484 AllianceGenome:MGI:3612860
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Summary
Predicted to enable 2-oxoglutarate-dependent dioxygenase activity. Orthologous to human PHYHD1 (phytanoyl-CoA dioxygenase domain containing 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in liver adult (RPKM 32.3), kidney adult (RPKM 25.2) and 26 other tissues See more
Orthologs
human all
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Genomic context

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Location:
2 B; 2 21.46 cM
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (30156215..30172161)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (30266203..30282149)

Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA 1700084E18 gene Neighboring gene STARR-positive B cell enhancer ABC_E7804 Neighboring gene STARR-seq mESC enhancer starr_04091 Neighboring gene leucine rich repeat containing 8A VRAC subunit A Neighboring gene STARR-positive B cell enhancer ABC_E7805 Neighboring gene nucleoporin 188 Neighboring gene dolichol kinase Neighboring gene predicted gene, 39780

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Phyhd1, an XPhyH-like homologue, is induced in mouse T cells upon T cell stimulation. Furusawa Y, et al. Biochem Biophys Res Commun, 2016 Apr 8. PMID 26970303
  2. A molecular profile of a hematopoietic stem cell niche. Hackney JA, et al. Proc Natl Acad Sci U S A, 2002 Oct 1. PMID 12226475, Free PMC Article
  3. Libraries enriched for alternatively spliced exons reveal splicing patterns in melanocytes and melanomas. Watahiki A, et al. Nat Methods, 2004 Dec. PMID 15782199
  4. Large-scale gene trapping in C57BL/6N mouse embryonic stem cells. Hansen GM, et al. Genome Res, 2008 Oct. PMID 18799693, Free PMC Article
  5. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (2) 

General gene information

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Markers

Potential readthrough

Included gene: Lrrc8a

Homology

Clone Names

  • MGC49146

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables 2-oxoglutarate-dependent dioxygenase activity ISO
Inferred from Sequence Orthology
more info
  
enables dioxygenase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables oxidoreductase activity IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in cellular_component ND
No biological Data available
more info
  

General protein information

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Preferred Names
phytanoyl-CoA dioxygenase domain-containing protein 1
NP_001239497.1
NP_001239499.1
NP_001239500.1
NP_001268758.1
NP_758471.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001252568.2 → NP_001239497.1  phytanoyl-CoA dioxygenase domain-containing protein 1 isoform 2

    See identical proteins and their annotated locations for NP_001239497.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site and lacks an exon in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AK005293, AK138607, AL954388, BC145356
    UniProtKB/TrEMBL
    B7ZNN8
    Conserved Domains (1) summary
    pfam05721
    Location:32 → 256
    PhyH; Phytanoyl-CoA dioxygenase (PhyH)

  2. NM_001252570.1 → NP_001239499.1  phytanoyl-CoA dioxygenase domain-containing protein 1 isoform 3

    See identical proteins and their annotated locations for NP_001239499.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1. Both variants 3 and 5 encode the same isoform (3).
    Source sequence(s)
    AK138607, AL845258, AL954388, BQ829083
    Consensus CDS
    CCDS57163.1
    UniProtKB/Swiss-Prot
    A2AQZ4, Q80V68, Q9DB26
    UniProtKB/TrEMBL
    A2AQZ2
    Related
    ENSMUSP00000121371.2, ENSMUST00000154647.8
    Conserved Domains (1) summary
    pfam05721
    Location:12 → 259
    PhyH; Phytanoyl-CoA dioxygenase (PhyH)

  3. NM_001252571.1 → NP_001239500.1  phytanoyl-CoA dioxygenase domain-containing protein 1 isoform 4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region and an internal coding exon, and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
    Source sequence(s)
    AL845258, AL954388
    Consensus CDS
    CCDS57164.1
    UniProtKB/TrEMBL
    A2AQZ5, A2AQZ7
    Related
    ENSMUSP00000109273.2, ENSMUST00000113643.8
    Conserved Domains (1) summary
    pfam05721
    Location:12 → 238
    PhyH; Phytanoyl-CoA dioxygenase (PhyH)

  4. NM_001281829.1 → NP_001268758.1  phytanoyl-CoA dioxygenase domain-containing protein 1 isoform 3

    See identical proteins and their annotated locations for NP_001268758.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1. Both variants 3 and 5 encode the same isoform (3).
    Source sequence(s)
    AI182929, AL954388, BE945679, BY196857, CO041185, CX235839
    Consensus CDS
    CCDS57163.1
    UniProtKB/Swiss-Prot
    A2AQZ4, Q80V68, Q9DB26
    UniProtKB/TrEMBL
    A2AQZ2
    Related
    ENSMUSP00000109275.2, ENSMUST00000113645.8
    Conserved Domains (1) summary
    pfam05721
    Location:12 → 259
    PhyH; Phytanoyl-CoA dioxygenase (PhyH)

  5. NM_172267.4 → NP_758471.1  phytanoyl-CoA dioxygenase domain-containing protein 1 isoform 1

    See identical proteins and their annotated locations for NP_758471.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AK005293, AK138607, AL954388
    Consensus CDS
    CCDS15876.1
    UniProtKB/TrEMBL
    A0A0R4J137
    Related
    ENSMUSP00000088663.7, ENSMUST00000091132.13
    Conserved Domains (1) summary
    pfam05721
    Location:32 → 279
    PhyH; Phytanoyl-CoA dioxygenase (PhyH)

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000068.8 Reference GRCm39 C57BL/6J

    Range
    30156215..30172161
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9DB26.2 GenPept UniProtKB/Swiss-Prot:Q9DB26

Gene LinkOut

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