U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

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

    Summary

    Go to the top of the page Help
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    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

    Go to the top of the page Help

    Alleles

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

    General gene information

    Go to the top of the page Help

    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

    Go to the top of the page Help
    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)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous