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    PHYHD1 phytanoyl-CoA dioxygenase domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 254295, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PHYHD1provided by HGNC
    Official Full Name
    phytanoyl-CoA dioxygenase domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:23396
    See related
    Ensembl:ENSG00000175287 MIM:620042; AllianceGenome:HGNC:23396
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Enables 2-oxoglutarate-dependent dioxygenase activity. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in kidney (RPKM 11.6), thyroid (RPKM 9.8) and 23 other tissues See more
    Orthologs
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    Genomic context

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    See PHYHD1 in Genome Data Viewer
    Location:
    9q34.11
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (128920982..128942041)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (141125761..141145449)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (131683261..131704320)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene KYAT1-SPOUT1 readthrough Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:131600611-131601111 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:131607420-131607646 Neighboring gene kynurenine aminotransferase 1 Neighboring gene Sharpr-MPRA regulatory region 9337 Neighboring gene Sharpr-MPRA regulatory region 7409 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29094 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20355 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131647725-131648487 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:131654523-131655130 Neighboring gene leucine rich repeat containing 8 VRAC subunit A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29095 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:131666020-131666192 Neighboring gene uncharacterized LOC101929291 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131672021-131672804 Neighboring gene Sharpr-MPRA regulatory region 12425 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:131704025-131704223 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131708642-131709204 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131709205-131709766 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:131709767-131710328 Neighboring gene nucleoporin 188 Neighboring gene dolichol kinase Neighboring gene uncharacterized LOC101929314

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Human phytanoyl-CoA dioxygenase domain-containing 1 (PHYHD1) is a putative oxygen sensor associated with RNA and carbohydrate metabolism. Ala-Nisula T, et al. FEBS Lett, 2023 Jun. PMID 37235702
    2. Crystal structure of PHYHD1A, a 2OG oxygenase related to phytanoyl-CoA hydroxylase. Zhang Z, et al. Biochem Biophys Res Commun, 2011 May 20. PMID 21530488
    3. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Denoeud F, et al. Genome Res, 2007 Jun. PMID 17567994, Free PMC Article
    4. Protein array based interactome analysis of amyloid-β indicates an inhibition of protein translation. Virok DP, et al. J Proteome Res, 2011 Apr 1. PMID 21244100
    5. Genome-wide YFP fluorescence complementation screen identifies new regulators for telomere signaling in human cells. Lee OH, et al. Mol Cell Proteomics, 2011 Feb. PMID 21044950, Free PMC Article

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Potential readthrough

    Included gene: NUP188

    Homology

    Clone Names

    • MGC16638

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 2-oxoglutarate-dependent dioxygenase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    phytanoyl-CoA dioxygenase domain-containing protein 1
    NP_001094346.1
    NP_001094347.1
    NP_777593.2

    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_001100876.2 → NP_001094346.1  phytanoyl-CoA dioxygenase domain-containing protein 1 isoform a

      See identical proteins and their annotated locations for NP_001094346.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes isoform a.
      Source sequence(s)
      AK095000, BM689360
      Consensus CDS
      CCDS43885.1
      UniProtKB/Swiss-Prot
      A6PWN9, A6PWP0, B3KT57, B4E3X8, Q5SRE7, Q5SRE9, Q5SRF0, Q7Z623, Q7Z7P9, Q96GM4
      Related
      ENSP00000361673.3, ENST00000372592.8
      Conserved Domains (1) summary
      pfam05721
      Location:12 → 259
      PhyH; Phytanoyl-CoA dioxygenase (PhyH)

    2. NM_001100877.1 → NP_001094347.1  phytanoyl-CoA dioxygenase domain-containing protein 1 isoform c

      See identical proteins and their annotated locations for NP_001094347.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame coding exon, compared to variant 1. The resulting protein (isoform c) is shorter than isoform a.
      Source sequence(s)
      AK095000, BC051300, BM689360
      Consensus CDS
      CCDS43886.1
      UniProtKB/Swiss-Prot
      Q5SRE7
      Related
      ENSP00000409928.2, ENST00000421063.6
      Conserved Domains (1) summary
      pfam05721
      Location:12 → 238
      PhyH; Phytanoyl-CoA dioxygenase (PhyH)

    3. NM_174933.4 → NP_777593.2  phytanoyl-CoA dioxygenase domain-containing protein 1 isoform b

      See identical proteins and their annotated locations for NP_777593.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate coding exon, compared to variant 1, that causes a frameshift. The resulting protein (isoform b) has a longer and distinct C-terminus, compared to isoform a.
      Source sequence(s)
      AK095000, BC009373, BM689360
      Consensus CDS
      CCDS6914.1
      Related
      ENSP00000309515.5, ENST00000308941.9
      Conserved Domains (1) summary
      cl21496
      Location:12 → 147
      2OG-FeII_Oxy; 2OG-Fe(II) oxygenase superfamily

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      128920982..128942041
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      141125761..141145449
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5SRE7.2 GenPept UniProtKB/Swiss-Prot:Q5SRE7

    Gene LinkOut

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

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