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    prdm1 PR domain 1 [ Xenopus tropicalis (tropical clawed frog) ]

    Gene ID: 493207, updated on 4-Nov-2024

    Summary

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    Official Symbol
    prdm1provided by Xenbase
    Official Full Name
    PR domain 1provided by Xenbase
    Primary source
    Xenbase:XB-GENE-853254
    See related
    Ensembl:ENSXETG00000008674 AllianceGenome:Xenbase:XB-GENE-853254
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Xenopus tropicalis
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Silurana
    Also known as
    blimp1; xblimp1; prdi-bf1
    Summary
    Predicted to enable several functions, including DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and metal ion binding activity. Acts upstream of or within swimming. Predicted to be located in cytoplasm and nucleus. Human ortholog(s) of this gene implicated in hepatocellular carcinoma and lung adenocarcinoma. Orthologous to human PRDM1 (PR/SET domain 1). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See prdm1 in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    104 current UCB_Xtro_10.0 (GCF_000004195.4) 5 NC_030681.2 (79507411..79524423, complement)
    103 previous assembly Xenopus_tropicalis_v9.1 (GCF_000004195.3) 5 NC_030681.1 (77124249..77141257, complement)

    Chromosome 5 - NC_030681.2Genomic Context describing neighboring genes Neighboring gene crystallin beta-gamma domain containing 1 Neighboring gene neurofilament medium polypeptide-like Neighboring gene autophagy related 5 Neighboring gene protein FAM135A-like Neighboring gene prolyl endopeptidase

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Defining synphenotype groups in Xenopus tropicalis by use of antisense morpholino oligonucleotides. Rana AA, et al. PLoS Genet, 2006 Nov 17. PMID 17112317, Free PMC Article
    2. Genetic and genomic tools for Xenopus research: The NIH Xenopus initiative. Klein SL, et al. Dev Dyn, 2002 Dec. PMID 12454917
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Clone Names

    • MGC52536

    Gene Ontology Provided by Xenbase

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within cell fate commitment IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within cellular developmental process IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within swimming IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    PR domain zinc finger protein 1
    Names
    PR domain containing 1, with ZNF domain

    NCBI Reference Sequences (RefSeq)

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    RefSeqs of Annotated Genomes: Xenopus tropicalis Annotation Release 104 details...Open this link in a new tab

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

    Reference UCB_Xtro_10.0 Primary Assembly

    Genomic

    1. NC_030681.2 Reference UCB_Xtro_10.0 Primary Assembly

      Range
      79507411..79524423 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_002937157.5 → XP_002937203.1  PR domain zinc finger protein 1

      See identical proteins and their annotated locations for XP_002937203.1

      UniProtKB/TrEMBL
      F6RF85
      Conserved Domains (4) summary
      COG5048
      Location:446 → 647
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:536 → 556
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:576 → 601
      zf-H2C2_2; Zinc-finger double domain
      cd19187
      Location:45 → 172
      PR-SET_PRDM1; PR-SET domain found in PR domain zinc finger protein 1 (PRDM1) and similar proteins

    2. XM_004914548.4 → XP_004914605.1  PR domain zinc finger protein 1

      See identical proteins and their annotated locations for XP_004914605.1

      UniProtKB/TrEMBL
      F6RF85
      Related
      ENSXETP00000018988.3, ENSXETT00000018988.4
      Conserved Domains (4) summary
      COG5048
      Location:446 → 647
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:536 → 556
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:576 → 601
      zf-H2C2_2; Zinc-finger double domain
      cd19187
      Location:45 → 172
      PR-SET_PRDM1; PR-SET domain found in PR domain zinc finger protein 1 (PRDM1) and similar proteins

    3. XM_012963549.3 → XP_012819003.1  PR domain zinc finger protein 1

      See identical proteins and their annotated locations for XP_012819003.1

      UniProtKB/TrEMBL
      F6RF85
      Conserved Domains (4) summary
      COG5048
      Location:446 → 647
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:536 → 556
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:576 → 601
      zf-H2C2_2; Zinc-finger double domain
      cd19187
      Location:45 → 172
      PR-SET_PRDM1; PR-SET domain found in PR domain zinc finger protein 1 (PRDM1) and similar proteins
    Nucleotide Protein Strain
    Heading Accession and Version

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