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    Zcchc4 zinc finger CCHC-type containing 4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 360946, updated on 21-Dec-2024

    Summary

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    Official Symbol
    Zcchc4provided by RGD
    Official Full Name
    zinc finger CCHC-type containing 4provided by RGD
    Primary source
    RGD:1311414
    See related
    EnsemblRapid:ENSRNOG00000029064 AllianceGenome:RGD:1311414
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable S-adenosyl-L-methionine binding activity; rRNA (adenine-N6-)-methyltransferase activity; and zinc ion binding activity. Predicted to be involved in positive regulation of translation and rRNA methylation. Predicted to be located in nucleus. Predicted to be active in cytoplasm and nucleolus. Orthologous to human ZCCHC4 (zinc finger CCHC-type containing 4). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 47.8), Heart (RPKM 47.6) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Zcchc4 in Genome Data Viewer
    Location:
    14q11
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 14 NC_086032.1 (62378261..62419899, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 14 NC_051349.1 (58165467..58207071, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 14 NC_005113.4 (60511494..60553167, complement)

    Chromosome 14 - NC_086032.1Genomic Context describing neighboring genes Neighboring gene eukaryotic translation initiation factor 4E family member 2, pseudogene 1 Neighboring gene anaphase promoting complex subunit 4 Neighboring gene phosphatidylinositol 4-kinase type 2 beta Neighboring gene uncharacterized LOC134481754 Neighboring gene Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. The human methyltransferase ZCCHC4 catalyses N6-methyladenosine modification of 28S ribosomal RNA. Pinto R, et al. Nucleic Acids Res, 2020 Jan 24. PMID 31799605, Free PMC Article
    2. Structure and regulation of ZCCHC4 in m(6)A-methylation of 28S rRNA. Ren W, et al. Nat Commun, 2019 Nov 6. PMID 31695039, Free PMC Article
    3. N(6-)Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation. Ma H, et al. Nat Chem Biol, 2019 Jan. PMID 30531910, Free PMC Article
    4. The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112. van Tran N, et al. Nucleic Acids Res, 2019 Sep 5. PMID 31328227, Free PMC Article
    5. 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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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables S-adenosyl-L-methionine binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables S-adenosyl-L-methionine binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables S-adenosyl-L-methionine binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables rRNA (adenine-N6-)-methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables rRNA (adenine-N6-)-methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables rRNA (adenine-N6-)-methyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables rRNA (adenine-N6-)-methyltransferase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables zinc ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in positive regulation of translation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of translation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of translation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in rRNA methylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in rRNA methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in rRNA methylation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in rRNA methylation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in nucleolus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleolus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    rRNA N(6)-adenosine-methyltransferase ZCCHC4; rRNA N6-adenosine-methyltransferase ZCCHC4
    Names
    zinc finger CCHC domain-containing protein 4
    zinc finger, CCHC domain containing 4
    NP_001388357.1
    XP_038948116.1
    XP_038948117.1
    XP_038948118.1
    XP_038948119.1
    XP_063129423.1
    XP_063129424.1

    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_001401428.1 → NP_001388357.1  rRNA N(6)-adenosine-methyltransferase ZCCHC4

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000014
      UniProtKB/Swiss-Prot
      D3ZV31
      UniProtKB/TrEMBL
      A0A8I6APM1
      Related
      ENSRNOP00000051233.4, ENSRNOT00000042757.5

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086032.1 Reference GRCr8

      Range
      62378261..62419899 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063273353.1 → XP_063129423.1  rRNA N6-adenosine-methyltransferase ZCCHC4 isoform X3

      UniProtKB/TrEMBL
      A6IJG9, A6IJH0, R9PXZ6

    2. XM_063273354.1 → XP_063129424.1  rRNA N6-adenosine-methyltransferase ZCCHC4 isoform X3

      UniProtKB/TrEMBL
      A6IJG9, A6IJH0, R9PXZ6

    3. XM_039092190.2 → XP_038948118.1  rRNA N6-adenosine-methyltransferase ZCCHC4 isoform X2

      UniProtKB/TrEMBL
      A6IJG9
      Conserved Domains (1) summary
      pfam10237
      Location:1 → 79
      N6-adenineMlase; Probable N6-adenine methyltransferase

    4. XM_039092188.2 → XP_038948116.1  rRNA N6-adenosine-methyltransferase ZCCHC4 isoform X1

      UniProtKB/TrEMBL
      A0A8I6APM1
      Conserved Domains (2) summary
      pfam06839
      Location:37 → 81
      zf-GRF; GRF zinc finger
      pfam10237
      Location:168 → 295
      N6-adenineMlase; Probable N6-adenine methyltransferase

    5. XM_039092191.2 → XP_038948119.1  rRNA N6-adenosine-methyltransferase ZCCHC4 isoform X2

      UniProtKB/TrEMBL
      A6IJG9
      Conserved Domains (1) summary
      pfam10237
      Location:1 → 79
      N6-adenineMlase; Probable N6-adenine methyltransferase

    6. XM_039092189.2 → XP_038948117.1  rRNA N6-adenosine-methyltransferase ZCCHC4 isoform X2

      UniProtKB/TrEMBL
      A6IJG9
      Conserved Domains (1) summary
      pfam10237
      Location:1 → 79
      N6-adenineMlase; Probable N6-adenine methyltransferase

    RNA

    1. XR_010057386.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001108360.1: Suppressed sequence

      Description
      NM_001108360.1: This RefSeq was removed because currently there is insufficient support for the transcript.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    D3ZV31.1 GenPept UniProtKB/Swiss-Prot:D3ZV31

    Gene LinkOut

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

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