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    Zcchc4 zinc finger, CCHC domain containing 4 [ Mus musculus (house mouse) ]

    Gene ID: 78796, updated on 12-May-2024

    Summary

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    Official Symbol
    Zcchc4provided by MGI
    Official Full Name
    zinc finger, CCHC domain containing 4provided by MGI
    Primary source
    MGI:MGI:1926046
    See related
    Ensembl:ENSMUSG00000029179 AllianceGenome:MGI:1926046
    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
    Also known as
    4930449I23Rik
    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. Is expressed in central nervous system and sensory organ. Orthologous to human ZCCHC4 (zinc finger CCHC-type containing 4). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 2.3), limb E14.5 (RPKM 2.3) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    5 C1; 5 28.7 cM
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (52932751..52982008)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (52775409..52824666)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_13066 Neighboring gene Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase Neighboring gene STARR-seq mESC enhancer starr_13067 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:53060867-53061054 Neighboring gene STARR-seq mESC enhancer starr_13069 Neighboring gene phosphatidylinositol 4-kinase type 2 beta Neighboring gene STARR-positive B cell enhancer ABC_E3575 Neighboring gene anaphase promoting complex subunit 4 Neighboring gene STARR-seq mESC enhancer starr_13070 Neighboring gene predicted gene, 30241

    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. Oncogenic RAS directs silencing of tumor suppressor genes through ordered recruitment of transcriptional repressors. Wajapeyee N, et al. Genes Dev, 2013 Oct 15. PMID 24105743, Free PMC Article
    2. A genome-wide in situ hybridization map of RNA-binding proteins reveals anatomically restricted expression in the developing mouse brain. McKee AE, et al. BMC Dev Biol, 2005 Jul 20. PMID 16033648, Free PMC Article
    3. BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. Pourhaghighi R, et al. Cell Syst, 2020 Apr 22. PMID 32325033, Free PMC Article
    4. A conditional knockout resource for the genome-wide study of mouse gene function. Skarnes WC, et al. Nature, 2011 Jun 15. PMID 21677750, 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 (3) 
    • Targeted (3) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables S-adenosyl-L-methionine binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables methyltransferase activity IEA
    Inferred from Electronic Annotation
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in methylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of translation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in rRNA methylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in rRNA methylation ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleolus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    rRNA N6-adenosine-methyltransferase ZCCHC4
    Names
    zinc finger CCHC domain-containing protein 4
    NP_001295073.1
    NP_001296374.1
    NP_084461.1
    XP_006504252.1
    XP_006504255.1
    XP_036021508.1
    XP_036021509.1
    XP_036021510.1

    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_001308144.1 → NP_001295073.1  rRNA N6-adenosine-methyltransferase ZCCHC4 isoform 2

      See identical proteins and their annotated locations for NP_001295073.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region and contains an alternate 3' terminal exon, compared to variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AK019621, AK138997, CD773830
      Consensus CDS
      CCDS80282.1
      UniProtKB/Swiss-Prot
      Q8BKW4
      Related
      ENSMUSP00000109537.3, ENSMUST00000113904.9
      Conserved Domains (3) summary
      pfam06839
      Location:37 → 81
      zf-GRF; GRF zinc finger
      pfam10237
      Location:171 → 327
      N6-adenineMlase; Probable N6-adenine methyltransferase
      cl19890
      Location:407 → 436
      zf-DHHC; DHHC palmitoyltransferase

    2. NM_001309445.1 → NP_001296374.1  rRNA N6-adenosine-methyltransferase ZCCHC4 isoform 3

      See identical proteins and their annotated locations for NP_001296374.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) has multiple differences, compared to variant 1. These differences result in distinct 5' and 3' UTRs, the use of an in-frame downstream start codon, and a novel 3' coding region, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, and a shorter and distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AC158585, AK019621, CD773830
      UniProtKB/TrEMBL
      Q08EK6
      Conserved Domains (1) summary
      pfam10237
      Location:1 → 125
      N6-adenineMlase; Probable N6-adenine methyltransferase

    3. NM_030185.3 → NP_084461.1  rRNA N6-adenosine-methyltransferase ZCCHC4 isoform 1

      See identical proteins and their annotated locations for NP_084461.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK049511, AK138997, BF466409, BM942023, BQ442984, CB527151
      Consensus CDS
      CCDS39087.1
      UniProtKB/Swiss-Prot
      Q3UTX6, Q8BKW4, Q9D2I1
      Related
      ENSMUSP00000031077.9, ENSMUST00000031077.13
      Conserved Domains (2) summary
      pfam06839
      Location:37 → 81
      zf-GRF; GRF zinc finger
      pfam10237
      Location:171 → 327
      N6-adenineMlase; Probable N6-adenine methyltransferase

    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_000071.7 Reference GRCm39 C57BL/6J

      Range
      52932751..52982008
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006504189.4 → XP_006504252.1  rRNA N6-adenosine-methyltransferase ZCCHC4 isoform X1

      See identical proteins and their annotated locations for XP_006504252.1

      UniProtKB/TrEMBL
      Q08EK6
      Conserved Domains (1) summary
      pfam10237
      Location:1 → 125
      N6-adenineMlase; Probable N6-adenine methyltransferase

    2. XM_036165615.1 → XP_036021508.1  rRNA N6-adenosine-methyltransferase ZCCHC4 isoform X2

      Conserved Domains (1) summary
      pfam10237
      Location:12 → 124
      N6-adenineMlase; Probable N6-adenine methyltransferase

    3. XM_036165617.1 → XP_036021510.1  rRNA N6-adenosine-methyltransferase ZCCHC4 isoform X3

    4. XM_036165616.1 → XP_036021509.1  rRNA N6-adenosine-methyltransferase ZCCHC4 isoform X2

      Conserved Domains (1) summary
      pfam10237
      Location:12 → 124
      N6-adenineMlase; Probable N6-adenine methyltransferase

    5. XM_006504192.5 → XP_006504255.1  rRNA N6-adenosine-methyltransferase ZCCHC4 isoform X1

      See identical proteins and their annotated locations for XP_006504255.1

      UniProtKB/TrEMBL
      Q08EK6
      Conserved Domains (1) summary
      pfam10237
      Location:1 → 125
      N6-adenineMlase; Probable N6-adenine methyltransferase

    RNA

    1. XR_001784758.3 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8BKW4.1 GenPept UniProtKB/Swiss-Prot:Q8BKW4

    Gene LinkOut

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