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

Gene ID: 78796, updated on 25-May-2024

Summary

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
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Genomic context

See Zcchc4 in Genome Data Viewer
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

Expression

  • 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

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (3) 
  • Targeted (3) 

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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

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_001308144.1NP_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:3781
    zf-GRF; GRF zinc finger
    pfam10237
    Location:171327
    N6-adenineMlase; Probable N6-adenine methyltransferase
    cl19890
    Location:407436
    zf-DHHC; DHHC palmitoyltransferase
  2. NM_001309445.1NP_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:1125
    N6-adenineMlase; Probable N6-adenine methyltransferase
  3. NM_030185.3NP_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:3781
    zf-GRF; GRF zinc finger
    pfam10237
    Location:171327
    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_006504189.4XP_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:1125
    N6-adenineMlase; Probable N6-adenine methyltransferase
  2. XM_036165615.1XP_036021508.1  rRNA N6-adenosine-methyltransferase ZCCHC4 isoform X2

    Conserved Domains (1) summary
    pfam10237
    Location:12124
    N6-adenineMlase; Probable N6-adenine methyltransferase
  3. XM_036165617.1XP_036021510.1  rRNA N6-adenosine-methyltransferase ZCCHC4 isoform X3

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

    Conserved Domains (1) summary
    pfam10237
    Location:12124
    N6-adenineMlase; Probable N6-adenine methyltransferase
  5. XM_006504192.5XP_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:1125
    N6-adenineMlase; Probable N6-adenine methyltransferase

RNA

  1. XR_001784758.3 RNA Sequence