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    Rcl1 RNA terminal phosphate cyclase-like 1 [ Mus musculus (house mouse) ]

    Gene ID: 59028, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Rcl1provided by MGI
    Official Full Name
    RNA terminal phosphate cyclase-like 1provided by MGI
    Primary source
    MGI:MGI:1913275
    See related
    Ensembl:ENSMUSG00000024785 AllianceGenome:MGI:1913275
    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
    Rnac; RPCL1; 2310040A02Rik
    Summary
    Predicted to enable RNA endonuclease activity. Acts upstream of or within endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) and endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Located in nucleolus. Is expressed in several structures, including axial musculature; cerebral cortex; gut; liver lobe; and submandibular gland primordium. Orthologous to human RCL1 (RNA terminal phosphate cyclase like 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in liver adult (RPKM 24.1), liver E18 (RPKM 16.5) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Rcl1 in Genome Data Viewer
    Location:
    19 C1; 19 23.61 cM
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 19 NC_000085.7 (29078761..29121251)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 19 NC_000085.6 (29101375..29143851)

    Chromosome 19 - NC_000085.7Genomic Context describing neighboring genes Neighboring gene adenylate kinase 3 Neighboring gene RIKEN cDNA 1700018L02 gene Neighboring gene STARR-positive B cell enhancer ABC_E1523 Neighboring gene STARR-seq mESC enhancer starr_45878 Neighboring gene predicted gene 9895 Neighboring gene STARR-positive B cell enhancer ABC_E3249 Neighboring gene STARR-seq mESC enhancer starr_45880 Neighboring gene microRNA 101b Neighboring gene STARR-seq mESC enhancer starr_45881 Neighboring gene predicted gene 5518 Neighboring gene predicted gene, 41829 Neighboring gene Janus kinase 2

    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 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. Rcl1p, the yeast protein similar to the RNA 3'-phosphate cyclase, associates with U3 snoRNP and is required for 18S rRNA biogenesis. Billy E, et al. EMBO J, 2000 May 2. PMID 10790377, Free PMC Article
    2. Two orthogonal cleavages separate subunit RNAs in mouse ribosome biogenesis. Wang M, et al. Nucleic Acids Res, 2014. PMID 25190460, Free PMC Article
    3. Development of an efficient screening system to identify novel bone metabolism-related genes using the exchangeable gene trap mutagenesis mouse models. Kurogi S, et al. Sci Rep, 2017 Jan 20. PMID 28106071, Free PMC Article
    4. The level of the transcription factor Pax6 is essential for controlling the balance between neural stem cell self-renewal and neurogenesis. Sansom SN, et al. PLoS Genet, 2009 Jun. PMID 19521500, Free PMC Article
    5. Characterization of an exchangeable gene trap using pU-17 carrying a stop codon-beta geo cassette. Taniwaki T, et al. Dev Growth Differ, 2005 Apr. PMID 15840001

    See all (26) 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)
    • Gene trapped (2) 

    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 RNA endonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    NOT enables RNA-3'-phosphate cyclase activity ISA
    Inferred from Sequence Alignment
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within rRNA processing ISA
    Inferred from Sequence Alignment
    more info
    		 PubMed 
    involved_in ribosomal small subunit biogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in ribosomal small subunit biogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleolus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of small-subunit processome ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of small-subunit processome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    RNA 3'-terminal phosphate cyclase-like protein
    Names
    RNA cyclase homolog

    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_021525.2 → NP_067500.1  RNA 3'-terminal phosphate cyclase-like protein

      See identical proteins and their annotated locations for NP_067500.1

      Status: VALIDATED

      Source sequence(s)
      AK009709
      Consensus CDS
      CCDS29731.1
      UniProtKB/Swiss-Prot
      Q9JJT0
      UniProtKB/TrEMBL
      Q3THS8
      Related
      ENSMUSP00000067579.6, ENSMUST00000064393.6
      Conserved Domains (1) summary
      TIGR03400
      Location:8 → 371
      18S_RNA_Rcl1p; 18S rRNA biogenesis protein RCL1

    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_000085.7 Reference GRCm39 C57BL/6J

      Range
      29078761..29121251
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006527246.5 → XP_006527309.1  RNA 3'-terminal phosphate cyclase-like protein isoform X1

      Conserved Domains (1) summary
      TIGR03400
      Location:17 → 192
      18S_RNA_Rcl1p; 18S rRNA biogenesis protein RCL1

    RNA

    1. XR_004940164.1 RNA Sequence

    2. XR_004940165.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9JJT0.1 GenPept UniProtKB/Swiss-Prot:Q9JJT0

    Gene LinkOut

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

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