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

Gene ID: 59028, updated on 9-Dec-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, Dec 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
  • 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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