U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Rtca RNA 3'-terminal phosphate cyclase [ Mus musculus (house mouse) ]

    Gene ID: 66368, updated on 11-Apr-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Rtcaprovided by MGI
    Official Full Name
    RNA 3'-terminal phosphate cyclaseprovided by MGI
    Primary source
    MGI:MGI:1913618
    See related
    Ensembl:ENSMUSG00000000339 AllianceGenome:MGI:1913618
    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
    RPC; Rtcd1; 2310009A18Rik
    Summary
    Predicted to enable RNA-3'-phosphate cyclase activity. Predicted to be involved in RNA processing. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Is expressed in dorsal root ganglion; retina; and retina ganglion cell layer. Orthologous to human RTCA (RNA 3'-terminal phosphate cyclase). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in testis adult (RPKM 35.2), CNS E11.5 (RPKM 29.0) and 28 other tissues See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Rtca in Genome Data Viewer
    Location:
    3 G1; 3 50.35 cM
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (116282612..116301852, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (116488963..116508203, complement)

    Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 22361 Neighboring gene predicted gene, 26358 Neighboring gene STARR-positive B cell enhancer ABC_E656 Neighboring gene STARR-positive B cell enhancer ABC_E2680 Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:116216204-116216387 Neighboring gene dihydrolipoamide branched chain transacylase E2 Neighboring gene ubiquitin-conjugating enzyme E2D 3 (UBC4/5 homolog, yeast) pseudogene Neighboring gene splicing factor, arginine/serine-rich pseudogene

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Regulation of axon regeneration by the RNA repair and splicing pathway. Song Y, et al. Nat Neurosci, 2015 Jun. PMID 25961792, Free PMC Article
    2. Widespread and dynamic translational control of red blood cell development. Alvarez-Dominguez JR, et al. Blood, 2017 Feb 2. PMID 27899360, Free PMC Article
    3. ATG5 is required for B cell polarization and presentation of particulate antigens. Arbogast F, et al. Autophagy, 2019 Feb. PMID 30196744, Free PMC Article
    4. Database resources of the National Center for Biotechnology Information. Wheeler DL, et al. Nucleic Acids Res, 2001 Jan 1. PMID 11125038, Free PMC Article
    5. Fancd2 in vivo interaction network reveals a non-canonical role in mitochondrial function. Zhang T, et al. Sci Rep, 2017 Apr 5. PMID 28378742, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

    Go to the top of the page Help

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (1) 

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Clone Names

    • MGC102342

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA-3'-phosphate cyclase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA-3'-phosphate cyclase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables catalytic activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ligase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in RNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of optical nerve axon regeneration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    RNA 3'-terminal phosphate cyclase
    Names
    RNA cyclase
    RNA terminal phosphate cyclase domain 1
    RNA terminal phosphate cyclase domain-containing protein 1
    RNA-3'-phosphate cyclase
    NP_079793.2
    XP_006501946.1
    XP_006501947.1
    XP_030108613.1

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_025517.3 → NP_079793.2  RNA 3'-terminal phosphate cyclase

      See identical proteins and their annotated locations for NP_079793.2

      Status: VALIDATED

      Source sequence(s)
      AK152129, AK159961, BM899781
      Consensus CDS
      CCDS17786.1
      UniProtKB/Swiss-Prot
      Q3TVV2, Q9D7H3
      UniProtKB/TrEMBL
      Q3TIJ4, Q3UAE6, Q5BLJ4
      Related
      ENSMUSP00000000348.9, ENSMUST00000000348.15
      Conserved Domains (2) summary
      cd00874
      Location:8 → 340
      RNA_Cyclase_Class_II; RNA 3' phosphate cyclase domain (class II). These proteins function as RNA cyclase to catalyze the ATP-dependent conversion of 3'-phosphate to a 2'.3'-cyclic phosphodiester at the end of RNA molecule. A conserved catalytic histidine residue is found in ...
      pfam01137
      Location:12 → 338
      RTC; RNA 3'-terminal phosphate cyclase

    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_000069.7 Reference GRCm39 C57BL/6J

      Range
      116282612..116301852 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006501884.3 → XP_006501947.1  RNA 3'-terminal phosphate cyclase isoform X2

      See identical proteins and their annotated locations for XP_006501947.1

      Conserved Domains (1) summary
      pfam01137
      Location:1 → 232
      RTC; RNA 3'-terminal phosphate cyclase

    2. XM_006501883.2 → XP_006501946.1  RNA 3'-terminal phosphate cyclase isoform X1

      UniProtKB/TrEMBL
      Q3TIJ4, Q3UAE6, Q5BLJ4
      Conserved Domains (1) summary
      pfam01137
      Location:2 → 281
      RTC; RNA 3'-terminal phosphate cyclase

    3. XM_030252753.2 → XP_030108613.1  RNA 3'-terminal phosphate cyclase isoform X2

      Conserved Domains (1) summary
      pfam01137
      Location:1 → 232
      RTC; RNA 3'-terminal phosphate cyclase

    RNA

    1. XR_001783733.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9D7H3.2 GenPept UniProtKB/Swiss-Prot:Q9D7H3

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools