U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Tsr3 TSR3 20S rRNA accumulation [ Mus musculus (house mouse) ]

    Gene ID: 68327, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Tsr3provided by MGI
    Official Full Name
    TSR3 20S rRNA accumulationprovided by MGI
    Primary source
    MGI:MGI:1915577
    See related
    Ensembl:ENSMUSG00000015126 AllianceGenome:MGI:1915577
    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
    0610007P22Rik; 1110014B11Rik
    Summary
    Predicted to enable 18S rRNA aminocarboxypropyltransferase activity. Predicted to be involved in enzyme-directed rRNA pseudouridine synthesis and maturation of SSU-rRNA. Predicted to be located in cytoplasm. Is expressed in forebrain. Orthologous to human TSR3 (TSR3 ribosome maturation factor). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 26.8), CNS E14 (RPKM 18.6) 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 Tsr3 in Genome Data Viewer
    Location:
    17 A3.3; 17 12.53 cM
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 17 NC_000083.7 (25459120..25461773)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (25240141..25242799)

    Chromosome 17 - NC_000083.7Genomic Context describing neighboring genes Neighboring gene CapStarr-seq enhancer MGSCv37_chr17:25321285-25321526 Neighboring gene ubiquinol-cytochrome c reductase complex assembly factor 4 Neighboring gene predicted gene, 52286 Neighboring gene unkempt family like zinc finger Neighboring gene N-acetylglucosamine-1-phosphotransferase, gamma subunit Neighboring gene BAI1-associated protein 3 Neighboring gene microRNA 3547 Neighboring gene ubiquitin-conjugating enzyme E2I Neighboring gene STARR-positive B cell enhancer ABC_E8659 Neighboring gene predicted gene, 17801

    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. A genomic atlas of mouse hypothalamic development. Shimogori T, et al. Nat Neurosci, 2010 Jun. PMID 20436479, Free PMC Article
    2. Isolation of novel tissue-specific genes from cDNA libraries representing the individual tissue constituents of the gastrulating mouse embryo. Harrison SM, et al. Development, 1995 Aug. PMID 7671812
    3. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548
    4. A high-resolution anatomical atlas of the transcriptome in the mouse embryo. Diez-Roux G, et al. PLoS Biol, 2011 Jan 18. PMID 21267068, Free PMC Article
    5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Gerhard DS, et al. Genome Res, 2004 Oct. PMID 15489334, Free PMC Article

    See all (14) 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) 

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Clone Names

    • MGC113771

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables 18S rRNA aminocarboxypropyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables 18S rRNA aminocarboxypropyltransferase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables S-adenosyl-L-methionine binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transferase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in enzyme-directed rRNA pseudouridine synthesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in enzyme-directed rRNA pseudouridine synthesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in maturation of SSU-rRNA IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    18S rRNA aminocarboxypropyltransferase
    Names
    20S S rRNA accumulation protein 3 homolog
    probable ribosome biogenesis protein C16orf42 homolog
    ribosome biogenesis protein TSR3 homolog
    NP_001157190.1
    NP_080952.2
    XP_006524903.1
    XP_006524905.1
    XP_011244888.1
    XP_030105876.1
    XP_036016652.1
    XP_036016653.1
    XP_036016654.1
    XP_036016655.1
    XP_036016656.1
    XP_036016657.1

    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_001163718.1 → NP_001157190.1  18S rRNA aminocarboxypropyltransferase isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 3' end of an exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AK158743, BC089019, CA979987
      UniProtKB/TrEMBL
      A0AAA9WW46, A0AAA9WWH4
      Related
      ENSMUSP00000159935.1, ENSMUST00000249830.1
      Conserved Domains (3) summary
      PRK02287
      Location:65 → 216
      PRK02287; hypothetical protein; Provisional
      pfam04034
      Location:96 → 212
      DUF367; Domain of unknown function (DUF367)
      pfam04068
      Location:60 → 92
      RLI; Possible Fer4-like domain in RNase L inhibitor, RLI

    2. NM_026676.3 → NP_080952.2  18S rRNA aminocarboxypropyltransferase isoform 1

      See identical proteins and their annotated locations for NP_080952.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK158743, BC089019
      Consensus CDS
      CCDS28512.1
      UniProtKB/Swiss-Prot
      Q5HZH2, Q9DD00
      UniProtKB/TrEMBL
      A0AAA9WWH4
      Related
      ENSMUSP00000068511.7, ENSMUST00000063574.8
      Conserved Domains (3) summary
      PRK02287
      Location:65 → 223
      PRK02287; hypothetical protein; Provisional
      pfam04034
      Location:96 → 219
      DUF367; Domain of unknown function (DUF367)
      pfam04068
      Location:60 → 92
      RLI; Possible Fer4-like domain in RNase L inhibitor, RLI

    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_000083.7 Reference GRCm39 C57BL/6J

      Range
      25459120..25461773
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006524842.4 → XP_006524905.1  18S rRNA aminocarboxypropyltransferase isoform X7

      Conserved Domains (1) summary
      pfam04034
      Location:1 → 85
      Ribo_biogen_C; Ribosome biogenesis protein, C-terminal

    2. XM_036160763.1 → XP_036016656.1  18S rRNA aminocarboxypropyltransferase isoform X5

      Conserved Domains (1) summary
      pfam04034
      Location:1 → 85
      Ribo_biogen_C; Ribosome biogenesis protein, C-terminal

    3. XM_006524840.4 → XP_006524903.1  18S rRNA aminocarboxypropyltransferase isoform X4

      Conserved Domains (2) summary
      pfam04034
      Location:35 → 160
      Ribo_biogen_C; Ribosome biogenesis protein, C-terminal
      pfam04068
      Location:1 → 31
      RLI; Possible Fer4-like domain in RNase L inhibitor, RLI

    4. XM_036160759.1 → XP_036016652.1  18S rRNA aminocarboxypropyltransferase isoform X1

      UniProtKB/TrEMBL
      A0AAA9WW50, A0AAA9WWH1
      Related
      ENSMUSP00000159936.1, ENSMUST00000249831.1
      Conserved Domains (2) summary
      pfam04034
      Location:96 → 221
      Ribo_biogen_C; Ribosome biogenesis protein, C-terminal
      pfam04068
      Location:60 → 92
      RLI; Possible Fer4-like domain in RNase L inhibitor, RLI

    5. XM_030250016.2 → XP_030105876.1  18S rRNA aminocarboxypropyltransferase isoform X6

      UniProtKB/TrEMBL
      A0AAA9WUT5, Q8CHV1
      Related
      ENSMUSP00000159937.1, ENSMUST00000249833.1
      Conserved Domains (1) summary
      pfam04034
      Location:12 → 126
      Ribo_biogen_C; Ribosome biogenesis protein, C-terminal

    6. XM_036160760.1 → XP_036016653.1  18S rRNA aminocarboxypropyltransferase isoform X2

      UniProtKB/TrEMBL
      A0AAA9WW50
      Conserved Domains (2) summary
      pfam04034
      Location:35 → 160
      Ribo_biogen_C; Ribosome biogenesis protein, C-terminal
      pfam04068
      Location:1 → 31
      RLI; Possible Fer4-like domain in RNase L inhibitor, RLI

    7. XM_011246586.4 → XP_011244888.1  18S rRNA aminocarboxypropyltransferase isoform X6

      See identical proteins and their annotated locations for XP_011244888.1

      UniProtKB/TrEMBL
      A0AAA9WUT5, Q8CHV1
      Conserved Domains (1) summary
      pfam04034
      Location:12 → 126
      Ribo_biogen_C; Ribosome biogenesis protein, C-terminal

    8. XM_036160761.1 → XP_036016654.1  18S rRNA aminocarboxypropyltransferase isoform X3

      Conserved Domains (1) summary
      pfam04034
      Location:12 → 126
      Ribo_biogen_C; Ribosome biogenesis protein, C-terminal

    9. XM_036160764.1 → XP_036016657.1  18S rRNA aminocarboxypropyltransferase isoform X6

      UniProtKB/TrEMBL
      A0AAA9WUT5, Q8CHV1
      Conserved Domains (1) summary
      pfam04034
      Location:12 → 126
      Ribo_biogen_C; Ribosome biogenesis protein, C-terminal

    10. XM_036160762.1 → XP_036016655.1  18S rRNA aminocarboxypropyltransferase isoform X3

      Conserved Domains (1) summary
      pfam04034
      Location:12 → 126
      Ribo_biogen_C; Ribosome biogenesis protein, C-terminal
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5HZH2.1 GenPept UniProtKB/Swiss-Prot:Q5HZH2

    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