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    Pdcd11 programmed cell death 11 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 309458, updated on 30-Mar-2024

    Summary

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    Official Symbol
    Pdcd11provided by RGD
    Official Full Name
    programmed cell death 11provided by RGD
    Primary source
    RGD:1304933
    See related
    Ensembl:ENSRNOG00000020304 AllianceGenome:RGD:1304933
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable RNA binding activity. Predicted to be involved in mRNA processing and rRNA processing. Predicted to be located in cytosol and nucleus. Predicted to be part of small-subunit processome. Predicted to be active in nucleolus. Orthologous to human PDCD11 (programmed cell death 11). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Adrenal (RPKM 129.2), Thymus (RPKM 126.8) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Pdcd11 in Genome Data Viewer
    Location:
    1q54
    Exon count:
    37
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (255922198..255963336)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (245980840..246021999)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (266866931..266908042)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene polycomb group ring finger 6 Neighboring gene TATA-box binding protein associated factor 5 Neighboring gene ATP synthase membrane subunit K Neighboring gene calcium homeostasis modulator family member 2 Neighboring gene calcium homeostasis modulator 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Regulation of Fas ligand expression and cell death by apoptosis-linked gene 4. Lacana E, et al. Nat Med, 1999 May. PMID 10229231
    2. Identification of a novel protein from glial cells based on its ability to interact with NF-kappaB subunits. Sweet T, et al. J Cell Biochem, 2003 Dec 1. PMID 14624448
    3. Both endonucleolytic and exonucleolytic cleavage mediate ITS1 removal during human ribosomal RNA processing. Sloan KE, et al. J Cell Biol, 2013 Mar 4. PMID 23439679, Free PMC Article
    4. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Baltz AG, et al. Mol Cell, 2012 Jun 8. PMID 22681889
    5. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Castello A, et al. Cell, 2012 Jun 8. PMID 22658674

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables NF-kappaB binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in rRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleolus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of small-subunit processome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    protein RRP5 homolog
    Names
    programmed cell death protein 11

    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_001107604.2 → NP_001101074.2  protein RRP5 homolog

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/TrEMBL
      D3ZNI3
      Related
      ENSRNOP00000027512.4, ENSRNOT00000027512.4
      Conserved Domains (16) summary
      COG0457
      Location:1592 → 1797
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      COG0539
      Location:65 → 633
      RpsA; Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
      cd04461
      Location:715 → 797
      S1_Rrp5_repeat_hs8_sc7; S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct ...
      cd05693
      Location:80 → 176
      S1_Rrp5_repeat_hs1_sc1; S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats ...
      cd05694
      Location:183 → 263
      S1_Rrp5_repeat_hs2_sc2; S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats ...
      cd05695
      Location:281 → 344
      S1_Rrp5_repeat_hs3; S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in ...
      cd05696
      Location:365 → 435
      S1_Rrp5_repeat_hs4; S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in ...
      cd05697
      Location:453 → 521
      S1_Rrp5_repeat_hs5; S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in ...
      cd05698
      Location:542 → 611
      S1_Rrp5_repeat_hs6_sc5; S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats ...
      cd05699
      Location:636 → 707
      S1_Rrp5_repeat_hs7; S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in ...
      cd05702
      Location:1041 → 1110
      S1_Rrp5_repeat_hs11_sc8; S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats ...
      cd05703
      Location:1154 → 1228
      S1_Rrp5_repeat_hs12_sc9; S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats ...
      cd05704
      Location:1232 → 1303
      S1_Rrp5_repeat_hs13; S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in ...
      sd00006
      Location:1696 → 1723
      TPR; TPR repeat [structural motif]
      pfam05843
      Location:1731 → 1871
      Suf; Suppressor of forked protein (Suf)
      cl09927
      Location:925 → 993
      S1_like; S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. ...

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086019.1 Reference GRCr8

      Range
      255922198..255963336
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063265069.1 → XP_063121139.1  protein RRP5 homolog isoform X1

    RNA

    1. XR_005487588.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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

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