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

Gene ID: 309458, updated on 2-Nov-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
EnsemblRapid: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 NF-kappaB binding activity and RNA binding activity. Predicted to be involved in 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, Nov 2024]
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 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, ENSRNOT00000027512.5
    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

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