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    Pdcd11 programmed cell death 11 [ Mus musculus (house mouse) ]

    Gene ID: 18572, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Pdcd11provided by MGI
    Official Full Name
    programmed cell death 11provided by MGI
    Primary source
    MGI:MGI:1341788
    See related
    Ensembl:ENSMUSG00000025047 AllianceGenome:MGI:1341788
    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
    ALG-4; Pdcd7; mKIAA0185; 1110021I22Rik
    Summary
    Predicted to enable RNA binding activity. Predicted to be involved in mRNA processing. Predicted to act upstream of or within rRNA processing. Located in cytosol. Is expressed in several structures, including blastocyst; early embryo; extraembryonic component; limb mesenchyme; and thymus primordium. Orthologous to human PDCD11 (programmed cell death 11). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 10.0), limb E14.5 (RPKM 6.7) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    19 C3; 19 39.24 cM
    Exon count:
    36
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 19 NC_000085.7 (47079183..47119585)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 19 NC_000085.6 (47090735..47131146)

    Chromosome 19 - NC_000085.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 23140 Neighboring gene STARR-positive B cell enhancer ABC_E1979 Neighboring gene TATA-box binding protein associated factor 5 Neighboring gene STARR-positive B cell enhancer ABC_E11038 Neighboring gene ATP synthase membrane subunit k Neighboring gene STARR-positive B cell enhancer ABC_E11039 Neighboring gene STARR-positive B cell enhancer ABC_E8754 Neighboring gene STARR-seq mESC enhancer starr_46339 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: 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. 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. Characterization of gene expression in mouse blastocyst using single-pass sequencing of 3995 clones. Sasaki N, et al. Genomics, 1998 Apr 15. PMID 9598303
    4. Venus trap in the mouse embryo reveals distinct molecular dynamics underlying specification of first embryonic lineages. Dietrich JE, et al. EMBO Rep, 2015 Aug. PMID 26142281, Free PMC Article
    5. A collection of cDNAs enriched in upper cortical layers of the embryonic mouse brain. García-Frigola C, et al. Brain Res Mol Brain Res, 2004 Mar 30. PMID 15010206

    See all (31) 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 (1)  1 citation
    • Endonuclease-mediated (2) 

    Pathways from PubChem

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    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 NF-kappaB binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in RNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within rRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in rRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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
    apoptosis-linked gene 4 protein
    programmed cell death protein 11
    programmed cell death protein 7

    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_011053.2 → NP_035183.2  protein RRP5 homolog

      See identical proteins and their annotated locations for NP_035183.2

      Status: VALIDATED

      Source sequence(s)
      BC055276, BC070468, BY729453
      Consensus CDS
      CCDS29888.1
      UniProtKB/Swiss-Prot
      Q3TSU4, Q3UGG2, Q3URK0, Q6NS46, Q6PIA8, Q6ZQH2, Q7TPE2, Q9CTD8, Q9R1Z2, Q9WTU7
      Related
      ENSMUSP00000072008.3, ENSMUST00000072141.4
      Conserved Domains (15) summary
      COG0457
      Location:1579 → 1784
      TPR; Tetratricopeptide (TPR) repeat [General function prediction only]
      COG0539
      Location:183 → 798
      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:284 → 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 ...
      cd05702
      Location:1047 → 1116
      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:1160 → 1234
      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:1238 → 1309
      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:1683 → 1710
      TPR; TPR repeat [structural motif]
      pfam05843
      Location:1718 → 1858
      Suf; Suppressor of forked protein (Suf)
      cl09927
      Location:636 → 707
      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_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
      47079183..47119585
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_003952752.2 RNA Sequence

    2. XR_877666.3 RNA Sequence

    3. XR_003952751.2 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_028635.1: Suppressed sequence

      Description
      NM_028635.1: This RefSeq record was removed by NCBI staff. Contact info@ncbi.nlm.nih.gov for further information.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6NS46.2 GenPept UniProtKB/Swiss-Prot:Q6NS46

    Gene LinkOut

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

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