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

Gene ID: 18572, updated on 27-Nov-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 NF-kappaB binding activity and RNA binding activity. Predicted to be involved in rRNA processing. Located in cytosol. Is expressed in several structures, including blastocyst; brain; early embryo; olfactory epithelium; and thymus primordium. Orthologous to human PDCD11 (programmed cell death 11). [provided by Alliance of Genome Resources, Nov 2024]
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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See Pdcd11 in Genome Data Viewer
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 (32) 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)
  • Endonuclease-mediated (2) 
  • Gene trapped (1)  1 citation

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 IEA
Inferred from Electronic Annotation
more info
  
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 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 nucleolus IEA
Inferred from Electronic Annotation
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 [email protected] 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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