PDCD11 is a NF-kappa-B (NFKB1; 164011)-binding protein that colocalizes with U3 RNA (MIM 180710) in the nucleolus and is required for rRNA maturation and generation of 18S rRNA (Sweet et al., 2003 [PubMed 14624448]; Sweet et al., 2008 [PubMed 17654514]).[supplied by OMIM, Oct 2008] See more...

Aliases for PDCD11 Gene

Aliases for PDCD11 Gene

  • Programmed Cell Death 11 2 3 5
  • Programmed Cell Death Protein 11 3 4
  • NF-Kappa-B-Binding Protein 3 4
  • Protein RRP5 Homolog 3 4
  • NFBP 3 4
  • Apoptosis-Linked Gene 4 3
  • KIAA0185 4
  • ALG-4 3
  • ALG4 3
  • RRP5 3

External Ids for PDCD11 Gene

Previous GeneCards Identifiers for PDCD11 Gene

  • GC10P104049
  • GC10P104390
  • GC10P105287
  • GC10P104821
  • GC10P104819
  • GC10P105146
  • GC10U900633
  • GC10P098787
  • GC10P105156

Summaries for PDCD11 Gene

Entrez Gene Summary for PDCD11 Gene

  • PDCD11 is a NF-kappa-B (NFKB1; 164011)-binding protein that colocalizes with U3 RNA (MIM 180710) in the nucleolus and is required for rRNA maturation and generation of 18S rRNA (Sweet et al., 2003 [PubMed 14624448]; Sweet et al., 2008 [PubMed 17654514]).[supplied by OMIM, Oct 2008]

GeneCards Summary for PDCD11 Gene

PDCD11 (Programmed Cell Death 11) is a Protein Coding gene. Diseases associated with PDCD11 include Autosomal Dominant Non-Syndromic Intellectual Disability 1 and Epididymo-Orchitis. Among its related pathways are rRNA processing in the nucleus and cytosol and Gene Expression. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and transcription factor binding.

UniProtKB/Swiss-Prot Summary for PDCD11 Gene

  • Essential for the generation of mature 18S rRNA, specifically necessary for cleavages at sites A0, 1 and 2 of the 47S precursor. Directly interacts with U3 snoRNA.
  • Involved in the biogenesis of rRNA.

Additional gene information for PDCD11 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PDCD11 Gene

Genomics for PDCD11 Gene

GeneHancer (GH) Regulatory Elements for PDCD11 Gene

Promoters and enhancers for PDCD11 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PDCD11 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PDCD11

Top Transcription factor binding sites by QIAGEN in the PDCD11 gene promoter:
  • AML1a
  • CUTL1
  • Evi-1
  • FOXO3
  • FOXO3a
  • FOXO3b
  • Nkx2-5
  • POU3F2
  • RP58
  • SRY

Genomic Locations for PDCD11 Gene

Genomic Locations for PDCD11 Gene
chr10:103,396,624-103,446,295
(GRCh38/hg38)
Size:
49,672 bases
Orientation:
Plus strand
chr10:105,156,405-105,206,049
(GRCh37/hg19)
Size:
49,645 bases
Orientation:
Plus strand

Genomic View for PDCD11 Gene

Genes around PDCD11 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDCD11 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDCD11 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDCD11 Gene

Proteins for PDCD11 Gene

  • Protein details for PDCD11 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q14690-RRP5_HUMAN
    Recommended name:
    Protein RRP5 homolog
    Protein Accession:
    Q14690
    Secondary Accessions:
    • Q2TA92
    • Q5W093
    • Q6P2J3
    • Q86VQ8
    • Q9H4P1

    Protein attributes for PDCD11 Gene

    Size:
    1871 amino acids
    Molecular mass:
    208701 Da
    Quaternary structure:
    • Interacts with NF-kappa-B p50/NFKB1 and NF-kappa-B p65/RELA.
    SequenceCaution:
    • Sequence=AAG01992.1; Type=Erroneous translation; Note=Wrong choice of frame.; Evidence={ECO:0000305}; Sequence=AAH49838.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=AAH64486.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=AAH80560.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=AAI11041.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAA11502.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAA11502.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PDCD11 Gene

neXtProt entry for PDCD11 Gene

Post-translational modifications for PDCD11 Gene

  • Ubiquitination at Lys219 and Lys1781
  • Modification sites at PhosphoSitePlus

Other Protein References for PDCD11 Gene

No data available for DME Specific Peptides for PDCD11 Gene

Domains & Families for PDCD11 Gene

Gene Families for PDCD11 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for PDCD11 Gene

Blocks:
  • RNA-processing protein, HAT helix
  • RNA binding S1
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PDCD11 Gene

GenScript: Design optimal peptide antigens:
  • Programmed cell death protein 11 (RRP5_HUMAN)
genes like me logo Genes that share domains with PDCD11: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for PDCD11 Gene

Function for PDCD11 Gene

Molecular function for PDCD11 Gene

UniProtKB/Swiss-Prot Function:
Essential for the generation of mature 18S rRNA, specifically necessary for cleavages at sites A0, 1 and 2 of the 47S precursor. Directly interacts with U3 snoRNA.
UniProtKB/Swiss-Prot Function:
Involved in the biogenesis of rRNA.

Phenotypes From GWAS Catalog for PDCD11 Gene

Gene Ontology (GO) - Molecular Function for PDCD11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22658674
GO:0005515 protein binding IPI,IEA 14624448
GO:0008134 transcription factor binding IPI 14624448
genes like me logo Genes that share ontologies with PDCD11: view
genes like me logo Genes that share phenotypes with PDCD11: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDCD11

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PDCD11 Gene

Localization for PDCD11 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDCD11 Gene

Nucleus, nucleolus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PDCD11 gene
Compartment Confidence
nucleus 5
cytosol 4
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (3)
  • Vesicles (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PDCD11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 14624448
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IBA 21873635
GO:0005829 cytosol IEA --
GO:0032040 small-subunit processome IBA 21873635
genes like me logo Genes that share ontologies with PDCD11: view

Pathways & Interactions for PDCD11 Gene

genes like me logo Genes that share pathways with PDCD11: view

Gene Ontology (GO) - Biological Process for PDCD11 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006364 rRNA processing TAS --
GO:0006396 RNA processing IEA --
GO:0006397 mRNA processing IEA --
genes like me logo Genes that share ontologies with PDCD11: view

No data available for SIGNOR curated interactions for PDCD11 Gene

Drugs & Compounds for PDCD11 Gene

No Compound Related Data Available

Transcripts for PDCD11 Gene

mRNA/cDNA for PDCD11 Gene

1 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDCD11

Alternative Splicing Database (ASD) splice patterns (SP) for PDCD11 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18 ^
SP1:
SP2:
SP3:
SP4: -
SP5: -
SP6:
SP7: - -
SP8:
SP9:
SP10:

ExUns: 19 ^ 20 ^ 21 ^ 22 ^ 23a · 23b ^ 24 ^ 25a · 25b ^ 26a · 26b ^ 27a · 27b ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33 ^ 34
SP1: - - -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:

Relevant External Links for PDCD11 Gene

GeneLoc Exon Structure for
PDCD11

Expression for PDCD11 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PDCD11 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PDCD11 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (18.3), Brain (12.8), CD8 Tcells (6.6), and Heart (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PDCD11 Gene



Protein tissue co-expression partners for PDCD11 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PDCD11

SOURCE GeneReport for Unigene cluster for PDCD11 Gene:

Hs.239499

Evidence on tissue expression from TISSUES for PDCD11 Gene

  • Nervous system(4.4)
  • Bone marrow(4.1)
  • Blood(2.4)
genes like me logo Genes that share expression patterns with PDCD11: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PDCD11 Gene

Orthologs for PDCD11 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PDCD11 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PDCD11 31 30
  • 99.5 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PDCD11 31 30
  • 88.12 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PDCD11 31 30
  • 87.03 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Pdcd11 17 31 30
  • 82.96 (n)
rat
(Rattus norvegicus)
Mammalia Pdcd11 30
  • 82.85 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 78 (a)
OneToMany
-- 31
  • 62 (a)
OneToMany
-- 31
  • 58 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia PDCD11 31
  • 65 (a)
OneToOne
chicken
(Gallus gallus)
Aves PDCD11 31 30
  • 62.82 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PDCD11 31
  • 55 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pdcd11 30
  • 58.72 (n)
zebrafish
(Danio rerio)
Actinopterygii pdcd11 31 30
  • 54.77 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG5728 31
  • 25 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea let-716 31
  • 23 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RRP5 33 31
  • 26 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G11964 30
  • 44.8 (n)
rice
(Oryza sativa)
Liliopsida Os07g0203300 30
  • 48.57 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 41 (a)
OneToOne
Species where no ortholog for PDCD11 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PDCD11 Gene

ENSEMBL:
Gene Tree for PDCD11 (if available)
TreeFam:
Gene Tree for PDCD11 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PDCD11: view image

Paralogs for PDCD11 Gene

No data available for Paralogs for PDCD11 Gene

Variants for PDCD11 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PDCD11 Gene

SNP ID Clinical significance and condition Chr 10 pos Variation AA Info Type
rs11591914 - p.Ala780Ser
rs11598673 - p.Ala623Ser
rs150893869 - p.Lys45Glu
rs2274289 - p.Pro1453Ser
rs2986014 - p.Leu1216Phe

Additional dbSNP identifiers (rs#s) for PDCD11 Gene

Structural Variations from Database of Genomic Variants (DGV) for PDCD11 Gene

Variant ID Type Subtype PubMed ID
dgv280e212 CNV gain 25503493
dgv965n100 CNV gain 25217958
dgv966n100 CNV gain 25217958
esv3577694 CNV gain 25503493
esv3624413 CNV gain 21293372
esv3624414 CNV gain 21293372
nsv1047382 CNV gain 25217958
nsv518987 CNV loss 19592680
nsv524966 CNV loss 19592680
nsv7529 CNV insertion 18451855

Variation tolerance for PDCD11 Gene

Residual Variation Intolerance Score: 8.67% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 18.50; 98.59% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PDCD11 Gene

Human Gene Mutation Database (HGMD)
PDCD11
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDCD11

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDCD11 Gene

Disorders for PDCD11 Gene

MalaCards: The human disease database

(5) MalaCards diseases for PDCD11 Gene - From: DISEASES

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PDCD11

genes like me logo Genes that share disorders with PDCD11: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PDCD11 Gene

Publications for PDCD11 Gene

  1. Evidence for involvement of NFBP in processing of ribosomal RNA. (PMID: 17654514) Sweet T … Amini S (Journal of cellular physiology 2008) 2 3 4 54
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54
  3. Identification of a novel protein from glial cells based on its ability to interact with NF-kappaB subunits. (PMID: 14624448) Sweet T … Amini S (Journal of cellular biochemistry 2003) 3 4 54
  4. Functional proteomic analysis of human nucleolus. (PMID: 12429849) Scherl A … Diaz JJ (Molecular biology of the cell 2002) 3 4 54
  5. Regulation of Fas ligand expression and cell death by apoptosis-linked gene 4. (PMID: 10229231) Lacana E … D'Adamio L (Nature medicine 1999) 2 3 54

Products for PDCD11 Gene

Sources for PDCD11 Gene