Human Gene PDCD11 (ENST00000369797.8_8) from GENCODE V47lift37
  Description: programmed cell death 11 (from RefSeq NM_014976.2)
Gencode Transcript: ENST00000369797.8_8
Gencode Gene: ENSG00000148843.15_13
Transcript (Including UTRs)
   Position: hg19 chr10:105,156,383-105,206,051 Size: 49,669 Total Exon Count: 36 Strand: +
Coding Region
   Position: hg19 chr10:105,158,184-105,205,306 Size: 47,123 Coding Exon Count: 35 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:105,156,383-105,206,051)mRNA (may differ from genome)Protein (1871 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RRP5_HUMAN
DESCRIPTION: RecName: Full=Protein RRP5 homolog; AltName: Full=NF-kappa-B-binding protein; Short=NFBP; AltName: Full=Programmed cell death protein 11;
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.
FUNCTION: Involved in the biogenesis of rRNA (By similarity).
SUBUNIT: Interacts with NF-kappa-B p50/NFKB1 and NF-kappa-B p65/RELA.
INTERACTION: P19838:NFKB1; NbExp=2; IntAct=EBI-300028, EBI-300010;
SUBCELLULAR LOCATION: Nucleus, nucleolus.
SIMILARITY: Contains 4 HAT repeats.
SIMILARITY: Contains 12 S1 motif domains.
SEQUENCE CAUTION: Sequence=AAG01992.1; Type=Erroneous translation; Note=Wrong choice of frame; Sequence=AAH49838.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=AAH64486.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=AAH80560.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=AAI11041.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence; Sequence=BAA11502.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: PDCD11
Diseases sorted by gene-association score: epididymo-orchitis (16)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 19.81 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 330.39 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -45.70116-0.394 Picture PostScript Text
3' UTR -294.20745-0.395 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR003107 - HAT
IPR012340 - NA-bd_OB-fold
IPR016027 - NA-bd_OB-fold-like
IPR003029 - Rbsml_prot_S1_RNA-bd_dom
IPR022967 - RNA-binding_domain_S1
IPR008847 - Suf
IPR013026 - TPR-contain_dom
IPR011990 - TPR-like_helical

Pfam Domains:
PF00575 - S1 RNA binding domain
PF01535 - PPR repeat
PF05843 - Suppressor of forked protein (Suf)

SCOP Domains:
81901 - HCP-like
48439 - Protein prenylyltransferase
48452 - TPR-like
50249 - Nucleic acid-binding proteins

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1WI5 - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q14690
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologGenome Browser
Gene DetailsGene Details Gene Details Gene Details
Gene SorterGene Sorter Gene Sorter Gene Sorter
 RGDEnsembl  SGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008134 transcription factor binding

Biological Process:
GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0000466 maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0006364 rRNA processing
GO:0006396 RNA processing
GO:0006397 mRNA processing

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005829 cytosol
GO:0032040 small-subunit processome


-  Descriptions from all associated GenBank mRNAs
  AK293772 - Homo sapiens cDNA FLJ61218 complete cds, highly similar to RRP5 protein homolog.
AK294971 - Homo sapiens cDNA FLJ54437 partial cds, highly similar to RRP5 protein homolog.
AK307418 - Homo sapiens cDNA, FLJ97366.
BC049838 - Homo sapiens programmed cell death 11, mRNA (cDNA clone IMAGE:5535193), partial cds.
BC064486 - Homo sapiens programmed cell death 11, mRNA (cDNA clone IMAGE:5930738), partial cds.
BC080560 - Homo sapiens programmed cell death 11, mRNA (cDNA clone IMAGE:6305061), partial cds.
BC111040 - Homo sapiens programmed cell death 11, mRNA (cDNA clone IMAGE:5534097), partial cds.
D80007 - Homo sapiens KIAA0185 mRNA, complete cds.
AB384444 - Synthetic construct DNA, clone: pF1KA0185, Homo sapiens PDCD11 gene for RRP5 protein homolog, complete cds, without stop codon, in Flexi system.
BC172442 - Synthetic construct Homo sapiens clone IMAGE:100069136, MGC:199147 programmed cell death 11 (PDCD11) mRNA, encodes complete protein.
BC023615 - Homo sapiens programmed cell death 11, mRNA (cDNA clone IMAGE:4646031), partial cds.
BC007698 - Homo sapiens programmed cell death 11, mRNA (cDNA clone IMAGE:3956692), partial cds.
JD066980 - Sequence 48004 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q14690 (Reactome details) participates in the following event(s):

R-HSA-6790906 EMG1 of the SSU processome methylates pseudouridine-1248 of 18S rRNA yielding N(1)-methylpseudouridine-1248
R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-6790901 rRNA modification in the nucleus and cytosol
R-HSA-8868773 rRNA processing in the nucleus and cytosol
R-HSA-72312 rRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000369797.1, ENST00000369797.2, ENST00000369797.3, ENST00000369797.4, ENST00000369797.5, ENST00000369797.6, ENST00000369797.7, KIAA0185, NM_014976, Q14690, Q2TA92, Q5W093, Q6P2J3, Q86VQ8, Q9H4P1, RRP5_HUMAN, uc318hwa.1, uc318hwa.2
UCSC ID: ENST00000369797.8_8
RefSeq Accession: NM_014976.2
Protein: Q14690 (aka RRP5_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.