Aliases for PNLDC1 Gene

Aliases for PNLDC1 Gene

  • PARN Like, Ribonuclease Domain Containing 1 2 3 5
  • Poly(A)-Specific Ribonuclease (PARN)-Like Domain Containing 1 2 3
  • Poly(A)-Specific Ribonuclease Domain-Containing Protein 1 3 4
  • PARN-Like Domain-Containing Protein 1 3 4
  • Poly(A)-Specific Ribonuclease PNLDC1 3 4
  • HsPNLDC1 3 4
  • Poly(A)-Specific Ribonuclease PARN-Like Domain-Containing Protein 1 3
  • EC 3.1.13.4 4

External Ids for PNLDC1 Gene

Previous GeneCards Identifiers for PNLDC1 Gene

  • GC06P160054
  • GC06P160130
  • GC06P160191
  • GC06P157691
  • GC06P160221

Summaries for PNLDC1 Gene

GeneCards Summary for PNLDC1 Gene

PNLDC1 (PARN Like, Ribonuclease Domain Containing 1) is a Protein Coding gene. Among its related pathways are Deadenylation-dependent mRNA decay. Gene Ontology (GO) annotations related to this gene include nucleic acid binding. An important paralog of this gene is PARN.

UniProtKB/Swiss-Prot Summary for PNLDC1 Gene

  • 3'-exoribonuclease that has a preference for poly(A) tails of mRNAs, thereby efficiently degrading poly(A) tails (PubMed:27515512). Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs and is also used to silence certain maternal mRNAs translationally during oocyte maturation and early embryonic development (PubMed:27515512). May act as a regulator of multipotency in embryonic stem cells (By similarity).

Additional gene information for PNLDC1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PNLDC1 Gene

Genomics for PNLDC1 Gene

GeneHancer (GH) Regulatory Elements for PNLDC1 Gene

Promoters and enhancers for PNLDC1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J159801 Promoter 0.6 EPDnew 512.9 +0.0 18 0.1 POLR2G GABPB1 ZBTB33 AGO2 AGO1 POLR2A PNLDC1 piR-59425-028 MRPL18
GH06J159800 Promoter 0.6 EPDnew 500.7 -0.1 -95 0.1 POLR2G GABPB1 ZBTB33 AGO2 AGO1 POLR2A PNLDC1 piR-59425-028 MRPL18 HSALNG0054782
GH06J159725 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 23.8 -72.1 -72063 5.6 EP300 FOXK2 ZBTB40 ZNF217 SIN3A NRF1 TCF12 POLR2G USF1 SP1 WTAP lnc-TCP1-2 SOD2 MRPL18 TCP1 PNLDC1 ACAT2 SNORA29 SNORA20 LOC729603
GH06J159690 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 17 -106.9 -106850 5.8 FOXK2 HNRNPK CTCF SIN3A NRF1 TCF12 POLR2G SP1 NCOR1 BCLAF1 SOD2 JA662193 lnc-WTAP-4 lnc-TCP1-5 WTAP MRPL18 PNLDC1 LOC729603 ACAT2 SNORA29
GH06J159759 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 10.4 -38.5 -38546 4.2 ZBTB40 EP300 ZSCAN5C SIN3A NRF1 POLR2G SP1 NCOR1 TEAD4 FOS ACAT2 ENSG00000285441 SOD2-OT1 MRPL18 WTAP LOC729603 PNLDC1 SOD2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PNLDC1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PNLDC1

Top Transcription factor binding sites by QIAGEN in the PNLDC1 gene promoter:
  • Egr-2
  • IRF-1
  • Lmo2
  • p53
  • Pax-4a
  • SRY
  • USF-1
  • USF-1:USF-2
  • USF1

Genomic Locations for PNLDC1 Gene

Genomic Locations for PNLDC1 Gene
chr6:159,800,249-159,820,704
(GRCh38/hg38)
Size:
20,456 bases
Orientation:
Plus strand
chr6:160,221,298-160,241,736
(GRCh37/hg19)
Size:
20,439 bases
Orientation:
Plus strand

Genomic View for PNLDC1 Gene

Genes around PNLDC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PNLDC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PNLDC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PNLDC1 Gene

Proteins for PNLDC1 Gene

  • Protein details for PNLDC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NA58-PNDC1_HUMAN
    Recommended name:
    Poly(A)-specific ribonuclease PNLDC1
    Protein Accession:
    Q8NA58
    Secondary Accessions:
    • Q5TAP7
    • Q8N7X5

    Protein attributes for PNLDC1 Gene

    Size:
    520 amino acids
    Molecular mass:
    60124 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PNLDC1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PNLDC1 Gene

Post-translational modifications for PNLDC1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PNLDC1 Gene

Domains & Families for PNLDC1 Gene

Gene Families for PNLDC1 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted membrane proteins

Protein Domains for PNLDC1 Gene

Blocks:
  • CAF1 family ribonuclease
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PNLDC1 Gene

GenScript: Design optimal peptide antigens:
  • Poly(A)-specific ribonuclease PARN-like domain-containing protein 1 (PNDC1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8NA58

UniProtKB/Swiss-Prot:

PNDC1_HUMAN :
  • Belongs to the CAF1 family.
Family:
  • Belongs to the CAF1 family.
genes like me logo Genes that share domains with PNLDC1: view

Function for PNLDC1 Gene

Molecular function for PNLDC1 Gene

UniProtKB/Swiss-Prot Function:
3'-exoribonuclease that has a preference for poly(A) tails of mRNAs, thereby efficiently degrading poly(A) tails (PubMed:27515512). Exonucleolytic degradation of the poly(A) tail is often the first step in the decay of eukaryotic mRNAs and is also used to silence certain maternal mRNAs translationally during oocyte maturation and early embryonic development (PubMed:27515512). May act as a regulator of multipotency in embryonic stem cells (By similarity).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=Exonucleolytic cleavage of poly(A) to 5'-AMP.; EC=3.1.13.4; Evidence=. ;.

Enzyme Numbers (IUBMB) for PNLDC1 Gene

Phenotypes From GWAS Catalog for PNLDC1 Gene

Gene Ontology (GO) - Molecular Function for PNLDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000175 3'-5'-exoribonuclease activity IBA 21873635
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IEA --
GO:0004518 nuclease activity IEA --
GO:0004527 exonuclease activity IEA --
genes like me logo Genes that share ontologies with PNLDC1: view
genes like me logo Genes that share phenotypes with PNLDC1: view

Animal Model Products

miRNA for PNLDC1 Gene

miRTarBase miRNAs that target PNLDC1

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PNLDC1 Gene

Localization for PNLDC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PNLDC1 Gene

Endoplasmic reticulum membrane; Single-pass membrane protein. Note=Localizes mainly in the endoplasmic reticulum (PubMed:27515512). {ECO:0000269 PubMed:27515512}.

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 PNLDC1 gene
Compartment Confidence
endoplasmic reticulum 5
mitochondrion 1
nucleus 1
plasma membrane 0
golgi apparatus 0

Gene Ontology (GO) - Cellular Components for PNLDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA 21873635
GO:0005783 endoplasmic reticulum IDA,IBA 27515512
GO:0005789 endoplasmic reticulum membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PNLDC1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PNLDC1 Gene

Pathways & Interactions for PNLDC1 Gene

PathCards logo

SuperPathways for PNLDC1 Gene

SuperPathway Contained pathways
1 Deadenylation-dependent mRNA decay
genes like me logo Genes that share pathways with PNLDC1: view

Pathways by source for PNLDC1 Gene

1 KEGG pathway for PNLDC1 Gene

Gene Ontology (GO) - Biological Process for PNLDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay IEA --
GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening IDA,IBA 27515512
GO:0001825 blastocyst formation IEA --
GO:0090305 nucleic acid phosphodiester bond hydrolysis IEA --
GO:0090503 RNA phosphodiester bond hydrolysis, exonucleolytic IEA --
genes like me logo Genes that share ontologies with PNLDC1: view

No data available for SIGNOR curated interactions for PNLDC1 Gene

Drugs & Compounds for PNLDC1 Gene

No Compound Related Data Available

Transcripts for PNLDC1 Gene

mRNA/cDNA for PNLDC1 Gene

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

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PNLDC1 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19
SP1: -
SP2: - -
SP3:
SP4: - -

Relevant External Links for PNLDC1 Gene

GeneLoc Exon Structure for
PNLDC1

Expression for PNLDC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PNLDC1 Gene

mRNA differential expression in normal tissues according to GTEx for PNLDC1 Gene

This gene is overexpressed in Testis (x12.9), Brain - Caudate (basal ganglia) (x4.7), and Brain - Putamen (basal ganglia) (x4.0).

Protein differential expression in normal tissues from HIPED for PNLDC1 Gene

This gene is overexpressed in Heart (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PNLDC1 Gene



Protein tissue co-expression partners for PNLDC1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PNLDC1

SOURCE GeneReport for Unigene cluster for PNLDC1 Gene:

Hs.349077

Evidence on tissue expression from TISSUES for PNLDC1 Gene

  • Nervous system(4.1)
genes like me logo Genes that share expression patterns with PNLDC1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PNLDC1 Gene

Orthologs for PNLDC1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PNLDC1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PNLDC1 31 30
  • 99.18 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PNLDC1 31 30
  • 86.1 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PNLDC1 31 30
  • 85.85 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Pnldc1 17 31 30
  • 84.03 (n)
oppossum
(Monodelphis domestica)
Mammalia PNLDC1 31
  • 73 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PNLDC1 31
  • 59 (a)
OneToOne
chicken
(Gallus gallus)
Aves PNLDC1 31 30
  • 63.67 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PNLDC1 31
  • 57 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea parn-1 31
  • 18 (a)
OneToMany
Species where no ortholog for PNLDC1 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)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • zebrafish (Danio rerio)

Evolution for PNLDC1 Gene

ENSEMBL:
Gene Tree for PNLDC1 (if available)
TreeFam:
Gene Tree for PNLDC1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PNLDC1: view image

Paralogs for PNLDC1 Gene

Paralogs for PNLDC1 Gene

genes like me logo Genes that share paralogs with PNLDC1: view

Variants for PNLDC1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PNLDC1 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
721294 Likely Benign: not provided 159,816,014(+) G/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for PNLDC1 Gene

Structural Variations from Database of Genomic Variants (DGV) for PNLDC1 Gene

Variant ID Type Subtype PubMed ID
esv3576237 CNV gain 25503493

Variation tolerance for PNLDC1 Gene

Residual Variation Intolerance Score: 40.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.52; 29.45% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PNLDC1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PNLDC1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PNLDC1 Gene

Disorders for PNLDC1 Gene

Additional Disease Information for PNLDC1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for PNLDC1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PNLDC1 Gene

Publications for PNLDC1 Gene

  1. Mammalian PNLDC1 is a novel poly(A) specific exonuclease with discrete expression during early development. (PMID: 27515512) Anastasakis D … Stathopoulos C (Nucleic acids research 2016) 3 4 54
  2. Association of genetic variants with hemorrhagic stroke in Japanese individuals. (PMID: 20198315) Yoshida T … Yamada Y (International journal of molecular medicine 2010) 3 41 54
  3. Assessment of a polymorphism of SDK1 with hypertension in Japanese Individuals. (PMID: 19851296) Oguri M … Yamada Y (American journal of hypertension 2010) 3 41 54
  4. Association of gene polymorphisms with chronic kidney disease in Japanese individuals. (PMID: 19724895) Yoshida T … Yamada Y (International journal of molecular medicine 2009) 3 41 54
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54

Products for PNLDC1 Gene

Sources for PNLDC1 Gene