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Aliases for POLR1D Gene

Aliases for POLR1D Gene

  • RNA Polymerase I Subunit D 2 3 5
  • Polymerase (RNA) I Polypeptide D, 16kDa 2 3
  • DNA-Directed RNA Polymerase I Subunit D 3 4
  • RNA Polymerases I And III Subunit AC2 3 4
  • RPA16 3 4
  • RPC16 3 4
  • AC19 3 4
  • DNA-Directed RNA Polymerases I And III Subunit RPAC2 3
  • RNA Polymerase I 16 KDa Subunit 4
  • Polymerase (RNA) I Subunit D 3
  • Protein POLR1D 3
  • POLR1C 3
  • RPO1-3 3
  • HRPA19 4
  • RPAC2 3
  • RPA9 3
  • TCS2 3

External Ids for POLR1D Gene

Previous GeneCards Identifiers for POLR1D Gene

  • GC13P022176
  • GC13P027125
  • GC13P025994
  • GC13P025993
  • GC13P027093
  • GC13P028194
  • GC13P009017

Summaries for POLR1D Gene

Entrez Gene Summary for POLR1D Gene

  • The protein encoded by this gene is a component of the RNA polymerase I and RNA polymerase III complexes, which function in the synthesis of ribosomal RNA precursors and small RNAs, respectively. Mutations in this gene are a cause of Treacher Collins syndrome (TCS), a craniofacial development disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2011]

GeneCards Summary for POLR1D Gene

POLR1D (RNA Polymerase I Subunit D) is a Protein Coding gene. Diseases associated with POLR1D include Treacher Collins Syndrome 2 and Treacher Collins Syndrome 1. Among its related pathways are Pyrimidine metabolism (KEGG) and Innate Immune System. Gene Ontology (GO) annotations related to this gene include protein dimerization activity and RNA polymerase I activity.

UniProtKB/Swiss-Prot for POLR1D Gene

  • DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common core component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively.

Gene Wiki entry for POLR1D Gene

Additional gene information for POLR1D Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for POLR1D Gene

Genomics for POLR1D Gene

GeneHancer (GH) Regulatory Elements for POLR1D Gene

Promoters and enhancers for POLR1D 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
GH13I027617 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 581.7 -0.2 -203 5.3 HDGF PKNOX1 CLOCK FOXA2 ZFP64 ARID4B NEUROD1 SIN3A FEZF1 DMAP1 POLR1D LNX2 PAN3 RNU6-63P
GH13I027599 Enhancer 1 Ensembl ENCODE 36.3 -20.6 -20592 1.4 TEAD4 TAL1 JUN BMI1 ZNF7 RFX5 TEAD3 FOSL1 ZNF335 TCF12 POLR1D LNX2 RNU6-63P
GH13I027641 Enhancer 1.2 Ensembl ENCODE dbSUPER 25.2 +22.8 22847 3.8 ELF3 FOXA2 ARID4B DMAP1 RAD21 ZNF48 RARA CREM MIXL1 HMG20B POLR1D LNX2 RNU6-63P GC13P027624 LOC105370128
GH13I028136 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 10.8 +519.2 519157 6.1 HDGF PKNOX1 SMAD1 ARID4B SIN3A DMAP1 YY1 POLR2B ZNF213 ZNF207 PAN3 PAN3-AS1 RNU6-82P SNORA27 POLR1D EEF1A1P3
GH13I027578 Enhancer 0.6 ENCODE 30.7 -42.0 -41958 0.8 SCRT1 PKNOX1 FOXA2 HLF SIN3A MNT FOXA1 CTBP1 SCRT2 FOS POLR1D LNX2 RNU6-63P
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around POLR1D on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the POLR1D gene promoter:

Genomic Locations for POLR1D Gene

Genomic Locations for POLR1D Gene
chr13:27,620,742-27,744,237
(GRCh38/hg38)
Size:
123,496 bases
Orientation:
Plus strand
chr13:28,194,880-28,241,559
(GRCh37/hg19)

Genomic View for POLR1D Gene

Genes around POLR1D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
POLR1D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for POLR1D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for POLR1D Gene

Proteins for POLR1D Gene

  • Protein details for POLR1D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P0DPB5-RPC22_HUMAN
    Recommended name:
    Protein POLR1D, isoform 2
    Protein Accession:
    P0DPB5
    Secondary Accessions:
    • Q5TBX2
    • Q96BR3
    • Q9Y2S0

    Protein attributes for POLR1D Gene

    Size:
    122 amino acids
    Molecular mass:
    14332 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for POLR1D Gene

    UniProtKB/Swiss-Prot:
  • Protein details for POLR1D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P0DPB6-RPAC2_HUMAN
    Recommended name:
    DNA-directed RNA polymerases I and III subunit RPAC2
    Protein Accession:
    P0DPB6
    Secondary Accessions:
    • Q5TBX2
    • Q96BR3
    • Q9Y2S0

    Protein attributes for POLR1D Gene

    Size:
    133 amino acids
    Molecular mass:
    15237 Da
    Quaternary structure:
    • Component of the RNA polymerase I (Pol I) and RNA polymerase III (Pol III) complexes consisting of at least 13 and 17 subunits, respectively.

    Alternative splice isoforms for POLR1D Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for POLR1D Gene

Post-translational modifications for POLR1D Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for POLR1D Gene

Domains & Families for POLR1D Gene

Gene Families for POLR1D Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for POLR1D Gene

Suggested Antigen Peptide Sequences for POLR1D Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P0DPB6

UniProtKB/Swiss-Prot:

RPAC2_HUMAN :
  • Belongs to the archaeal RpoL/eukaryotic RPB11/RPC19 RNA polymerase subunit family.
Family:
  • Belongs to the archaeal RpoL/eukaryotic RPB11/RPC19 RNA polymerase subunit family.
genes like me logo Genes that share domains with POLR1D: view

Function for POLR1D Gene

Molecular function for POLR1D Gene

UniProtKB/Swiss-Prot Function:
DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common core component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively.

Phenotypes From GWAS Catalog for POLR1D Gene

Gene Ontology (GO) - Molecular Function for POLR1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003899 DNA-directed 5-3 RNA polymerase activity IEA --
GO:0046983 protein dimerization activity IEA --
genes like me logo Genes that share ontologies with POLR1D: view
genes like me logo Genes that share phenotypes with POLR1D: view

Human Phenotype Ontology for POLR1D Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for POLR1D Gene

Localization for POLR1D Gene

Subcellular locations from UniProtKB/Swiss-Prot for POLR1D Gene

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 POLR1D gene
Compartment Confidence
nucleus 5
cytosol 2
golgi apparatus 2
plasma membrane 1
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for POLR1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with POLR1D: view

Pathways & Interactions for POLR1D Gene

genes like me logo Genes that share pathways with POLR1D: view

Gene Ontology (GO) - Biological Process for POLR1D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with POLR1D: view

No data available for SIGNOR curated interactions for POLR1D Gene

Drugs & Compounds for POLR1D Gene

(8) Drugs for POLR1D Gene - From: ApexBio and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Cytidine triphosphate Experimental Pharma 0
Guanosine triphosphate Experimental Pharma 0
Uridine triphosphate Experimental, Investigational Pharma 0
ATP Investigational Nutra Agonist 0

(1) Additional Compounds for POLR1D Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
pyrophosphate
  • (4-)Diphosphoric acid ion
  • (P2O74-)Diphosphate
  • Diphosphate
  • Diphosphoric acid
  • PPi
14000-31-8

(3) ApexBio Compounds for POLR1D Gene

Compound Action Cas Number
BMH-21 RNA polymerase I Inhibitior 896705-16-1
CX-5461 Pol I-mediated rRNA synthesis inhibitor 1138549-36-6
Foscarnet Sodium 63585-09-1
genes like me logo Genes that share compounds with POLR1D: view

Drug Products

Transcripts for POLR1D Gene

Unigene Clusters for POLR1D Gene

Polymerase (RNA) I polypeptide D, 16kDa:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for POLR1D Gene

ExUns: 1 ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c
SP1: - -
SP2: - - - - - -
SP3: - - -
SP4: -
SP5:

Relevant External Links for POLR1D Gene

GeneLoc Exon Structure for
POLR1D
ECgene alternative splicing isoforms for
POLR1D

Expression for POLR1D Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for POLR1D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for POLR1D Gene

This gene is overexpressed in Islet of Langerhans (12.9), Peripheral blood mononuclear cells (12.8), Retina (6.7), Adrenal (6.5), and CD4 Tcells (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for POLR1D Gene



Protein tissue co-expression partners for POLR1D Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of POLR1D Gene:

POLR1D

SOURCE GeneReport for Unigene cluster for POLR1D Gene:

Hs.507584

Evidence on tissue expression from TISSUES for POLR1D Gene

  • Nervous system(3.6)
  • Blood(2.6)
  • Lung(2.5)
  • Lymph node(2.2)
  • Eye(2.1)
  • Spleen(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for POLR1D Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • inner ear
  • jaw
  • mandible
  • maxilla
  • middle ear
  • mouth
  • neck
  • nose
  • outer ear
  • pharynx
  • scalp
  • skull
  • tooth
Thorax:
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
Pelvis:
  • pelvis
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • hair
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with POLR1D: view

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for POLR1D Gene

Orthologs for POLR1D Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for POLR1D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia POLR1D 33 34
  • 100 (n)
dog
(Canis familiaris)
Mammalia POLR1D 33 34
  • 97.74 (n)
cow
(Bos Taurus)
Mammalia -- 34
  • 94 (a)
OneToMany
POLR1D 33 34
  • 91.23 (n)
mouse
(Mus musculus)
Mammalia Polr1d 33 16 34
  • 92.48 (n)
oppossum
(Monodelphis domestica)
Mammalia POLR1D 34
  • 80 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia POLR1D 34
  • 72 (a)
OneToOne
chicken
(Gallus gallus)
Aves POLR1D 33 34
  • 74.69 (n)
lizard
(Anolis carolinensis)
Reptilia POLR1D 34
  • 63 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100495369 33
  • 74.77 (n)
zebrafish
(Danio rerio)
Actinopterygii polr1d 33 34
  • 67.27 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009644 33
  • 56.59 (n)
fruit fly
(Drosophila melanogaster)
Insecta l(2)37Cg 33 34
  • 54.51 (n)
worm
(Caenorhabditis elegans)
Secernentea rpac-19 34
  • 26 (a)
OneToOne
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F23760g 33
  • 59.06 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RPC19 33 34 36
  • 55.46 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFL220C 33
  • 55.45 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes rpc19 33
  • 62.03 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU00419 33
  • 54.96 (n)
Species where no ortholog for POLR1D was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • 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)
  • wheat (Triticum aestivum)

Evolution for POLR1D Gene

ENSEMBL:
Gene Tree for POLR1D (if available)
TreeFam:
Gene Tree for POLR1D (if available)

Paralogs for POLR1D Gene

(4) SIMAP similar genes for POLR1D Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with POLR1D: view

No data available for Paralogs for POLR1D Gene

Variants for POLR1D Gene

Sequence variations from dbSNP and Humsavar for POLR1D Gene

SNP ID Clin Chr 13 pos Variation AA Info Type
rs1014318222 uncertain-significance, Treacher Collins Syndrome, Dominant 27,623,341(+) A/G 3_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant
rs1014369151 Collins syndrome 2 (TCS2) [MIM:613717] 27,623,014(+) C/T coding_sequence_variant, genic_upstream_transcript_variant, intron_variant, missense_variant
rs116927792 likely-benign, Treacher Collins Syndrome, Dominant 27,623,411(+) C/T 3_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant
rs138090002 uncertain-significance, Treacher Collins Syndrome, Dominant 27,623,362(+) C/T 3_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant
rs190867386 likely-benign, Treacher Collins Syndrome, Dominant 27,623,397(+) A/C/G 3_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for POLR1D Gene

Variant ID Type Subtype PubMed ID
nsv1039183 CNV loss 25217958
nsv523599 CNV loss 19592680
nsv561388 CNV loss 21841781

Variation tolerance for POLR1D Gene

Residual Variation Intolerance Score: 41.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.22; 4.83% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for POLR1D Gene

Human Gene Mutation Database (HGMD)
POLR1D
SNPedia medical, phenotypic, and genealogical associations of SNPs for
POLR1D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for POLR1D Gene

Disorders for POLR1D Gene

MalaCards: The human disease database

(2) MalaCards diseases for POLR1D Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
treacher collins syndrome 2
  • tcs2
treacher collins syndrome 1
  • tcs1
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

RPAC2_HUMAN
  • Treacher Collins syndrome 2 (TCS2) [MIM:613717]: A form of Treacher Collins syndrome, a disorder of craniofacial development. Treacher Collins syndrome is characterized by a combination of bilateral downward slanting of the palpebral fissures, colobomas of the lower eyelids with a paucity of eyelashes medial to the defect, hypoplasia of the facial bones, cleft palate, malformation of the external ears, atresia of the external auditory canals, and bilateral conductive hearing loss. {ECO:0000269 PubMed:21131976}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for POLR1D

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with POLR1D: view

No data available for Genatlas for POLR1D Gene

Publications for POLR1D Gene

  1. Common variants on 14q32 and 13q12 are associated with DLBCL susceptibility. (PMID: 21471979) Kumar V … Matsuda K (Journal of human genetics 2011) 3 44 58
  2. Assessment of a polymorphism of SDK1 with hypertension in Japanese Individuals. (PMID: 19851296) Oguri M … Yamada Y (American journal of hypertension 2010) 3 44 58
  3. Association of genetic variants with hemorrhagic stroke in Japanese individuals. (PMID: 20198315) Yoshida T … Yamada Y (International journal of molecular medicine 2010) 3 44 58
  4. Sequential use of transcriptional profiling, expression quantitative trait mapping, and gene association implicates MMP20 in human kidney aging. (PMID: 19834535) Wheeler HE … Kim SK (PLoS genetics 2009) 3 44 58
  5. Association of gene polymorphisms with chronic kidney disease in Japanese individuals. (PMID: 19724895) Yoshida T … Yamada Y (International journal of molecular medicine 2009) 3 44 58

Products for POLR1D Gene

Sources for POLR1D Gene

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