Aliases for RCN3 Gene

Aliases for RCN3 Gene

  • Reticulocalbin 3 2 3 5
  • Reticulocalbin 3, EF-Hand Calcium Binding Domain 2 3
  • EF-Hand Calcium-Binding Protein RLP49 3 4
  • Reticulocalbin-3 3 4
  • RLP49 2 3
  • Reticulocabin 3
  • RCN3 5

External Ids for RCN3 Gene

Previous GeneCards Identifiers for RCN3 Gene

  • GC19P054706
  • GC19P054722
  • GC19P050030
  • GC19P046407

Summaries for RCN3 Gene

GeneCards Summary for RCN3 Gene

RCN3 (Reticulocalbin 3) is a Protein Coding gene. Diseases associated with RCN3 include Neonatal Respiratory Failure and Myopathy, Distal, 3. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is RCN1.

UniProtKB/Swiss-Prot Summary for RCN3 Gene

  • Probable molecular chaperone assisting protein biosynthesis and transport in the endoplasmic reticulum (PubMed:16433634, PubMed:28939891). Required for the proper biosynthesis and transport of pulmonary surfactant-associated protein A/SP-A, pulmonary surfactant-associated protein D/SP-D and the lipid transporter ABCA3 (By similarity). By regulating both the proper expression and the degradation through the endoplasmic reticulum-associated protein degradation pathway of these proteins plays a crucial role in pulmonary surfactant homeostasis (By similarity). Has an anti-fibrotic activity by negatively regulating the secretion of type I and type III collagens (PubMed:28939891). This calcium-binding protein also transiently associates with immature PCSK6 and regulates its secretion (PubMed:16433634).

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RCN3 Gene

Genomics for RCN3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RCN3 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
GH19J049527 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 +0.8 767 2.5 TBP SIX5 NR2C1 MNT ETS1 BHLHE40 HCFC1 VEZF1 ZEB2 EBF1 HSALNG0127004 RCN3 FCGRT PRRG2
GH19J049511 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 14.8 -13.2 -13223 5.7 ZBTB10 MXD4 NR2C1 IKZF1 ZIC2 THAP11 SIN3A ZNF511 SMAD4 SAP130 FCGRT NONHSAG026245.2 PRR12 RCN3 SNORD32A SNORD33 SNORD34 SNORD35A RPL13A PRRG2
GH19J049532 Promoter/Enhancer 1.3 ENCODE CraniofacialAtlas 17.1 +6.2 6240 2.3 MNT SMAD5 HES1 MBD2 BHLHE40 ZIC2 SIN3A ZNF395 CTCF MAX RF00005-082 TRK-TTT12-1 RCN3 FCGRT PRR12 HSALNG0127004 PRRG2
GH19J049558 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE dbSUPER 12.9 +33.1 33068 4.5 MNT VEZF1 ADNP NFE2 FOXK2 NRF1 EGR1 ZNF664 ESRRA ZMYM3 NOSIP lnc-RRAS-1-002 piR-49035 PRR12 RCN3 FCGRT MIR150 RPS11 SNORD35B SNORD34
GH19J049552 Promoter/Enhancer 1.4 Ensembl ENCODE CraniofacialAtlas dbSUPER 12.9 +27.8 27771 5.7 ZNF623 VEZF1 SAP130 ZNF146 ADNP CBX1 SUPT5H ZNF205 HNF4A ZBTB33 NOSIP PRR12 FCGRT RCN3 PRRG2 MIR150 RPS11 SNORD35B SNORD33 SNORD34
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RCN3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RCN3

Top Transcription factor binding sites by QIAGEN in the RCN3 gene promoter:
  • Bach1
  • Bach2
  • E2F
  • E2F-1
  • Egr-2
  • Egr-4
  • Elk-1
  • ISGF-3
  • Sp1
  • STAT5A

Genomic Locations for RCN3 Gene

Latest Assembly
chr19:49,527,579-49,546,962
(GRCh38/hg38)
Size:
19,384 bases
Orientation:
Plus strand

Previous Assembly
chr19:50,031,260-50,046,890
(GRCh37/hg19 by Entrez Gene)
Size:
15,631 bases
Orientation:
Plus strand

chr19:50,030,875-50,050,219
(GRCh37/hg19 by Ensembl)
Size:
19,345 bases
Orientation:
Plus strand

Genomic View for RCN3 Gene

Genes around RCN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RCN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RCN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RCN3 Gene

Proteins for RCN3 Gene

  • Protein details for RCN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96D15-RCN3_HUMAN
    Recommended name:
    Reticulocalbin-3
    Protein Accession:
    Q96D15
    Secondary Accessions:
    • Q9HBZ8

    Protein attributes for RCN3 Gene

    Size:
    328 amino acids
    Molecular mass:
    37493 Da
    Quaternary structure:
    • Interacts with PCSK6 (immature form including the propeptide); probably involved in the maturation and the secretion of PCSK6.

neXtProt entry for RCN3 Gene

Post-translational modifications for RCN3 Gene

Other Protein References for RCN3 Gene

No data available for DME Specific Peptides for RCN3 Gene

Domains & Families for RCN3 Gene

Gene Families for RCN3 Gene

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

Protein Domains for RCN3 Gene

Suggested Antigen Peptide Sequences for RCN3 Gene

GenScript: Design optimal peptide antigens:
  • EF-hand calcium-binding protein RLP49 (RCN3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96D15

UniProtKB/Swiss-Prot:

RCN3_HUMAN :
  • Belongs to the CREC family.
Family:
  • Belongs to the CREC family.
genes like me logo Genes that share domains with RCN3: view

Function for RCN3 Gene

Molecular function for RCN3 Gene

UniProtKB/Swiss-Prot Function:
Probable molecular chaperone assisting protein biosynthesis and transport in the endoplasmic reticulum (PubMed:16433634, PubMed:28939891). Required for the proper biosynthesis and transport of pulmonary surfactant-associated protein A/SP-A, pulmonary surfactant-associated protein D/SP-D and the lipid transporter ABCA3 (By similarity). By regulating both the proper expression and the degradation through the endoplasmic reticulum-associated protein degradation pathway of these proteins plays a crucial role in pulmonary surfactant homeostasis (By similarity). Has an anti-fibrotic activity by negatively regulating the secretion of type I and type III collagens (PubMed:28939891). This calcium-binding protein also transiently associates with immature PCSK6 and regulates its secretion (PubMed:16433634).
UniProtKB/Swiss-Prot Induction:
Down-regulated by aldosterone (at protein level). No effect at the transcript level.

Phenotypes From GWAS Catalog for RCN3 Gene

Gene Ontology (GO) - Molecular Function for RCN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA,IDA 16433634
GO:0005515 protein binding IPI 16189514
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with RCN3: view
genes like me logo Genes that share phenotypes with RCN3: view

Animal Models for RCN3 Gene

MGI Knock Outs for RCN3:
  • Rcn3 Rcn3<tm1b(EUCOMM)Hmgu>
  • Rcn3 Rcn3<tm1Rzm>

miRNA for RCN3 Gene

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RCN3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RCN3 Gene

Localization for RCN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RCN3 Gene

Endoplasmic reticulum lumen.

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 RCN3 gene
Compartment Confidence
endoplasmic reticulum 5
extracellular 2
mitochondrion 2
plasma membrane 1
cytoskeleton 1
nucleus 1
cytosol 1
golgi apparatus 1
peroxisome 0
lysosome 0

Subcellular locations from the

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

Gene Ontology (GO) - Cellular Components for RCN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IBA,IDA 16433634
GO:0005788 endoplasmic reticulum lumen IEA --
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with RCN3: view

Pathways & Interactions for RCN3 Gene

PathCards logo

SuperPathways for RCN3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RCN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0009306 protein secretion IMP 16433634
GO:0010952 positive regulation of peptidase activity IMP 28939891
GO:0015031 protein transport ISS --
GO:0032964 collagen biosynthetic process IMP 28939891
GO:0036503 ERAD pathway IEA,ISS --
genes like me logo Genes that share ontologies with RCN3: view

No data available for Pathways by source and SIGNOR curated interactions for RCN3 Gene

Drugs & Compounds for RCN3 Gene

No Compound Related Data Available

Transcripts for RCN3 Gene

mRNA/cDNA for RCN3 Gene

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

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RCN3

Alternative Splicing Database (ASD) splice patterns (SP) for RCN3 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c ^ 7
SP1:
SP2: -
SP3: -

Relevant External Links for RCN3 Gene

GeneLoc Exon Structure for
RCN3

Expression for RCN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RCN3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RCN3 Gene

This gene is overexpressed in Bone marrow stromal cell (56.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RCN3 Gene



Protein tissue co-expression partners for RCN3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RCN3

SOURCE GeneReport for Unigene cluster for RCN3 Gene:

Hs.567550

mRNA Expression by UniProt/SwissProt for RCN3 Gene:

Q96D15-RCN3_HUMAN
Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for RCN3 Gene

  • Lung(4.3)
  • Nervous system(4.2)
  • Liver(4.1)
genes like me logo Genes that share expression patterns with RCN3: view

Primer products for research

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for RCN3 Gene

Orthologs for RCN3 Gene

This gene was present in the common ancestor of animals.

Orthologs for RCN3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia RCN3 30 31
  • 98.88 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia RCN3 30 31
  • 90.65 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia RCN3 30 31
  • 90.45 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Rcn3 30 17 31
  • 87.2 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia RCN3 31
  • 87 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Rcn3 30
  • 86.69 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia RCN3 31
  • 66 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia RCN3 31
  • 61 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia rcn3 30
  • 63.05 (n)
Zebrafish
(Danio rerio)
Actinopterygii rcn3 30 31
  • 60.54 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta scf 31
  • 44 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea calu-1 31
  • 40 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 45 (a)
ManyToMany
-- 31
  • 41 (a)
ManyToMany
CSA.6945 31
  • 40 (a)
ManyToMany
Species where no ortholog for RCN3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • Chicken (Gallus gallus)
  • 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 (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • 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 RCN3 Gene

ENSEMBL:
Gene Tree for RCN3 (if available)
TreeFam:
Gene Tree for RCN3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RCN3: view image

Paralogs for RCN3 Gene

Paralogs for RCN3 Gene

(3) SIMAP similar genes for RCN3 Gene using alignment to 4 proteins:

  • RCN3_HUMAN
  • M0QYB8_HUMAN
  • M0QZH0_HUMAN
  • M0QZU3_HUMAN
genes like me logo Genes that share paralogs with RCN3: view

Variants for RCN3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RCN3 Gene

SNP ID Clinical significance and condition Chr 19 pos Variation AA Info Type
rs34654230 - p.Arg250Trp

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RCN3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for RCN3 Gene

Variant ID Type Subtype PubMed ID
nsv1160655 CNV deletion 26073780
nsv478163 CNV novel sequence insertion 20440878
nsv833862 CNV loss 17160897
nsv833863 CNV loss 17160897
nsv9739 CNV gain+loss 18304495

Variation tolerance for RCN3 Gene

Residual Variation Intolerance Score: 85.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.71; 78.66% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RCN3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RCN3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RCN3 Gene

Disorders for RCN3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for RCN3 Gene - From: COP

Disorder Aliases PubMed IDs
neonatal respiratory failure
  • respiratory failure of newborn
myopathy, distal, 3
  • mpd3
enchondromatosis, multiple, ollier type
  • ollier disease
- elite association - COSMIC cancer census association via MalaCards
Search RCN3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RCN3

genes like me logo Genes that share disorders with RCN3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RCN3 Gene

Publications for RCN3 Gene

  1. A proteomic approach reveals transient association of reticulocalbin-3, a novel member of the CREC family, with the precursor of subtilisin-like proprotein convertase, PACE4. (PMID: 16433634) Tsuji A … Matsuda Y (The Biochemical journal 2006) 3 4 23
  2. Differential Proteomics Identifies Reticulocalbin-3 as a Novel Negative Mediator of Collagen Production in Human Cardiac Fibroblasts. (PMID: 28939891) Martínez-Martínez E … López-Andrés N (Scientific reports 2017) 3 4
  3. 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
  4. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 3 4
  5. Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning. (PMID: 10931946) Hu RM … Chen JL (Proceedings of the National Academy of Sciences of the United States of America 2000) 3 4

Products for RCN3 Gene

Sources for RCN3 Gene