Aliases for RFPL3 Gene

Aliases for RFPL3 Gene

  • Ret Finger Protein Like 3 2 3 5
  • Ret Finger Protein-Like 3 3 4
  • RNF120 2 3
  • RFPL3 5

External Ids for RFPL3 Gene

Previous GeneCards Identifiers for RFPL3 Gene

  • GC22P029449
  • GC22P031075
  • GC22P031078
  • GC22P032750
  • GC22P015708

Summaries for RFPL3 Gene

GeneCards Summary for RFPL3 Gene

RFPL3 (Ret Finger Protein Like 3) is a Protein Coding gene. Diseases associated with RFPL3 include Myoclonic Epilepsy Of Lafora. An important paralog of this gene is RFPL1.

UniProtKB/Swiss-Prot Summary for RFPL3 Gene

  • (Microbial infection) Stimulates the activity of Human Immunodeficiency Virus 1/HIV-1 pre-integration complex.

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RFPL3 Gene

Genomics for RFPL3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RFPL3 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
GH22J032357 Promoter 0.7 EPDnew Ensembl 250.7 -0.3 -284 0.8 SLC5A4 RFPL3 lnc-RTCB-4 HSALNG0135026 RFPL2
GH22J032355 Enhancer 0.4 ENCODE 250.7 +1.1 1104 0.2 ZNF654 CTCF RAD21 SMC3 SLC5A4 ENSG00000271093 RFPL3 lnc-RTCB-2 lnc-RTCB-4 RTCB
GH22J032358 Enhancer 0.3 Ensembl 250.7 +1.4 1416 0.2 CTCF ENSG00000271093 RFPL3 SLC5A4 lnc-RTCB-2 lnc-RTCB-4 RTCB
GH22J032266 Enhancer 0.8 Ensembl ENCODE 10.7 -88.8 -88784 1 ZNF654 NFIC CTCF REST TRIM22 RAD21 SMC3 BATF NFIA ARID3A ENSG00000234626 RFPL3 IGLCOR22-2 IGLVIVOR22-2 LOC339666 RFPL3S ENSG00000241954 ENSG00000232218 SLC5A1 CPSF1P1
GH22J032473 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 3.5 +120.8 120834 4.7 ZNF207 ZNF654 IKZF1 JUND ATF2 POLR2A NFIC ZIC2 YY1 CTCF FBXO7 NONHSAG033755.2 BPIFC EIF4ENIF1 SLC5A4 RFPL3 C22orf42 RFPL2 HSALNG0135033 piR-52478
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RFPL3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RFPL3

Top Transcription factor binding sites by QIAGEN in the RFPL3 gene promoter:
  • LyF-1
  • POU2F1
  • POU2F1a
  • POU2F1b
  • POU2F1c

Genomic Locations for RFPL3 Gene

Latest Assembly
chr22:32,354,885-32,361,161
(GRCh38/hg38)
Size:
6,277 bases
Orientation:
Plus strand

Previous Assembly
chr22:32,750,872-32,757,148
(GRCh37/hg19 by Entrez Gene)
Size:
6,277 bases
Orientation:
Plus strand

chr22:32,750,872-32,757,148
(GRCh37/hg19 by Ensembl)
Size:
6,277 bases
Orientation:
Plus strand

Genomic View for RFPL3 Gene

Genes around RFPL3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RFPL3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RFPL3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RFPL3 Gene

Proteins for RFPL3 Gene

  • Protein details for RFPL3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75679-RFPL3_HUMAN
    Recommended name:
    Ret finger protein-like 3
    Protein Accession:
    O75679
    Secondary Accessions:
    • A2A279
    • Q6IC03
    • Q6IC04
    • Q6NSX3
    • Q8N5R4

    Protein attributes for RFPL3 Gene

    Size:
    317 amino acids
    Molecular mass:
    35386 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=CAA09046.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for RFPL3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RFPL3 Gene

Post-translational modifications for RFPL3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RFPL3 Gene

No data available for DME Specific Peptides for RFPL3 Gene

Domains & Families for RFPL3 Gene

Gene Families for RFPL3 Gene

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

Protein Domains for RFPL3 Gene

InterPro:
Blocks:
  • Zn-finger, RING
  • Butyrophylin C-terminal DUF signature
  • SPRY-associated domain

Suggested Antigen Peptide Sequences for RFPL3 Gene

GenScript: Design optimal peptide antigens:
  • Ret finger protein-like 3 (Q8N5R4_HUMAN)
  • Ret finger protein-like 3 (RFPL3_HUMAN)
genes like me logo Genes that share domains with RFPL3: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for RFPL3 Gene

Function for RFPL3 Gene

Molecular function for RFPL3 Gene

UniProtKB/Swiss-Prot Function:
(Microbial infection) Stimulates the activity of Human Immunodeficiency Virus 1/HIV-1 pre-integration complex.
GENATLAS Biochemistry:
ret finger protein-like 3,B box family

Phenotypes From GWAS Catalog for RFPL3 Gene

Gene Ontology (GO) - Molecular Function for RFPL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004842 ubiquitin-protein transferase activity IBA 21873635
GO:0005515 protein binding IPI 25416956
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with RFPL3: view
genes like me logo Genes that share phenotypes with RFPL3: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RFPL3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for RFPL3 Gene

Localization for RFPL3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RFPL3 Gene

Cytoplasm. Nucleus. Note=A higher concentration of RFPL3 is observed in the cytoplasm compared to the nucleus. {ECO:0000269 PubMed:25107902}.

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 RFPL3 gene
Compartment Confidence
nucleus 3
extracellular 2
mitochondrion 1
cytosol 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RFPL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000785 chromatin IBA 21873635
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IBA 21873635
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with RFPL3: view

Pathways & Interactions for RFPL3 Gene

PathCards logo

SuperPathways for RFPL3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RFPL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016032 viral process IEA --
GO:0016567 protein ubiquitination IEA --
GO:0045893 positive regulation of transcription, DNA-templated IBA 21873635
genes like me logo Genes that share ontologies with RFPL3: view

No data available for Pathways by source and SIGNOR curated interactions for RFPL3 Gene

Drugs & Compounds for RFPL3 Gene

No Compound Related Data Available

Transcripts for RFPL3 Gene

mRNA/cDNA for RFPL3 Gene

2 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
2 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 RFPL3

Alternative Splicing Database (ASD) splice patterns (SP) for RFPL3 Gene

No ASD Table

Relevant External Links for RFPL3 Gene

GeneLoc Exon Structure for
RFPL3

Expression for RFPL3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RFPL3 Gene

mRNA differential expression in normal tissues according to GTEx for RFPL3 Gene

This gene is overexpressed in Testis (x34.0) and Brain - Cerebellar Hemisphere (x4.3).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RFPL3

SOURCE GeneReport for Unigene cluster for RFPL3 Gene:

Hs.558455

mRNA Expression by UniProt/SwissProt for RFPL3 Gene:

O75679-RFPL3_HUMAN
Tissue specificity: Expressed during neurogenesis in differentiating human embryonic stem cells and in the developing human neocortex.

Evidence on tissue expression from TISSUES for RFPL3 Gene

  • Nervous system(4.4)
genes like me logo Genes that share expression patterns with RFPL3: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for RFPL3 Gene

Orthologs for RFPL3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for RFPL3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia RFPL3 29
  • 98.26 (n)
-- 30
  • 87 (a)
OneToMany
Dog
(Canis familiaris)
Mammalia -- 30
  • 57 (a)
OneToMany
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 40 (a)
OneToMany
Oppossum
(Monodelphis domestica)
Mammalia -- 30
  • 26 (a)
ManyToMany
Cow
(Bos Taurus)
Mammalia -- 30
  • 25 (a)
ManyToMany
Mouse
(Mus musculus)
Mammalia Mefv 30
  • 5 (a)
ManyToMany
Lizard
(Anolis carolinensis)
Reptilia -- 30
  • 13 (a)
ManyToMany
Species where no ortholog for RFPL3 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)
  • 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 Vase (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)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for RFPL3 Gene

ENSEMBL:
Gene Tree for RFPL3 (if available)
TreeFam:
Gene Tree for RFPL3 (if available)
Alliance of Genome Resources:
Additional Orthologs for RFPL3

Paralogs for RFPL3 Gene

(14) SIMAP similar genes for RFPL3 Gene using alignment to 1 proteins:

  • RFPL3_HUMAN

Pseudogenes.org Pseudogenes for RFPL3 Gene

genes like me logo Genes that share paralogs with RFPL3: view

Variants for RFPL3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RFPL3 Gene

SNP ID Clinical significance and condition Chr 22 pos Variation AA Info Type
rs16987625 -- p.Met83Thr
rs5749408 -- p.Tyr181Cys
rs9619258 -- p.Asp126Asn
rs9621427 -- p.Leu110Met

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RFPL3 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 RFPL3 Gene

Variant ID Type Subtype PubMed ID
esv2422247 CNV duplication 17116639
esv3575476 CNV gain 25503493
esv3893474 CNV gain 25118596
nsv459874 CNV gain 19166990
nsv588895 CNV gain 21841781
nsv964624 CNV duplication 23825009
nsv979671 CNV duplication 23825009

Variation tolerance for RFPL3 Gene

Residual Variation Intolerance Score: 92.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.32; 76.67% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RFPL3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RFPL3
Leiden Open Variation Database (LOVD)
RFPL3

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RFPL3 Gene

Disorders for RFPL3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for RFPL3 Gene - From: COP

Disorder Aliases PubMed IDs
myoclonic epilepsy of lafora
  • melf
- elite association - COSMIC cancer census association via MalaCards
Search RFPL3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RFPL3

genes like me logo Genes that share disorders with RFPL3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RFPL3 Gene

Publications for RFPL3 Gene

  1. Duplications on human chromosome 22 reveal a novel Ret Finger Protein-like gene family with sense and endogenous antisense transcripts. (PMID: 10508838) Seroussi E … Dumanski JP (Genome research 1999) 2 3 4 22
  2. Identification of RFPL3 protein as a novel E3 ubiquitin ligase modulating the integration activity of human immunodeficiency virus, type 1 preintegration complex using a microtiter plate-based assay. (PMID: 25107902) Tan BH … Suzuki Y (The Journal of biological chemistry 2014) 2 3 4
  3. Evolutionary forces shape the human RFPL1,2,3 genes toward a role in neocortex development. (PMID: 18656177) Bonnefont J … Krause KH (American journal of human genetics 2008) 3 4
  4. A genome annotation-driven approach to cloning the human ORFeome. (PMID: 15461802) Collins JE … Dunham I (Genome biology 2004) 3 4
  5. The DNA sequence of human chromosome 22. (PMID: 10591208) Dunham I … O'Brien KP (Nature 1999) 3 4

Products for RFPL3 Gene

Sources for RFPL3 Gene