Free for academic non-profit institutions. Other users need a Commercial license

Aliases for RFPL3 Gene

Aliases for RFPL3 Gene

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

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. An important paralog of this gene is RFPL1.

UniProtKB/Swiss-Prot for RFPL3 Gene

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

Additional gene information for RFPL3 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RFPL3 Gene

Genomics for RFPL3 Gene

GeneHancer (GH) Regulatory Elements for RFPL3 Gene

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
GH22I032354 Promoter 0.6 EPDnew 550.8 0.0 -27 0.1 POLR2A SLC5A4 RFPL3
GH22I032356 Enhancer 0.5 Ensembl 550.8 +0.4 415 0.2 SP1 NFATC3 ASH1L FOS IGLCOR22-2 RFPL3 SLC5A4 RTCB
GH22I032355 Enhancer 0.4 ENCODE 550.8 +1.1 1104 0.2 CTCF ZNF654 RAD21 IGLCOR22-2 RFPL3 SLC5A4
GH22I032473 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 3.5 +120.8 120834 4.7 PKNOX1 FOXA2 ARID4B SIN3A DMAP1 YY1 SLC30A9 POLR2B ZNF207 ZNF143 FBXO7 BPIFC SLC5A4 RFPL3 C22orf42 RFPL2 PIR46477
GH22I032266 Enhancer 0.8 Ensembl ENCODE 10.7 -88.6 -88629 0.5 CTCF ZNF654 NFIA TRIM22 REST BATF RAD21 YY1 NFIC ZNF692 ENSG00000234626 RFPL3 IGLVIVOR22-2 LOC339666 ENSG00000241954 RFPL3S LOC100422292 SLC5A1 CPSF1P1 RFPL2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RFPL3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RFPL3 gene promoter:

Genomic Locations for RFPL3 Gene

Genomic Locations for RFPL3 Gene
chr22:32,354,885-32,361,161
(GRCh38/hg38)
Size:
6,277 bases
Orientation:
Plus strand
chr22:32,750,872-32,757,148
(GRCh37/hg19)

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

Suggested Antigen Peptide Sequences for RFPL3 Gene

Graphical View of Domain Structure for InterPro Entry

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

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

Function for RFPL3 Gene

Molecular function for RFPL3 Gene

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

Gene Ontology (GO) - Molecular Function for RFPL3 Gene

GO ID Qualified GO term Evidence PubMed IDs
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

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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 4
extracellular 2
mitochondrion 1
cytosol 1

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:0005634 nucleus IEA --
GO:0005737 cytoplasm IEA --
genes like me logo Genes that share ontologies with RFPL3: view

Pathways & Interactions for RFPL3 Gene

SuperPathways for RFPL3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RFPL3 Gene

None

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

(3) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(10) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for RFPL3 Gene

Ret finger protein-like 3:
Representative Sequences:

Clone Products

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

No ASD Table

Relevant External Links for RFPL3 Gene

GeneLoc Exon Structure for
RFPL3
ECgene alternative splicing isoforms for
RFPL3

Expression for RFPL3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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).

NURSA nuclear receptor signaling pathways regulating expression of RFPL3 Gene:

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(4.3)
genes like me logo Genes that share expression patterns with RFPL3: view

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 33
  • 98.26 (n)
-- 34
  • 87 (a)
OneToMany
dog
(Canis familiaris)
Mammalia -- 34
  • 57 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 40 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 26 (a)
ManyToMany
cow
(Bos Taurus)
Mammalia -- 34
  • 25 (a)
ManyToMany
mouse
(Mus musculus)
Mammalia Mefv 34
  • 5 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 13 (a)
ManyToMany
Species where no ortholog for RFPL3 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)
  • 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 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)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for RFPL3 Gene

ENSEMBL:
Gene Tree for RFPL3 (if available)
TreeFam:
Gene Tree for RFPL3 (if available)

Paralogs for RFPL3 Gene

Paralogs for RFPL3 Gene

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

Pseudogenes.org Pseudogenes for RFPL3 Gene

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

Variants for RFPL3 Gene

Sequence variations from dbSNP and Humsavar for RFPL3 Gene

SNP ID Clin Chr 22 pos Variation AA Info Type
rs1000079594 -- 32,358,515(+) T/G coding_sequence_variant, intron_variant, synonymous_variant
rs1000201332 -- 32,354,326(+) T/A upstream_transcript_variant
rs1000587950 -- 32,355,456(+) C/T 5_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant
rs1001199618 -- 32,358,876(+) T/C 3_prime_UTR_variant, intron_variant
rs1001408569 -- 32,355,076(+) /T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for RFPL3 Gene

Additional Disease Information for RFPL3

No disorders were found for RFPL3 Gene.

No data available for MalaCards , 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 58
  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 58
  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 58
  4. A genome annotation-driven approach to cloning the human ORFeome. (PMID: 15461802) Collins JE … Dunham I (Genome biology 2004) 3 4 58
  5. The DNA sequence of human chromosome 22. (PMID: 10591208) Dunham I … O'Brien KP (Nature 1999) 3 4 58

Products for RFPL3 Gene

Sources for RFPL3 Gene

Content
Loading form....