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Aliases for ERVFRD-1 Gene

Aliases for ERVFRD-1 Gene

  • Endogenous Retrovirus Group FRD Member 1, Envelope 2 3 5
  • Endogenous Retrovirus Group FRD Member 1 2 3 4
  • HERV-FRD_6p24.1 Provirus Ancestral Env Polyprotein 3 4
  • Envelope Polyprotein 3 4
  • ERVFRDE1 3 4
  • HERV-FRD 3 4
  • HERV-FRD Provirus Ancestral Env Polyprotein 3
  • Endogenous Retrovirus Group FRD, Member 1 2
  • HERV-W/FRD 3
  • Syncytin 2 3
  • Syncytin-2 3
  • GLLL6191 3
  • UNQ6191 3
  • EnvFRD 3

External Ids for ERVFRD-1 Gene

Summaries for ERVFRD-1 Gene

Entrez Gene Summary for ERVFRD-1 Gene

  • Many different human endogenous retrovirus (HERV) families are expressed in normal placental tissue at high levels, suggesting that HERVs are functionally important in reproduction. This gene is part of a human endogenous retrovirus provirus on chromosome 6 that has inactivating mutations in the gag and pol genes. This gene is the envelope glycoprotein gene which appears to have been selectively preserved. The gene's protein product plays a major role in placental development and trophoblast fusion. The protein has the characteristics of a typical retroviral envelope protein, including a cleavage site that separates the surface (SU) and transmembrane (TM) proteins which form a heterodimer. [provided by RefSeq, Jun 2012]

GeneCards Summary for ERVFRD-1 Gene

ERVFRD-1 (Endogenous Retrovirus Group FRD Member 1, Envelope) is a Protein Coding gene. An important paralog of this gene is ERVW-1.

UniProtKB/Swiss-Prot for ERVFRD-1 Gene

  • This endogenous retroviral envelope protein has retained its original fusogenic properties and participates in trophoblast fusion and the formation of a syncytium during placenta morphogenesis. The interaction with MFSD2A is apparently important for this process (PubMed:18988732).

  • Endogenous envelope proteins may have kept, lost or modified their original function during evolution but this one can still make pseudotypes with MLV, HIV-1 or SIV-1 virions and confer infectivity. Retroviral envelope proteins mediate receptor recognition and membrane fusion during early infection. The surface protein mediates receptor recognition, while the transmembrane protein anchors the envelope heterodimer to the viral membrane through one transmembrane domain. The other hydrophobic domain, called fusion peptide, mediates fusion of the viral membrane with the target cell membrane (PubMed:14694139).

Gene Wiki entry for ERVFRD-1 Gene

Additional gene information for ERVFRD-1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ERVFRD-1 Gene

Genomics for ERVFRD-1 Gene

GeneHancer (GH) Regulatory Elements for ERVFRD-1 Gene

Promoters and enhancers for ERVFRD-1 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
GH06J011110 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 659.4 +0.1 125 2 HDAC1 MEIS2 PKNOX1 TEAD4 MAX CEBPG E4F1 CHAMP1 FOSL1 CC2D1A ERVFRD-1 SMIM13
GH06J010398 Promoter/Enhancer 3.4 VISTA UCNEbase EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9.7 +701.9 701943 22.9 FEZF1 YY1 ZNF213 ZNF143 ZNF548 ZNF263 SP3 MEF2D ZNF610 GLIS1 TFAP2A TFAP2A-AS1 RNA5SP203 ERVFRD-1 PAK1IP1 TMEM14C TMEM14B C6orf52 TFAP2A-AS2
GH06J010719 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 9.7 +389.1 389072 6.7 CLOCK MLX ZFP64 FEZF1 DMAP1 YY1 ZNF213 ZNF143 SP3 NFYC TMEM14C RNA5SP203 ENSG00000272097 ERVFRD-1 PAK1IP1 C6orf52
GH06J011458 Enhancer 1.3 FANTOM5 Ensembl ENCODE 15.3 -348.4 -348415 3.8 HDGF PKNOX1 RB1 STAT5A BMI1 YBX1 BATF KLF5 IRF4 RAD21 ERVFRD-1 ENSG00000247925 RNA5SP203 ENSG00000233656 TMEM170B NEDD9 ENSG00000242753 LOC105374928 LOC105374929
GH06J011042 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 9.9 +68.3 68331 2.3 PKNOX1 ARNT ARID4B SIN3A ZNF2 ZNF766 CBX5 ZNF213 ZNF416 ZNF143 ELOVL2 ELOVL2-AS1 PIR47110 RNA5SP203 TFAP2A-AS1 SYCP2L GCM2 ENSG00000235051 HIVEP1 ERVFRD-1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ERVFRD-1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for ERVFRD-1 Gene

Genomic Locations for ERVFRD-1 Gene
chr6:11,102,489-11,111,838
(GRCh38/hg38)
Size:
9,350 bases
Orientation:
Minus strand
chr6:11,102,722-11,112,071
(GRCh37/hg19)
Size:
9,350 bases
Orientation:
Minus strand

Genomic View for ERVFRD-1 Gene

Genes around ERVFRD-1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ERVFRD-1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ERVFRD-1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ERVFRD-1 Gene

Proteins for ERVFRD-1 Gene

  • Protein details for ERVFRD-1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P60508-SYCY2_HUMAN
    Recommended name:
    Syncytin-2
    Protein Accession:
    P60508

    Protein attributes for ERVFRD-1 Gene

    Size:
    538 amino acids
    Molecular mass:
    59523 Da
    Quaternary structure:
    • The surface and transmembrane proteins form a heterodimer. They are attached by non-covalent interactions or by a labile interchain disulfide bond (By similarity). Interacts with MFSD2A.
    Miscellaneous:
    • HERV-FRD subgenomic RNA has been observed.
    • Ortholog in old-world and new-world monkeys, but not in prosimians.
    • The human genome contains a high percentage of proviral-like elements, also called endogenous retroviruses (ERVs) that are the genomic traces of ancient infections of the germline by exogenous retroviruses. Although most of these elements are defective, some have conserved a functional envelope (env) gene, most probably diverted by the host for its benefit.

    Three dimensional structures from OCA and Proteopedia for ERVFRD-1 Gene

neXtProt entry for ERVFRD-1 Gene

Post-translational modifications for ERVFRD-1 Gene

  • Specific enzymatic cleavages in vivo yield the mature SU and TM proteins.
  • The CXXC motif is highly conserved across a broad range of retroviral envelope proteins. It is thought to participate in the formation of a labile disulfide bond possibly with the CX6CC motif present in the transmembrane protein. Isomerization of the intersubunit disulfide bond to an SU intrachain disulfide bond is thought to occur upon receptor recognition in order to allow membrane fusion (By similarity).
  • Glycosylation at isoforms=443, isoforms=332, Asn312, isoforms=247, Asn241, Asn220, isoforms=177, isoforms=146, and Asn133
  • Modification sites at PhosphoSitePlus

Other Protein References for ERVFRD-1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ERVFRD-1 Gene

Domains & Families for ERVFRD-1 Gene

Gene Families for ERVFRD-1 Gene

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

Protein Domains for ERVFRD-1 Gene

Suggested Antigen Peptide Sequences for ERVFRD-1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P60508

UniProtKB/Swiss-Prot:

SYCY2_HUMAN :
  • Contains the CKS-17 immunosuppressive domain present in many retroviral envelope proteins. As a synthetic peptide, it inhibits immune function in vitro and in vivo (By similarity).
  • Belongs to the gamma type-C retroviral envelope protein family. HERV class-I FRD env subfamily.
Domain:
  • Contains the CKS-17 immunosuppressive domain present in many retroviral envelope proteins. As a synthetic peptide, it inhibits immune function in vitro and in vivo (By similarity).
Family:
  • Belongs to the gamma type-C retroviral envelope protein family. HERV class-I FRD env subfamily.
genes like me logo Genes that share domains with ERVFRD-1: view

Function for ERVFRD-1 Gene

Molecular function for ERVFRD-1 Gene

UniProtKB/Swiss-Prot Function:
This endogenous retroviral envelope protein has retained its original fusogenic properties and participates in trophoblast fusion and the formation of a syncytium during placenta morphogenesis. The interaction with MFSD2A is apparently important for this process (PubMed:18988732).
UniProtKB/Swiss-Prot Function:
Endogenous envelope proteins may have kept, lost or modified their original function during evolution but this one can still make pseudotypes with MLV, HIV-1 or SIV-1 virions and confer infectivity. Retroviral envelope proteins mediate receptor recognition and membrane fusion during early infection. The surface protein mediates receptor recognition, while the transmembrane protein anchors the envelope heterodimer to the viral membrane through one transmembrane domain. The other hydrophobic domain, called fusion peptide, mediates fusion of the viral membrane with the target cell membrane (PubMed:14694139).

Phenotypes From GWAS Catalog for ERVFRD-1 Gene

genes like me logo Genes that share phenotypes with ERVFRD-1: view

Animal Models for ERVFRD-1 Gene

MGI Knock Outs for ERVFRD-1:
  • Synb Synb<tm1.2Ics>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ERVFRD-1

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for ERVFRD-1 Gene

Localization for ERVFRD-1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ERVFRD-1 Gene

Virion.
Surface protein: Cell membrane; Peripheral membrane protein. Note=The surface protein is not anchored to the membrane, but localizes to the extracellular surface through its binding to TM. {ECO:0000250 UniProtKB:Q9UQF0}.
Transmembrane protein: Cell membrane; Single-pass membrane protein.

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 ERVFRD-1 gene
Compartment Confidence
plasma membrane 5

Gene Ontology (GO) - Cellular Components for ERVFRD-1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with ERVFRD-1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for ERVFRD-1 Gene

Pathways & Interactions for ERVFRD-1 Gene

SuperPathways for ERVFRD-1 Gene

No Data Available

Interacting Proteins for ERVFRD-1 Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000420174%0d%0a9606.ENSP00000261674%0d%0a
Selected Interacting proteins: P60508-SYCY2_HUMAN ENSP00000420174 for ERVFRD-1 Gene via IID STRING

Gene Ontology (GO) - Biological Process for ERVFRD-1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000768 syncytium formation by plasma membrane fusion IDA 14557543
GO:0006949 syncytium formation IDA 23492904
GO:0045026 plasma membrane fusion IDA 14557543
genes like me logo Genes that share ontologies with ERVFRD-1: view

No data available for Pathways by source and SIGNOR curated interactions for ERVFRD-1 Gene

Drugs & Compounds for ERVFRD-1 Gene

No Compound Related Data Available

Transcripts for ERVFRD-1 Gene

mRNA/cDNA for ERVFRD-1 Gene

(1) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(47) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for ERVFRD-1 Gene

Endogenous retrovirus group FRD, member 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ERVFRD-1

Alternative Splicing Database (ASD) splice patterns (SP) for ERVFRD-1 Gene

No ASD Table

Relevant External Links for ERVFRD-1 Gene

GeneLoc Exon Structure for
ERVFRD-1
ECgene alternative splicing isoforms for
ERVFRD-1

Expression for ERVFRD-1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ERVFRD-1 Gene

mRNA differential expression in normal tissues according to GTEx for ERVFRD-1 Gene

This gene is overexpressed in Esophagus - Gastroesophageal Junction (x5.1) and Esophagus - Muscularis (x4.6).

Protein differential expression in normal tissues from HIPED for ERVFRD-1 Gene

This gene is overexpressed in Placenta (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for ERVFRD-1 Gene



Protein tissue co-expression partners for ERVFRD-1 Gene

- Elite partner

SOURCE GeneReport for Unigene cluster for ERVFRD-1 Gene:

Hs.631996

mRNA Expression by UniProt/SwissProt for ERVFRD-1 Gene:

P60508-SYCY2_HUMAN
Tissue specificity: Expressed at higher level in placenta. Expressed at lower level in adrenal, bone marrow, brain, breast, colon, kidney, lung, ovary, peripheral blood lymphocytes, prostate, skin, spleen, testis, thymus, thyroid, trachea.
genes like me logo Genes that share expression patterns with ERVFRD-1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for ERVFRD-1 Gene

Orthologs for ERVFRD-1 Gene

This gene was present in the common ancestor of mammals.

Orthologs for ERVFRD-1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia ERVFRDE1 34
  • 100 (a)
OneToOne
ERVFRD-1 33
  • 99.5 (n)
rat
(Rattus norvegicus)
Mammalia Ervfrd-1 33
  • 45.74 (n)
mouse
(Mus musculus)
Mammalia Synb 16 33
  • 44.94 (n)
Gm14226 34
  • 13 (a)
OneToMany
D17H6S56E-5 34
  • 10 (a)
OneToMany
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 23 (a)
OneToMany
-- 34
  • 22 (a)
OneToMany
-- 34
  • 20 (a)
OneToMany
-- 34
  • 19 (a)
OneToMany
-- 34
  • 19 (a)
OneToMany
-- 34
  • 19 (a)
OneToMany
-- 34
  • 18 (a)
OneToMany
-- 34
  • 18 (a)
OneToMany
-- 34
  • 17 (a)
OneToMany
-- 34
  • 17 (a)
OneToMany
-- 34
  • 16 (a)
OneToMany
-- 34
  • 15 (a)
OneToMany
-- 34
  • 14 (a)
OneToMany
-- 34
  • 13 (a)
OneToMany
-- 34
  • 13 (a)
OneToMany
-- 34
  • 12 (a)
OneToMany
-- 34
  • 12 (a)
OneToMany
-- 34
  • 11 (a)
OneToMany
dog
(Canis familiaris)
Mammalia ERVFRD-1 34
  • 18 (a)
OneToOne
Species where no ortholog for ERVFRD-1 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)
  • cow (Bos Taurus)
  • 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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • 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 ERVFRD-1 Gene

ENSEMBL:
Gene Tree for ERVFRD-1 (if available)
TreeFam:
Gene Tree for ERVFRD-1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ERVFRD-1: view image

Paralogs for ERVFRD-1 Gene

Paralogs for ERVFRD-1 Gene

(1) SIMAP similar genes for ERVFRD-1 Gene using alignment to 1 proteins:

  • EFRD1_HUMAN
genes like me logo Genes that share paralogs with ERVFRD-1: view

Variants for ERVFRD-1 Gene

Sequence variations from dbSNP and Humsavar for ERVFRD-1 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000019683 -- 11,105,671(-) A/G intron_variant
rs1000088105 -- 11,104,046(-) A/T coding_sequence_variant, missense_variant
rs1000209663 -- 11,102,869(-) A/G 3_prime_UTR_variant
rs1000454643 -- 11,105,282(-) A/G coding_sequence_variant, missense_variant
rs1000620017 -- 11,107,651(-) C/G intron_variant

Variation tolerance for ERVFRD-1 Gene

Gene Damage Index Score: 0.91; 18.92% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ERVFRD-1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ERVFRD-1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for ERVFRD-1 Gene

Disorders for ERVFRD-1 Gene

Additional Disease Information for ERVFRD-1

No disorders were found for ERVFRD-1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ERVFRD-1 Gene

Publications for ERVFRD-1 Gene

  1. Genomewide screening for fusogenic human endogenous retrovirus envelopes identifies syncytin 2, a gene conserved on primate evolution. (PMID: 14557543) Blaise S … Heidmann T (Proceedings of the National Academy of Sciences of the United States of America 2003) 2 3 4 22 58
  2. Crystal structure of a pivotal domain of human syncytin-2, a 40 million years old endogenous retrovirus fusogenic envelope gene captured by primates. (PMID: 16140326) Renard M … Heidmann T (Journal of molecular biology 2005) 3 4 22 58
  3. Survey of human genes of retroviral origin: identification and transcriptome of the genes with coding capacity for complete envelope proteins. (PMID: 12970426) de Parseval N … Heidmann T (Journal of virology 2003) 2 3 4 58
  4. A novel human endogenous retroviral protein inhibits cell-cell fusion. (PMID: 23492904) Sugimoto J … Schust D (Scientific reports 2013) 3 4 58
  5. A revised nomenclature for transcribed human endogenous retroviral loci. (PMID: 21542922) Mayer J … Seal RL (Mobile DNA 2011) 2 3 58

Products for ERVFRD-1 Gene

Sources for ERVFRD-1 Gene

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