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A revised nomenclature for transcribed human endogenous retroviral loci



Endogenous retroviruses (ERVs) and ERV-like sequences comprise 8% of the human genome. A hitherto unknown proportion of ERV loci are transcribed and thus contribute to the human transcriptome. A small proportion of these loci encode functional proteins. As the role of ERVs in normal and diseased biological processes is not yet established, transcribed ERV loci are of particular interest. As more transcribed ERV loci are likely to be identified in the near future, the development of a systematic nomenclature is important to ensure that all information on each locus can be easily retrieved.


Here we present a revised nomenclature of transcribed human endogenous retroviral loci that sorts loci into groups based on Repbase classifications. Each symbol is of the format ERV + group symbol + unique number. Group symbols are based on a mixture of Repbase designations and well-supported symbols used in the literature. The presented guidelines will allow newly identified loci to be easily incorporated into the scheme.


The naming system will be employed by the HUGO Gene Nomenclature Committee for naming transcribed human ERV loci. We hope that the system will contribute to clarifying a certain aspect of a sometimes confusing nomenclature for human endogenous retroviruses. The presented system may also be employed for naming transcribed loci of human non-ERV repeat loci.

Human endogenous retroviruses

Human endogenous retroviruses (ERVs) are remnants of infections of former exogenous retroviruses. Proviruses formed by numerous distinct exogenous retroviruses in the germline genome could be inherited by subsequent generations. About 8% of the human genome consists of sequences that are potentially of retroviral origin [1] and are distributed in about 700,000 different loci. In addition to proviruses, these sequences include solitary long terminal repeats (LTRs), nonretroviral sequences flanked by LTRs that may not be directly derived from infectious retroviruses and sequences similar to LTRs. ERVs and related sequences are thus part of the repetitive portions of the human genome, which comprise about 45% of the human genome mass, including mobile DNA such as L1, Alu and SVA elements.

Detailed analysis of the human genome sequence by wet-lab and bioinformatics approaches resulted in the definition of ERV groups, with the number depending on the methods used for defining groups: 31 groups were defined by Sperber et al.[2] and Blomberg et al.[3], 42 groups were defined by Mager and Medstrand [4], 30 groups were defined by Gifford and Tristem [5] and several hundred human ERV and LTR families were defined by Repbase [6].

Almost all human ERV loci no longer encode former retroviral proteins because of their ancient incorporation into the host genome and thus accumulation of nonsense mutations. Many loci are missing large proviral portions, and most loci have been reduced to so-called solitary LTRs by homologous recombination between proviral LTRs. For more detailed information on human ERVs, we refer interested readers to recent reviews on the topic and the references therein [710].

While protein coding capacity is very limited, many human ERV loci still are transcribed and usually are initiated by promoter sequences within the proviral LTRs. Obviously, mutations within LTRs have not yet rendered all LTRs in the human genome defective. In principle, promoters in flanking, non-ERV sequences may also contribute to transcription of those loci. Probably every human tissue and cell type, diseased or not, contains ERV transcripts [11, 12]. More than a single ERV group is usually found transcribed, and patterns of transcribed ERV groups differ between tissue and cell types. Transcription of ERV loci is thus regulated in some way. While expression of ERV sequences has been associated with a number of human diseases, such as germ cell tumours, melanoma and multiple sclerosis, the involvement of ERVs in human diseases remains to be elucidated. On the other side, some ERV loci very likely provide important biological functions, such as the syncytin [13] and syncytin 2 loci [14], referred to herein as ERVW-1 and ERVFRD-1, respectively. Other loci harbouring only partial open reading frames, such as a recently characterized HERV-W locus on chromosome Xq22.3 [15] (ERVW-2), may likewise produce partial retroviral proteins with potential biological functions. It is therefore of particular interest which ERV loci actually contribute to the human transcriptome.

Recent studies have identified transcribed ERV loci in normal and diseased human cells and tissues by means of reassigning ERV cDNA sequences to individual loci in the human reference genome sequence, employing characteristic nucleotide differences between individual loci of a regarded ERV group. Many more transcribed ERV loci are likely to be identified in future studies. It is therefore necessary to introduce a nomenclature for transcribed human ERV sequences.

Previous nomenclature used in the literature

The lack of an established nomenclature for transcribed ERV elements has led to confusion within the literature. These problems were previously reviewed in detail [16]. ERVs have been classified into groups (formerly known as "families", which is heresy to virologists because "family" refers to Retroviridae), although different classification systems have been used. For instance, some groups have been defined initially by molecular genetics means, others by sequence similarity and others by primer binding site sequences. Changing amounts of sequence information also showed that some ERV groups' designations needed to be revised. Different names have been used for the same ERV group. Likewise, individual loci have been referred to using a variety of different symbols (for example, see the aliases listed in Table 1 for the ERVK-6 locus). The use of different symbols for the same locus makes it difficult to retrieve all information on that particular locus.

Table 1 Nomenclature for transcribed human endogenous retrovirus loci

Previous ERV nomenclature and the Human Genome Organisation Gene Nomenclature Committee

The Human Genome Organisation (HUGO) Gene Nomenclature Committee (HGNC) works under the auspices of HUGO and is the only worldwide authority that assigns standardised nomenclature to human genes [17]. The HGNC has previously focused on approving nomenclature for protein-coding genes, pseudogenes, phenotypes and noncoding RNA. In the past, the committee has approved symbols for specific human ERVs only at the request of individual researchers. The symbols did not follow a systematic nomenclature: some symbols were of a simple format (for example, ERV1), some provided information on the group to which the ERV belonged (for example, ERVK2) and others included information on proteins encoded by the ERV (for example, ERVWE1 (endogenous retroviral family W, env(C7), member 1)). On reviewing the literature, it was clear that (1) many of the most frequently published loci were not represented by HGNC symbols, (2) by following more than one system, HGNC symbols were not serving the community, and (3) the nomenclature needed both updating and expansion.

HGNC editors curate relevant information for each gene that has approved nomenclature. In addition to approving a gene symbol and name for each transcribed human ERV, the HGNC records all known symbol aliases so that information on each gene can be retrieved using any known symbol. HGNC entries also include the chromosomal location of the ERV locus, links to GenBank, European Molecular Biology Laboratory (EMBL) and DNA Databank of Japan (DDBJ) sequence records and links to at least one PubMed reference. Where appropriate, links are also provided to annotation projects at both the genomic and proteomic levels. HGNC names are propagated to other major biological databases, such as Ensembl, UniProt and Entrez Gene. Therefore, this new nomenclature will provide a useful resource that is currently unavailable to the ERV community and other researchers concerned with ERVs.

A gene-based nomenclature

The primary definition of a gene used by the HGNC is "a DNA segment that contributes to phenotype/function" [18]. It is beyond the scope of this nomenclature effort to standardise the nomenclature of ERVs in general or to attempt to name every ERV element in the genome. As discussed above, there is evidence that some human ERVs encode functional proteins and that some encode transcripts and/or proteins which may be associated with disease, so the transcriptionally active loci come under the remit of the HGNC for naming. This category of ERVs represents most of the individual loci that have been published with individual names, so it is worth developing a standardised nomenclature for this subset. The three criteria for being accepted as a transcriptionally active ERV are as follows: (1) The ERV must be represented by an mRNA sequence in a public database, (2) the reported cDNA sequence must map unambiguously to the reference genome to allow identification and (3) the sequence must represent a viral gene rather than solely a solitary LTR. We acknowledge that there are sources of uncertainty. Many ERVs may be expressed at a low level [19], a "leakage" which can be hard to distinguish from perhaps more significant expression. Groups of recently integrated ERVs may be highly expressed, but their transcripts may be identical or almost identical and could be hard to map unambiguously. However, these difficulties should not prevent the naming of ERV loci which fulfil the criteria mentioned above. There is one symbol approved per ERV locus independently of how many viral genes the ERV may encode.

A systematic ERV nomenclature scheme

The nomenclature scheme described in this paper aims to be concise so that it is user-friendly. It also aims to be informative to researchers, including those who are less familiar with the field. To be informative, the nomenclature scheme is hierarchical, with each symbol beginning with the root symbol "ERV" so that the symbols are instantly recognisable and can be grouped together in searches. Note that many researchers have published papers using symbols beginning with "HERV", but it is against the guidelines of the HGNC ever to use H for "human" in symbols, mainly because this precludes the possibility of the nomenclature scheme's being extended to other species. Each ERV symbol, then, includes an identifier that represents the group to which the ERV belongs.

In order for the nomenclature scheme to be systematic, one method of sorting ERVs into groups needed to be selected. The Repbase system [6] is a widely known, comprehensive database of repetitive elements that groups ERVs together on the basis of sequence similarity. RepeatMasker annotations using Repbase designations are available on the University of California, Santa Cruz (UCSC) [20], and Ensembl [21] genome browsers, making these ERV groups highly accessible and recognisable to researchers in the field. Therefore, the nomenclature system uses the Repbase classification system for naming the ERVs within groups. Repbase groups, however, do not follow a systematic nomenclature and often contain an unallowable "H" for "human". When deciding on the group identifier to be included in each symbol, we compared Repbase symbols with those that have appeared frequently in the literature. In cases where there was a well-supported nomenclature present in the literature, we used this symbol in place of the Repbase symbol; for example, we used ERVW instead of the Repbase group designation HERV17, as we felt that these would be more likely to be used by the ERV community. For a comparison of the group symbols used in the new nomenclature scheme with Repbase designations, see Table 2.

Table 2 Comparison of Repbase group symbols with group symbols used in the nomenclature scheme presented herein

Finally, each ERV within a particular group is uniquely identified by a number, for example, ERVK-1. Numbers are assigned consecutively within each group to make the nomenclature system expandable. The number is used to make each symbol unique and has no intrinsic meaning. ERVK-2 has merely been assigned the next number following ERVK-1, but this provides no information on the position of the ERVs within the genome or the order in which an ERV may have been published. The use of numerical identifiers keeps the symbols as short as possible to encourage widespread use by researchers. Newly identified transcribed loci will take the next available consecutive number for their particular group; for example, if a newly transcribed ERVK locus is identified, it will take the symbol ERVK-26. Each symbol is accompanied by an expanded gene name which clearly and succinctly explains that derivation of the nomenclature; for example, the full name of ERVFRD-1 is "endogenous retrovirus group FRD, member 1".

We are aware that the proposed nomenclature scheme cannot encompass all conceivable (and sometimes known) unusual structures of ERV loci, such as hybrid loci consisting of different ERV groups and ERV insertions into existing ERV loci [22]. HGNC, after conferring with researchers who submit newly identified transcribed loci, will decide whether or how to name such unique loci on a case-by-case basis. For example, the scheme will not incorporate ERV locus transcripts that are part of another gene's transcript, as these elements will not be considered separate loci.

Table 1 lists transcribed human ERVs that have been named according to the new nomenclature system. All ERVs in the table either have been published or have been annotated by the RefSeq project. An initial list was sent to a number of researchers in the field for their comments. The list was expanded as these researchers suggested more loci. Where no transcript sequence was available, authors were asked to submit representative sequences to the GenBank, EMBL and DDBJ databases. We encourage researchers to contact the HGNC if they know of further ERVs that can be included in the scheme.

Finally, although only human gene nomenclature is under the remit of the HGNC, we wish to mention that the naming system introduced here for transcribed ERVs could, in principle, also be applied to other, non-ERV repetitive sequences in the human genome, as well as to repetitive DNA in nonhuman species. Future research will probably reveal numerous transcribed repetitive DNA sequences in various species. Judged just from ERV designations in different species, a standardised naming system for transcribed repeat loci may be highly beneficial to avoid future confusion.


  1. 1.

    Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al: Initial sequencing and analysis of the human genome. Nature. 2001, 409 (6822): 860-921. 10.1038/35057062.

    CAS  Article  PubMed  Google Scholar 

  2. 2.

    Sperber GO, Airola T, Jern P, Blomberg J: Automated recognition of retroviral sequences in genomic data--RetroTector. Nucleic Acids Res. 2007, 35 (15): 4964-4976. 10.1093/nar/gkm515.

    PubMed Central  CAS  Article  PubMed  Google Scholar 

  3. 3.

    Blomberg J, Goran S, Jern P, Benachenhou F: Towards a retrovirus database, RetroBank. Proceedings of the Centennial Retrovirus Meeting, 29 April - 4 May 2010. Edited by: Daniel R, Hejnar J, Skalka AM, Svoboda J Prague. 2010, Czech Republic: Medimond International Proceedings, 19-22.

    Google Scholar 

  4. 4.

    Mager DL, Medstrand P: Retroviral Repeat Sequences. Nature Encyclopedia of the Human Genome. Edited by: Cooper D. 2003, Hampshire, England: Macmillan Publishers Ltd, 5: 57-63.

    Google Scholar 

  5. 5.

    Gifford R, Tristem M: The evolution, distribution and diversity of endogenous retroviruses. Virus Genes. 2003, 26 (3): 291-315. 10.1023/A:1024455415443.

    CAS  Article  PubMed  Google Scholar 

  6. 6.

    Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J: Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005, 110 (1-4): 462-467. 10.1159/000084979.

    CAS  Article  PubMed  Google Scholar 

  7. 7.

    Blikstad V, Benachenhou F, Sperber GO, Blomberg J: Evolution of human endogenous retroviral sequences: a conceptual account. Cell Mol Life Sci. 2008, 65 (21): 3348-3365. 10.1007/s00018-008-8495-2.

    CAS  Article  PubMed  Google Scholar 

  8. 8.

    Kurth R, Bannert N: Beneficial and detrimental effects of human endogenous retroviruses. Int J Cancer. 2010, 126 (2): 306-314. 10.1002/ijc.24902.

    CAS  Article  PubMed  Google Scholar 

  9. 9.

    Mayer J, Meese E: Human endogenous retroviruses in the primate lineage and their influence on host genomes. Cytogenet Genome Res. 2005, 110 (1-4): 448-456. 10.1159/000084977.

    CAS  Article  PubMed  Google Scholar 

  10. 10.

    Ruprecht K, Mayer J, Sauter M, Roemer K, Mueller-Lantzsch N: Endogenous retroviruses and cancer. Cell Mol Life Sci. 2008, 65 (21): 3366-3382. 10.1007/s00018-008-8496-1.

    CAS  Article  PubMed  Google Scholar 

  11. 11.

    Hu L: Endogenous retroviral RNA expression in humans. PhD thesis. 2007, Department of Medical Sciences, Clinical Virology, Uppsala University

    Google Scholar 

  12. 12.

    Seifarth W, Frank O, Zeilfelder U, Spiess B, Greenwood AD, Hehlmann R, Leib-Mösch C: Comprehensive analysis of human endogenous retrovirus transcriptional activity in human tissues with a retrovirus-specific microarray. J Virol. 2005, 79 (1): 341-352. 10.1128/JVI.79.1.341-352.2005.

    PubMed Central  CAS  Article  PubMed  Google Scholar 

  13. 13.

    Mi S, Lee X, Li X, Veldman GM, Finnerty H, Racie L, LaVallie E, Tang XY, Edouard P, Howes S, et al: Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis. Nature. 2000, 403 (6771): 785-789. 10.1038/35001608.

    CAS  Article  PubMed  Google Scholar 

  14. 14.

    de Parseval N, Heidmann T: Human endogenous retroviruses: from infectious elements to human genes. Cytogenet Genome Res. 2005, 110 (1-4): 318-332. 10.1159/000084964.

    CAS  Article  PubMed  Google Scholar 

  15. 15.

    Roebke C, Wahl S, Laufer G, Stadelmann C, Sauter M, Mueller-Lantzsch N, Mayer J, Ruprecht K: An N-terminally truncated envelope protein encoded by a human endogenous retrovirus W locus on chromosome Xq22.3. Retrovirology. 2010, 7 (1): 69-10.1186/1742-4690-7-69.

    PubMed Central  Article  PubMed  Google Scholar 

  16. 16.

    Blomberg J, Benachenhou F, Blikstad V, Sperber G, Mayer J: Classification and nomenclature of endogenous retroviral sequences (ERVs): problems and recommendations. Gene. 2009, 448 (2): 115-123. 10.1016/j.gene.2009.06.007.

    CAS  Article  PubMed  Google Scholar 

  17. 17.

    Seal RL, Gordon SM, Lush MJ, Wright MW, Bruford EA: the HGNC resources in 2011. Nucleic Acids Res. 2011, D514-519. 39 Database

  18. 18.

    Wain HM, Bruford EA, Lovering RC, Lush MJ, Wright MW, Povey S: Guidelines for human gene nomenclature. Genomics. 2002, 79 (4): 464-470. 10.1006/geno.2002.6748.

    CAS  Article  PubMed  Google Scholar 

  19. 19.

    Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, et al: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007, 447 (7146): 799-816. 10.1038/nature05874.

    CAS  Article  PubMed  Google Scholar 

  20. 20.

    Mangan ME, Williams JM, Kuhn RM, Lathe WC: The UCSC genome browser: what every molecular biologist should know. Curr Protoc Mol Biol. 2009, Chapter 19: Unit19 19-

    Google Scholar 

  21. 21.

    Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S: Ensembl 2011. Nucleic Acids Res. 2011, D800-806. 39 Database

  22. 22.

    Flockerzi A, Burkhardt S, Schempp W, Meese E, Mayer J: Human Endogenous Retrovirus HERV-K14 Families: Status, Variants, Evolution, and Mobilization of Other Cellular Sequences. J Virol. 2005, 79 (5): 2941-2949. 10.1128/JVI.79.5.2941-2949.2005.

    PubMed Central  CAS  Article  PubMed  Google Scholar 

  23. 23.

    Flockerzi A, Ruggieri A, Frank O, Sauter M, Maldener E, Kopper B, Wullich B, Seifarth W, Muller-Lantzsch N, Leib-Mosch C, et al: Expression patterns of transcribed human endogenous retrovirus HERV-K(HML-2) loci in human tissues and the need for a HERV Transcriptome Project. BMC Genomics. 2008, 9: 354-10.1186/1471-2164-9-354.

    PubMed Central  Article  PubMed  Google Scholar 

  24. 24.

    Villesen P, Aagaard L, Wiuf C, Pedersen FS: Identification of endogenous retroviral reading frames in the human genome. Retrovirology. 2004, 1: 32-10.1186/1742-4690-1-32.

    PubMed Central  Article  PubMed  Google Scholar 

  25. 25.

    Sugimoto J, Matsuura N, Kinjo Y, Takasu N, Oda T, Jinno Y: Transcriptionally active HERV-K genes: identification, isolation, and chromosomal mapping. Genomics. 2001, 72 (2): 137-144. 10.1006/geno.2001.6473.

    CAS  Article  PubMed  Google Scholar 

  26. 26.

    Berkhout B, Jebbink M, Zsiros J: Identification of an active reverse transcriptase enzyme encoded by a human endogenous HERV-K retrovirus. J Virol. 1999, 73 (3): 2365-2375.

    PubMed Central  CAS  PubMed  Google Scholar 

  27. 27.

    de Parseval N, Lazar V, Casella JF, Benit L, Heidmann T: Survey of human genes of retroviral origin: identification and transcriptome of the genes with coding capacity for complete envelope proteins. J Virol. 2003, 77 (19): 10414-10422. 10.1128/JVI.77.19.10414-10422.2003.

    PubMed Central  CAS  Article  PubMed  Google Scholar 

  28. 28.

    Barbulescu M, Turner G, Seaman MI, Deinard AS, Kidd KK, Lenz J: Many human endogenous retrovirus K (HERV-K) proviruses are unique to humans. Curr Biol. 1999, 9 (16): 861-868. 10.1016/S0960-9822(99)80390-X.

    CAS  Article  PubMed  Google Scholar 

  29. 29.

    Turner G, Barbulescu M, Su M, Jensen-Seaman MI, Kidd KK, Lenz J: Insertional polymorphisms of full-length endogenous retroviruses in humans. Curr Biol. 2001, 11 (19): 1531-1535. 10.1016/S0960-9822(01)00455-9.

    CAS  Article  PubMed  Google Scholar 

  30. 30.

    Zsiros J, Jebbink MF, Lukashov VV, Voute PA, Berkhout B: Evolutionary relationships within a subgroup of HERV-K-related human endogenous retroviruses. J Gen Virol. 1998, 79 (Pt 1): 61-70.

    CAS  Article  PubMed  Google Scholar 

  31. 31.

    Tonjes RR, Czauderna F, Kurth R: Genome-wide screening, cloning, chromosomal assignment, and expression of full-length human endogenous retrovirus type K. J Virol. 1999, 73 (11): 9187-9195.

    PubMed Central  CAS  PubMed  Google Scholar 

  32. 32.

    Okahara G, Matsubara S, Oda T, Sugimoto J, Jinno Y, Kanaya F: Expression analyses of human endogenous retroviruses (HERVs): tissue-specific and developmental stage-dependent expression of HERVs. Genomics. 2004, 84 (6): 982-990. 10.1016/j.ygeno.2004.09.004.

    CAS  Article  PubMed  Google Scholar 

  33. 33.

    Frank O, Verbeke C, Schwarz N, Mayer J, Fabarius A, Hehlmann R, Leib-Mosch C, Seifarth W: Variable transcriptional activity of endogenous retroviruses in human breast cancer. J Virol. 2008, 82 (4): 1808-1818. 10.1128/JVI.02115-07.

    PubMed Central  CAS  Article  PubMed  Google Scholar 

  34. 34.

    Blaise S, de Parseval N, Benit L, Heidmann T: Genomewide screening for fusogenic human endogenous retrovirus envelopes identifies syncytin 2, a gene conserved on primate evolution. Proc Natl Acad Sci USA. 2003, 100 (22): 13013-13018. 10.1073/pnas.2132646100.

    PubMed Central  CAS  Article  PubMed  Google Scholar 

  35. 35.

    Cohen M, Powers M, O'Connell C, Kato N: The nucleotide sequence of the env gene from the human provirus ERV3 and isolation and characterization of an ERV3-specific cDNA. Virology. 1985, 147 (2): 449-458. 10.1016/0042-6822(85)90147-3.

    CAS  Article  PubMed  Google Scholar 

  36. 36.

    Larsson E, Andersson AC, Nilsson BO: Expression of an endogenous retrovirus (ERV3 HERV-R) in human reproductive and embryonic tissues--evidence for a function for envelope gene products. Ups J Med Sci. 1994, 99 (2): 113-120. 10.3109/03009739409179354.

    CAS  Article  PubMed  Google Scholar 

  37. 37.

    Blond JL, Beseme F, Duret L, Bouton O, Bedin F, Perron H, Mandrand B, Mallet F: Molecular characterization and placental expression of HERV-W, a new human endogenous retrovirus family. J Virol. 1999, 73 (2): 1175-1185.

    PubMed Central  CAS  PubMed  Google Scholar 

  38. 38.

    Laufer G, Mayer J, Mueller BF, Mueller-Lantzsch N, Ruprecht K: Analysis of transcribed human endogenous retrovirus W env loci clarifies the origin of multiple sclerosis-associated retrovirus env sequences. Retrovirology. 2009, 6: 37-10.1186/1742-4690-6-37.

    PubMed Central  Article  PubMed  Google Scholar 

  39. 39.

    Komurian-Pradel F, Paranhos-Baccala G, Bedin F, Ounanian-Paraz A, Sodoyer M, Ott C, Rajoharison A, Garcia E, Mallet F, Mandrand B, et al: Molecular cloning and characterization of MSRV-related sequences associated with retrovirus-like particles. Virology. 1999, 260 (1): 1-9. 10.1006/viro.1999.9792.

    CAS  Article  PubMed  Google Scholar 

  40. 40.

    Jeong BH, Lee YJ, Carp RI, Kim YS: The prevalence of human endogenous retroviruses in cerebrospinal fluids from patients with sporadic Creutzfeldt-Jakob disease. J Clin Virol. 2010, 47 (2): 136-142. 10.1016/j.jcv.2009.11.016.

    CAS  Article  PubMed  Google Scholar 

  41. 41.

    Yao Y, Schroder J, Nellaker C, Bottmer C, Bachmann S, Yolken RH, Karlsson H: Elevated levels of human endogenous retrovirus-W transcripts in blood cells from patients with first episode schizophrenia. Genes Brain Behav. 2008, 7 (1): 103-112.

    CAS  PubMed  Google Scholar 

  42. 42.

    de Parseval N, Diop G, Blaise S, Helle F, Vasilescu A, Matsuda F, Heidmann T: Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes. BMC Genomics. 2005, 6: 117-10.1186/1471-2164-6-117.

    PubMed Central  Article  PubMed  Google Scholar 

  43. 43.

    Yi JM, Kim HS: Expression and phylogenetic analyses of human endogenous retrovirus HC2 belonging to the HERV-T family in human tissues and cancer cells. J Hum Genet. 2007, 52 (4): 285-296. 10.1007/s10038-007-0115-8.

    CAS  Article  PubMed  Google Scholar 

  44. 44.

    Shiroma T, Sugimoto J, Oda T, Jinno Y, Kanaya F: Search for active endogenous retroviruses: identification and characterization of a HERV-E gene that is expressed in the pancreas and thyroid. J Hum Genet. 2001, 46 (11): 619-625. 10.1007/s100380170012.

    CAS  Article  PubMed  Google Scholar 

  45. 45.

    Prusty BK, zur Hausen H, Schmidt R, Kimmel R, de Villiers EM: Transcription of HERV-E and HERV-E-related sequences in malignant and non-malignant human haematopoietic cells. Virology. 2008, 382 (1): 37-45. 10.1016/j.virol.2008.09.006.

    CAS  Article  PubMed  Google Scholar 

  46. 46.

    Takahashi Y, Harashima N, Kajigaya S, Yokoyama H, Cherkasova E, McCoy JP, Hanada K, Mena O, Kurlander R, Tawab A, et al: Regression of human kidney cancer following allogeneic stem cell transplantation is associated with recognition of an HERV-E antigen by T cells. J Clin Invest. 2008, 118 (3): 1099-1109.

    PubMed Central  CAS  PubMed  Google Scholar 

  47. 47.

    Kjeldbjerg AL, Villesen P, Aagaard L, Pedersen FS: Gene conversion and purifying selection of a placenta-specific ERV-V envelope gene during simian evolution. BMC Evol Biol. 2008, 8: 266-10.1186/1471-2148-8-266.

    PubMed Central  Article  PubMed  Google Scholar 

  48. 48.

    Liang QY, Ding JY, Zheng S: Identification and detection of a novel human endogenous retrovirus-related gene, and structural characterization of its related elements. Genet Mol Biol. 2009, 32 (4): 704-U738. 10.1590/S1415-47572009005000082.

    PubMed Central  CAS  Article  PubMed  Google Scholar 

  49. 49.

    Patzke S, Lindeskog M, Munthe E, Aasheim HC: Characterization of a novel human endogenous retrovirus, HERV-H/F, expressed in human leukemia cell lines. Virology. 2002, 303 (1): 164-173. 10.1006/viro.2002.1615.

    CAS  Article  PubMed  Google Scholar 

  50. 50.

    Lindeskog M, Blomberg J: Spliced human endogenous retroviral HERV-H env transcripts in T-cell leukaemia cell lines and normal leukocytes: alternative splicing pattern of HERV-H transcripts. J Gen Virol. 1997, 78 (Pt 10): 2575-2585.

    CAS  Article  PubMed  Google Scholar 

  51. 51.

    Moles JP, Tesniere A, Guilhou JJ: A new endogenous retroviral sequence is expressed in skin of patients with psoriasis. Br J Dermatol. 2005, 153 (1): 83-89. 10.1111/j.1365-2133.2005.06555.x.

    CAS  Article  PubMed  Google Scholar 

  52. 52.

    La Mantia G, Pengue G, Maglione D, Pannuti A, Pascucci A, Lania L: Identification of new human repetitive sequences: characterization of the corresponding cDNAs and their expression in embryonal carcinoma cells. Nucleic Acids Res. 1989, 17 (15): 5913-5922. 10.1093/nar/17.15.5913.

    PubMed Central  CAS  Article  PubMed  Google Scholar 

  53. 53.

    Andersson ML, Lindeskog M, Medstrand P, Westley B, May F, Blomberg J: Diversity of human endogenous retrovirus class II-like sequences. J Gen Virol. 1999, 80 (Pt 1): 255-260.

    CAS  Article  PubMed  Google Scholar 

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Research in the laboratory of JM is supported by Deutsche Forschungsgemeinschaft (DFG) and Homburger Forschungsförderungsprogramm (HOMFOR) The HGNC is funded by The Wellcome Trust grant 081979/Z/07/Z and National Human Genome Research Institute grant P41 HG03345). We also acknowledge those who provided extra information for the list of transcribed ERV loci: Yoshihiro Jinno, Finn Skou Pedersen, Benoit Barbeau, Christine Leib-Mösch and Patrick M Alliel.

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All authors contributed to the presented nomenclature scheme and wrote the manuscript.

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Mayer, J., Blomberg, J. & Seal, R.L. A revised nomenclature for transcribed human endogenous retroviral loci. Mobile DNA 2, 7 (2011).

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  • Published:

  • DOI:


  • European Molecular Biology Laboratory
  • Human Genome Organisation
  • Nomenclature Scheme
  • Primer Binding Site Sequence
  • Partial Open Reading Frame