format-version: 1.2 date: 02:05:2014 08:22 saved-by: martinschiller auto-generated-by: OBO-Edit 2.3-beta7 default-namespace: HIV idspace: ROP http://purl.org/obo/owl/OBO_REL# idspace: ENVO http://purl.org/obo/owl/ENVO# idspace: snap http://www.ifomis.org/bfo/1.1/snap# idspace: VO http://purl.obolibrary.org/obo/VO idspace: RO http://www.obofoundry.org/ro/ro.owl# idspace: MOD http://www.berkeleybop.org/ontologies/mod.owl idspace: BFO http://www.ifomis.org/bfo/1.1/ idspace: MI http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/mod/data/PSI-MOD.obo idspace: IDO http://purl.obolibrary.org/obo/ido.owl idspace: CHEBI http://purl.org/obo/owl/CHEBI# idspace: PRO http://purl.org/obo/owl/PRO# idspace: PATO http://purl.org/obo/owl/PATO# idspace: birn_anat http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl# idspace: HPO http://purl.org/obo/owl/HP# idspace: UO http://purl.org/obo/owl/UO# idspace: NCBITaxon http://purl.org/obo/owl/NCBITaxon# idspace: OBI http://purl.obolibrary.org/obo/OBI_ idspace: SO http://purl.org/obo/owl/SO# idspace: FMA http://purl.org/obo/owl/FMA# idspace: IAO http://purl.obolibrary.org/obo/IAO idspace: UBERON http://purl.org/obo/owl/UBERON# idspace: GO http://purl.org/obo/owl/GO# idspace: OGMS http://ogms.googlecode.com/svn/releases/2011-09-20/ontology/ogms.owl idspace: CL http://purl.org/obo/owl/CL# idspace: span http://www.ifomis.org/bfo/1.1/span# remark: This version 1.3 contains additional sources and minor corrections in the spacing of some ids for the HIV Ontology remark: This version 1.3 is of 2014-04-25 [Term] id: HIV:00000 name: HIV def: "Human immunodeficiency virus (HIV) is a lentivirus that causes acquired immunodeficiency syndrome (AIDS), a condition in humans in which progressive failure of the immune system allows life-threatening opportunistic infections and cancers to thrive." [http://digitaljournal.com/article/363078] synonym: "HIV species" RELATED [PMID:24743531] synonym: "Human Immunodeficiency Virus" RELATED [PMID:24757518] xref: Source:NEWT\:11676 is_a: HIV:00029 ! retrovirus is_a: HIV:00043 ! lentivirus [Term] id: HIV:00001 name: HIV gene def: "A region (or regions) in the HIV genome that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:0000704] comment: A region of the HIV genome that encodes an RNA and/or protein. Definition adapted from SO:0000704. xref: Source:SO\:0000704 part_of: HIV:00029 part_of: HIV:00038 [Term] id: HIV:00002 name: HIV transcript def: "An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:0000673] comment: Definition adapted from SO:0000673. xref: Source:SO\:0000673 part_of: HIV:00029 is transcribed_from: HIV:00037 [Term] id: HIV:00003 name: HIV protein def: "A linear polymer of amino acids joined by peptide bonds in a specific sequence encoded by the HIV genome." [MI:0326] comment: Definition adapted from MI:03264. xref: Source:MI\:0326 is_transcribed_and_translated_from: HIV:00037 [Term] id: HIV:00004 name: antiretroviral drug def: "A compound that inhibits the replication of retroviruses. Medications for the treatment of infection by retroviruses, primarily HIV." [http://www.sciencedaily.com/articles/a/antiretroviral_drug.htm] [Term] id: HIV:00005 name: FDA-approved antiretroviral drug def: "An antiretroviral drug that has been approved by the Food and Drug Administration (FDA)." [http://medical-dictionary.thefreedictionary.com/Antiretroviral+drug] synonym: "FDA approved ARV drug" RELATED [http://medical-dictionary.thefreedictionary.com/Antiretroviral+drug] type_of: HIV:00004 [Term] id: HIV:00006 name: proteolytically processed protein def: "A HIV protein that is cleaved at one or more peptide bonds by a protease to create multiple proteins derived from the precursor." [PubMed:18688235] synonym: "processed" RELATED [PMID:18830418] synonym: "proteolytic cleavage" RELATED [PMID:24755218] xref: Source:GO\:0006508 xref: Source:MOD\:00000 [Term] id: HIV:00007 name: HIV protein domain def: "A HIV protein domain is a conserved part of a given HIV protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded." [http://bioportal.bioontology.org/ontologies/NCIT?p=classes&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C13379] Comment: part_of: HIV:00003 [Term] id: HIV:00008 name: HIV protein sequence motif def: "Signatures of protein families and can often be used as tools for the prediction of protein function." [PMID:8804823] part_of: HIV:00003 [Term] id: HIV:00009 name: HIV minimotif def: "Minimotifs are short peptide sequences which play important roles in many cellular functions." [PMID:19656396] synonym: "HIV protein minimotif." RELATED [PMID:19656396] synonym: "HIV Short Linear Motif" RELATED [PMID:19656396] synonym: "HIV SLiM" RELATED [PMID:19656396] part_of: HIV:00003 [Term] id: HIV:00010 name: HIV long terminal repeat def: "The long terminal repeat (LTR) of the human immunodeficiency virus (HIV) contains the viral promoter, which is responsible for viral gene expression in eukaryotic cells." [http://www.pnas.org/content/86/7/2157.full.pdf] synonym: "LTR" RELATED [http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C13251] part_of: HIV:00038 [Term] id: HIV:00011 name: HIV group def: "Scientists divide HIV types into groups. Each group is believed to represent an independent transmission of SIV into humans." [PMID:22229120] type_of: HIV:00000 [Term] id: HIV:00012 name: HIV subtype def: "Group is subdivided further into subtypes that are designated with a letter." [PMID:7723052] synonym: "HIV clade" RELATED [http://www.projecthalo.com/aura#Clade] type_of: HIV:00011 [Term] id: HIV:00013 name: HIV circulating recombinant form def: "CRFs derived from recombination between viruses of different subtypes which are each given a number." [http://www.avert.org/hiv-types.htm] synonym: "CRF" RELATED [http://www.avert.org/hiv-types.htm] Comment: CRF12_BF, for example, is a recombination between subtypes B and F. [Term] id: HIV:00014 name: HIV protein epitope def: "The simplest form of an antigenic determinant, on a complex antigenic molecule, which can combine with antibody or T cell receptor." [http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C13189] synonym: "antigenic determinant" RELATED [http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C13189] synonym: "binding determinants" RELATED [http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C13189] part_of: HIV:00003 [Term] id: HIV:00015 name: HIV drug binding site def: "The reactive parts of an HIV macromolecule that directly participate in its specific combination with a drug." [http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C13405] part_of: HIV:00003 [Term] id: HIV:00016 name: HIV posttranslational modification def: "The process of covalently altering one or more amino acids in a HIV protein after the protein has been completely translated and released from the ribosome." [GO:0043687] xref: GO:0043687 Comment: Definition adapted from GO. [GO:0043687] Synonym: "HIV post-translational modification"[PMID:20170637] Synonym: "HIV PTM"[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3738961/] part_of: HIV:00003 [Term] id: HIV:00017 name: host protein that interacts with an HIV protein def: "A human protein that binds to an HIV protein or covalently modifies a HIV protein." [PMID:18927109] comment: Definition modified from PMID:18927109. xref: [http://www.ncbi.nlm.nih.gov/projects/RefSeq/HIVInteractions/tat.html\][PMID\:18927109\] [Term] id: HIV:00018 name: host protein that interacts with an HIV RNA def: "A human protein that binds to an HIV RNA or covalently modifies a HIV RNA." [PMID:24554657] [Term] id: HIV:00019 name: host protein required for HIV replication def: "A class of human proteins that are essential for HIV replication, but are not lethal to the host cell when silenced." [PMID:21966263] synonym: "HDF" RELATED [PMID:21966263] synonym: "HIV dependency factor" RELATED [PMID:21966263] [Term] id: HIV:00020 name: HIV protein structure def: "The three-dimensional structure of an HIV protein, part of an HIV protein, or a complex of an HIV protein with another protein. The structure of a protein is characterized in four ways: The primary structure is the order of the different amino acids in a protein chain, whereas the secondary structure consists of the geometry of chain segments in forms such as helices or sheets. The tertiary structure describes how a protein folds in on itself; the quaternary structure of a protein describes how different protein chains hook up with each other." [http://dictionary.reference.com/browse/protein+structure] comment: Definition adapted from website source. xref: FIX:0000327 part_of: HIV:00003 [Term] id: HIV:00021 name: HIV protein structured region def: "Entire HIV proteins or regions that have a fixed tertiary structure." [PMID:24657436] part_of: HIV:00003 [Term] id: HIV:00022 name: HIV unstructured protein def: "Entire HIV proteins or regions of HIV proteins that lack a fixed tertiary structure." [:pondr.com/pondr-tut1.html] comment: Definition and synonyms adapted from sources indicated. synonym: "IDP" RELATED [PMID:24656084] synonym: "Intrinsically disorded proteins" RELATED [PMID:11381529] synonym: "Intrinsically unstructured proteins" RELATED [PMID:15738986] synonym: "IUP" RELATED [PMID:12368089] part_of: HIV:00003 [Term] id: HIV:00023 name: HIV isolate def: "A specific individual microbe and its genetically identical progeny separated on a single occasion from a sample taken from a host or culture system." [http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C53471] synonym: "HIV strain" RELATED [http://www.avert.org/hiv-types.htm] type_of: HIV:00000 [Term] id: HIV:00024 name: HIV protein subcellular localization def: "Any process in which a HIV protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell." [GO:0034613] comment: Definition adapted from GO:0034613. synonym: "cellular protein localisation " RELATED [GO:0034613] synonym: "cellular protein localization " RELATED [GO:0034613] synonym: "PSL" RELATED [PMID:19958518] GO: 0034613 [Term] id: HIV:00025 name: HIV protein-protein interaction def: "Interactions between HIV and human proteins." [http://www.ncbi.nlm.nih.gov/projects/RefSeq/HIVInteractions/index.html, PMID:18927109] comment: Database available at http://www.ncbi.nlm.nih.gov/projects/RefSeq/HIVInteractions/index.html. Definition adapted from PMID:18927109. [Term] id: HIV:00026 name: HIV protein-protein interaction residue synonym: "HIV protein-protein interaction amino acid" RELATED [PMID:23867278] definition: "Amino acids in HIV protein involved in the interactions between HIV and human proteins" [PMID:23702796] part_of: HIV:00003 part_of: HIV:00025 [Term] id: HIV:00027 name: HIV protein sequence feature def: "Regions or sites of interest in the protein sequence. In general this section lists post-translational modifications, binding sites, enzyme active sites, local secondary structure or other characteristics." [http://www.uniprot.org/manual/sequence_annotation] part_of: HIV:00003 [Term] id: HIV:00028 name: HIV drug binding site residue def: "Drugs interact with HIV or host target proteins by bonding at specific binding sites. These binding sites are composed of amino acids that contact the drug which are called drug binding sites residues." [http://www.bio-toolkit.com/HIVTolbox/user_guide] synonym: "HIV drug binding site amino acid" RELATED [http://www.merckmanuals.com/home/drugs/drug_dynamics/drug_action.html] part_of: HIV:00003 part_of: HIV:00015 Adapted from PMID: 24526384 [Term] id: HIV:00029 name: retrovirus def: "Retroviruses from the family Retroviridae are composed of numerous non-icosahedral, enveloped viruses which possess two copies of a single-stranded RNA genome that has a short dimerized region." [http://www.ncbi.nlm.nih.gov/retroviruses/] xref: Source:NEWT\:31931 is_a NCBITaxon: 10239 Adapted from PMCID: PMC3185594 PMID: 10774801 [Term] id: HIV:00030 name: reverse transcription def: "A DNA synthesis process that uses RNA as the initial template for synthesis of DNA, but which also includes an RNase activity to remove the RNA strand of an RNA-DNA heteroduplex produced by the RNA-dependent synthesis step and use of the initial DNA strand as a template for DNA synthesis." [GO:0001171] xref: Source:GO\:0001171 Adapted from PMID: 24525292 [Term] id: HIV:00031 name: provirus integration def: "A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage." [GO:0075713] xref: Source:GO\:0075713 Adapted from PMID: 24492253 [Term] id: HIV:00032 name: pre-integration complex def: "A nucleoprotein complex containing viral genetic material and associated viral and host proteins, which is capable of inserting a viral genome into a host genome." [GO:0019035] xref: Source:GO\:0019035 [Term] id: HIV:00033 name: viral budding def: "A viral process by which enveloped viruses acquire a host-derived membrane enriched in viral proteins to form their external envelope. The process starts when nucleocapsids, assembled or in the process of being built, induce formation of a membrane curvature in the host plasma or organelle membrane and wrap up in the forming bud. The process ends when the bud is eventually pinched off by membrane scission to release the enveloped particle into the lumenal or extracellular space." [GO:0046755] xref: Source:GO\:0046755 Adapted from PMID: 24034610 [Term] id: HIV:00034 name: viral assembly def: "A late phase of the viral life cycle during which all the components necessary for the formation of a mature virion collect at a particular site in the cell and the basic structure of the virus particle is formed." [GO:0019068] xref: Source:GO\:0019068 Adapted from PMID: 24507598 [Term] id: HIV:00035 name: viral envelope fusion def: "Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm." [GO:0019064] xref: Source:GO\:0019064 Adapted from PMID: 24335304 [Term] id: HIV:00036 name: viral maturation def: "The assembly of the component viral parts into an infectious virion." [GO:0019075] xref: Source:GO\:0019075 Adapted from PMID: 24472118 [Term] id: HIV:00037 name: genome def: "The entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of viruses, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA." [PMID:_18258610] [Term] id: HIV:00038 name: HIV genome def: "The entirety of HIV's hereditary information. It is encoded either in DNA as a provirus, or as RNA in the vision and host cell. The genome includes both the genes and the non-coding sequences of the DNA/RNA." [http://www.yale.edu/bio243/HIV/genome.html] is_a: HIV:00037 ! genome Comment: part_of: HIV:00029 [Term] id: HIV:00039 name: HIV RNA structure def: "HIV RNA structure is often divided into four different levels primary, secondary, tertiary and quaternary. Primary structure consists of a linear sequence of nucleotides that are linked together by phosphodiester bonds. It is this linear sequence of nucleotides that make up the primary structure of RNA. Secondary structure is the set of interactions between bases, i.e., parts of which is strands are bound to each other. Tertiary structure is the locations of the atoms in three-dimensional space, taking into consideration geometrical and steric constraints. The quaternary structure of nucleic acids is similar to that of protein quaternary structure. Although some of the concepts are not exactly the same, the quaternary structure refers to a higher-level of organization of RNA. Moreover, it refers to interactions of the nucleic acids with other molecules." [PMID:9430589] is_a: HIV:00037 ! genome is_a: HIV:00042 ! HIV RNA Comment: [Term] id: HIV:00040 name: HIV drug resistance mutation def: "Any mutation in the HIV genome that results in a change the susceptibility of HIV to one ore more antiretroviral drugs." [PMID:24746180] synonym: "DRM" RELATED [http://www.bio-toolkit.com/GoMap/user_guide/] [Term] id: HIV:00041 name: HIV drug resistance mutation type def: "There are six DRM categories of HIV drug resistance mutations(DRMs): (1) A primary DRM causes resistance without any other mutations; (2) A primary set DRM has two or more mutations that cause resistance only in the presence of other primary set mutation(s); (3) A secondary set DRM enhances resistance caused by a primary mutation; (4) A beneficial DRM attenuates/prevents resistance by overriding another mutation that promotes resistance; (5); A beneficial set DRM has two or more mutations that each normally cause resistance, override each other and attenuate/prevent resistance (6) ; and (6) A resistance precursor DRM has no effect on resistance, but must occur prior to another primary or primary set of mutations." [http://www.bio-toolkit.com/GoMap/user_guide/] synonym: "DRM" RELATED [http://www.bio-toolkit.com/GoMap/user_guide/] type_of HIV: 00040 [Term] id: HIV:00042 name: HIV RNA def: "RNA that is transcribed from HIV proviral DNA." [PMID:24753416] part_of: HIV:00038 [Term] id: HIV:00043 name: lentivirus def: "A genus of viruses of the Retroviridae family, characterized by a long incubation period." [PMID:24749361] is_a: HIV:00029 ! retrovirus [Term] id: HIV:00044 name: HIV RNA element def: "A RNA structure found in HIV RNA that plays a role in one or more steps of the replication cycle." [http://dx.doi.org/10.1016/j.chom.2013.01.007] [Term] id: HIV:00045 name: HIV structural protein def: "Protein products of gag, pol, and env genes which are essential components of the retroviral particle." [:LosAlamosHIVSequenceDatabaseCompendium2013] type_of: HIV:00003 [Term] id: HIV:00046 name: HIV regulatory protein def: "Tat and Rev proteins of HIV/SIV. They modulate transcriptional and posttranscriptional steps of virus gene expression and are essential for virus propagation." [:LosAlamosHIVSequenceDatabaseCompendium2013] is_transcribed_and_translated_from: HIV:00037 type_of: HIV:00003 [Term] id: HIV:00047 name: HIV accessory protein def: "Additional virion and non-virion-associated proteins produced by HIV/SIV retroviruses: Vif, Vpr, Vpu, Vpx, Nef. Although the accessory proteins are in general not necessary for viral propagation in tissue culture, they have been conserved in the different isolates; this conservation and experimental observations suggest that their role in vivo is very important. Their functional importance continues to be elucidated." [:LosAlamosHIVSequenceDatabaseCompendium2013] synonym: "HIV auxiliary protein" RELATED [PMID:2202146] is_transcribed_and_translated_from: HIV:00037 type_of: HIV:00003 [Term] id: HIV:00048 name: HIV RNA dimerization def: "The retroviral genome consists of two identical RNA molecules joined at their 5' ends." [PMID:2124274, PMID:22328732] synonym: "HIV dimerization" RELATED [PMID:2124274] [Term] id: HIV:00049 name: viral genome packaging def: "The encapsulation of the viral genome within the capsid." [GO:0019072] synonym: "encapsidation" RELATED [PMID:24688060] synonym: "packaging" RELATED [PMID:24530126] xref: GO:0019072 [Term] id: HIV:00050 name: viral enzyme def: "Products of pol genes, which are essential components of the retroviral particle that catalyze different reactions." [:LosAlamosHIVSequenceDatabaseCompendium2013] is_transcribed_and_translated_from: HIV:00037 type_of: HIV:00003 [Typedef] id: binds_to name: binds_to is_transitive: true [Typedef] id: is_a name: is_a [Typedef] id: is_transcribed_and_translated_from name: is_transcribed_and_translated_from [Typedef] id: is_transcribed_from name: is_transcribed_from [Typedef] id: is_translated_from name: is_translated_from [Typedef] id: part_of name: part_of is_transitive: true [Typedef] id: RO:instance_of name: instance_of is_transitive: true [Instance] id: HIV:00101 name: HIV-1 synonym: "HIV1" RELATED [] synonym: "HTLV-III" RELATED [] synonym: "Human Immunodeficiency Virus 1" RELATED [] synonym: "human immunodeficiency virus 1 HIV-1" RELATED [] synonym: "human immunodeficiency virus HIV-1" RELATED [] synonym: "human immunodeficiency virus type 1" RELATED [] synonym: "human immunodeficiency virus type 1 HIV 1" RELATED [] synonym: "human immunodeficiency virus type 1 HIV-1" RELATED [] synonym: "human immunodeficiency virus type 1 HIV1" RELATED [] synonym: "human immunodeficiency virus type 1, HIV-1" RELATED [] synonym: "human immunodeficiency virus type I HIV-1" RELATED [] synonym: "human immunodeficiency virus type-1 HIV-1" RELATED [] synonym: "human immunodeficiency virus-1 HIV-1" RELATED [] synonym: "LAV" RELATED [] xref: NCBITaxon:11676 instance_of: HIV:00010 property value: host_range human type_of: HIV:00000 [Instance] id: HIV:00102 name: HIV-2 synonym: "HIV2" RELATED [] synonym: "human immunodeficiency virus 1 HIV-2" RELATED [] synonym: "Human Immunodeficiency Virus 2" RELATED [] synonym: "human immunodeficiency virus HIV-2" RELATED [] synonym: "human immunodeficiency virus type 2" RELATED [] synonym: "human immunodeficiency virus type 2 HIV 2" RELATED [] synonym: "human immunodeficiency virus type 2 HIV-2" RELATED [] synonym: "human immunodeficiency virus type 2 HIV2" RELATED [] synonym: "human immunodeficiency virus type 2, HIV-2" RELATED [] synonym: "human immunodeficiency virus type II HIV-2" RELATED [] synonym: "human immunodeficiency virus type-2 HIV-2" RELATED [] synonym: "human immunodeficiency virus-2 HIV-2" RELATED [] xref: NCBITaxon:11709 instance_of: HIV:00010 property value: host_range human type_of: HIV:00000 [Instance] id: HIV:00103 name: HIV-3 synonym: "Human Immunodeficiency Virus 3" RELATED [] synonym: "Human Immunodeficiency Virus type 3" RELATED [] xref: NCBITaxon:35274 instance_of: HIV:00010 property value: host_range human type_of: HIV:00000 [Instance] id: HIV:00104 name: SHIV comment: The SHIV are a molecular construct with part of the genome coming from SIV to allow infection in monkeys, and part of the genome (envelope gene) coming from HIV-1 to study how it changes/mutates in an animal model. synonym: "SIV/HIV" RELATED [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=57667] xref: NCBITaxon:57667 instance_of: HIV:00010 property value: host_range simian, human type_of: HIV:00000 [Instance] id: HIV:00105 name: M namespace: HIV group synonym: "Group M" RELATED [] synonym: "HIV-1 Group M" RELATED [] xref: NCBITaxon:388795 instance_of: HIV:00011 type_of: HIV:00011 [Instance] id: HIV:00106 name: N namespace: HIV group synonym: "Group N" RELATED [] synonym: "HIV-1 Group N" RELATED [] instance_of: HIV:00011 type_of: HIV:00011 [Instance] id: HIV:00107 name: O namespace: HIV group synonym: "Group O" RELATED [] synonym: "HIV-1 Group O" RELATED [] instance_of: HIV:00011 type_of: HIV:00011 [Instance] id: HIV:00108 name: SIV comment: Retroviruses able to infect at least 45 species of African non-human primates, http://en.wikipedia.org/wiki/simian_immunodeficiency_virus. synonym: "Chimpanzee immunodeficiency virus" RELATED [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=11723&lvl=3&lin=f&keep=1&srchmode=1&unlock] synonym: "Chimpanzee immunodeficiency virus (SIV(CPZ))" RELATED [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=11723&lvl=3&lin=f&keep=1&srchmode=1&unlock] synonym: "Simian immunodeficiency virus SIV cps" RELATED [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=11723&lvl=3&lin=f&keep=1&srchmode=1&unlock] synonym: "simian immunodeficiency viruses SIV" RELATED [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=11723&lvl=3&lin=f&keep=1&srchmode=1&unlock] xref: NCBITaxon:11723 type_of: HIV:00029 type_of: HIV:00043 [Instance] id: HIV:01000 name: gag namespace: HIV gene xref: NCBI-Gene:NC_001722.1 xref: NCBI-Gene:NC_001802.1 instance_of: HIV:00001 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 [Instance] id: HIV:01001 name: pol namespace: HIV gene comment: Pol can be made by itself, but is most often made as a gag-pol fusion. xref: NCBI-Gene:NC_001722.1 xref: NCBI-Gene:NC_001802.1 instance_of: HIV:00001 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 part_of: HIV:00037 [Instance] id: HIV:01002 name: gp160 namespace: HIV gene synonym: "env" RELATED [] xref: NCBI-Gene:NC_001722.1 xref: NCBI-Gene:NC_001802.1 instance_of: HIV:00001 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 part_of: HIV:00037 [Instance] id: HIV:01003 name: tat namespace: HIV gene synonym: "p14" RELATED [] xref: NCBI-Gene:NC_001722.1 xref: NCBI-Gene:NC_001802.1 instance_of: HIV:00001 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 part_of: HIV:00037 [Instance] id: HIV:01004 name: rev namespace: HIV gene synonym: "p19" RELATED [] xref: NCBI-Gene:NC_001722.1 xref: NCBI-Gene:NC_001802.1 instance_of: HIV:00001 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 part_of: HIV:00037 [Instance] id: HIV:01005 name: nef namespace: HIV gene synonym: "p27" RELATED [] xref: NCBI-Gene:NC_001722.1 xref: NCBI-Gene:NC_001802.1 instance_of: HIV:00001 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 part_of: HIV:00037 [Instance] id: HIV:01006 name: vpr namespace: HIV gene synonym: "p15" RELATED [] xref: NCBI-Gene:NC_001722.1 xref: NCBI-Gene:NC_001802.1 instance_of: HIV:00001 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 part_of: HIV:00037 [Instance] id: HIV:01007 name: vif namespace: HIV gene synonym: "p23" RELATED [] xref: NCBI-Gene:NC_001722.1 xref: NCBI-Gene:NC_001802.1 instance_of: HIV:00001 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 part_of: HIV:00037 [Instance] id: HIV:01008 name: vpu namespace: HIV gene comment: Vpu is only present in HIV-1 and no other known HIV species. synonym: "p16" RELATED [] xref: NCBI-Gene:NC_001802.1 instance_of: HIV:00001 part_of: HIV:00101 part_of: HIV:00037 [Instance] id: HIV:01009 name: vpx namespace: HIV gene comment: Vpx is only present in HIV-2 and no other known HIV species. synonym: "p16" RELATED [] xref: NCBI-Gene:NC_001722.1 instance_of: HIV:00001 part_of: HIV:00001 part_of: HIV:00037 [Instance] id: HIV:01010 name: group-specific antigen protein namespace: HIV protein comment: Precursor to Matrix, Capsid, Spacer Protein 1, Nucleocapsid, Spacer Protein 2 and P6. synonym: "Gag " RELATED [] synonym: "Gag polyprotein" RELATED [] xref: RefSeq:NP_057849 instance_of: HIV:00003 is_transcribed_and_translated_from: HIV:01000 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 is_transcribed_and_translated_from: HIV:00037 [Instance] id: HIV:01011 name: Pol namespace: HIV protein comment: Pol can be made by itself, but is most often made as a Gag-Pol fusion. synonym: "Pol polyprotein" RELATED [] xref: RefSeq:NP_789740 instance_of: HIV:00003 is_transcribed_and_translated_from: HIV:01001 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 is_transcribed_and_translated_from: HIV:00037 [Instance] id: HIV:01012 name: envelope polyprotein namespace: HIV protein comment: Precursor to GP120 and GP41. synonym: "Env" RELATED [] synonym: "GP160" RELATED [] xref: RefSeq:NP_057856 instance_of: HIV:00003 is_transcribed_and_translated_from: HIV:01002 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 is_transcribed_and_translated_from: HIV:00037 [Instance] id: HIV:01013 name: envelope glycoprotein 120 namespace: HIV protein comment: Is derived from GP160. synonym: " GP120" RELATED [] synonym: "GP120 surface" RELATED [] xref: RefSeq:NP_0579894 instance_of: HIV:00006 is_transcribed_and_translated_from: HIV:01002 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 is_transcribed_and_translated_from: HIV:00037 [Instance] id: HIV:01014 name: envelope glycoprotein 41 namespace: HIV protein comment: Is derived from GP160. synonym: " GP41" RELATED [] synonym: "GP41 transmembrane" RELATED [] xref: RefSeq:NP_0579895 instance_of: HIV:00006 is_transcribed_and_translated_from: HIV:01002 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 is_transcribed_and_translated_from: HIV:00037 [Instance] id: HIV:01015 name: transactivating regulatory protein namespace: HIV protein synonym: "p14" RELATED [] synonym: "p14/p16" RELATED [] synonym: "p16" RELATED [] synonym: "Tat " RELATED [] synonym: "Tat protein p14/p16" RELATED [] xref: RefSeq:NP_057853 instance_of: HIV:00003 is_transcribed_and_translated_from: HIV:01003 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 is_transcribed_and_translated_from: HIV:00037 [Instance] id: HIV:01016 name: Rev namespace: HIV protein synonym: "anti-repression transactivator protein" RELATED [] synonym: "p19" RELATED [] synonym: "Rev protein" RELATED [] synonym: "Rev protein (p19)" RELATED [] xref: RefSeq:NP_057854 instance_of: HIV:00003 is_transcribed_and_translated_from: HIV:01004 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 is_transcribed_and_translated_from: HIV:00037 [Instance] id: HIV:01017 name: negative factor namespace: HIV protein synonym: "Nef" RELATED [] synonym: "Nef protein (p27/p25)" RELATED [] synonym: "p25" RELATED [] synonym: "p27" RELATED [] synonym: "p27/p25" RELATED [] xref: RefSeq:NP_057857 instance_of: HIV:00003 is_transcribed_and_translated_from: HIV:01005 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 is_transcribed_and_translated_from: HIV:00037 [Instance] id: HIV:01018 name: viral protein r namespace: HIV protein synonym: "p10" RELATED [] synonym: "p12" RELATED [] synonym: "p12/p10" RELATED [] synonym: "Vpr" RELATED [] xref: RefSeq:NP_057852 instance_of: HIV:00003 is_transcribed_and_translated_from: HIV:01006 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 is_transcribed_and_translated_from: HIV:00037 [Instance] id: HIV:01019 name: viral infectivity factor namespace: HIV protein synonym: "p23" RELATED [] synonym: "Vif" RELATED [] synonym: "Vif protein (p23)" RELATED [] xref: RefSeq:NP_057851 instance_of: HIV:00003 is_transcribed_and_translated_from: HIV:01007 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 is_transcribed_and_translated_from: HIV:00037 [Instance] id: HIV:01020 name: viral protein u namespace: HIV protein comment: Vpu is only present in HIV-1 and no other known HIV species. synonym: " Vpu" RELATED [] synonym: "p16" RELATED [] synonym: "Vpu protein (p16)" RELATED [] xref: RefSeq:NP_057855 instance_of: HIV:00003 is_transcribed_and_translated_from: HIV:01008 part_of: HIV:00000 is_transcribed_and_translated_from: HIV:00037 [Instance] id: HIV:01021 name: Vpx namespace: HIV protein comment: Vpx is only present in HIV-2 and no other known HIV species. synonym: "p16" RELATED [] synonym: "viral protein x" RELATED [] synonym: "vpx protein" RELATED [] instance_of: HIV:00006 is_transcribed_and_translated_from: HIV:01009 part_of: HIV:00102 is_transcribed_and_translated_from: HIV:00037 [Instance] id: HIV:01022 name: Capsid namespace: HIV protein comment: Derived from Gag or Gag-Pol. synonym: "CA" RELATED [] synonym: "capsid protein" RELATED [] synonym: "core antigen capsid protein" RELATED [] synonym: "p24" RELATED [] synonym: "p24 core antigen" RELATED [] xref: RefSeq:NP_579880 instance_of: HIV:00006 is_transcribed_and_translated_from: HIV:01000 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 is_transcribed_and_translated_from: HIV:00037 [Instance] id: HIV:01023 name: spacer protein 1 namespace: HIV protein comment: Derived from Gag or Gag-Pol. synonym: "p1" RELATED [] synonym: "p1 Gag protein" RELATED [] xref: RefSeq:NP_787042 instance_of: HIV:00006 is_transcribed_and_translated_from: HIV:01000 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 is_transcribed_and_translated_from: HIV:00037 [Instance] id: HIV:01024 name: spacer protein 2 namespace: HIV protein comment: Derived from Gag or Gag-Pol. synonym: "p2" RELATED [] synonym: "p2 Gag protein" RELATED [] xref: RefSeq:NP_579882 instance_of: HIV:00006 is_transcribed_and_translated_from: HIV:01000 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 is_transcribed_and_translated_from: HIV:00037 [Instance] id: HIV:01025 name: p6 namespace: HIV protein comment: Derived from Gag or Gag-Pol. synonym: "p6 Gag protein" RELATED [] synonym: "p6 Vpr binding protein" RELATED [] xref: RefSeq:NP_579883 instance_of: HIV:00006 is_transcribed_and_translated_from: HIV:01000 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 is_transcribed_and_translated_from: HIV:00037 [Instance] id: HIV:01026 name: Nucleocapsid namespace: HIV protein comment: Derived from a frameshift protein transcribed and translated from the Gag-Pol polyprotein. synonym: "NC" RELATED [] synonym: "P7" RELATED [] synonym: "P7 nucleo-capsid protein" RELATED [] synonym: "P7 nucleocapsid" RELATED [] xref: RefSeq:NP_579881 instance_of: HIV:00006 is_transcribed_and_translated_from: HIV:01000 is_transcribed_and_translated_from: HIV:01001 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 is_transcribed_and_translated_from: HIV:00037 [Instance] id: HIV:01027 name: Protease namespace: HIV protein comment: Derived from Gag or Gag-Pol. synonym: "p10" RELATED [] synonym: "PR" RELATED [] synonym: "retropepsin" RELATED [] xref: RefSeq:NP_705926 instance_of: HIV:00006 is_transcribed_and_translated_from: HIV:01001 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 is_transcribed_and_translated_from: HIV:00037 [Instance] id: HIV:01028 name: Reverse Transcriptase namespace: HIV protein comment: Derived from Gag or Gag-Pol. synonym: "p51" RELATED [] synonym: "p51 reverse transcriptase" RELATED [] synonym: "RT" RELATED [] xref: RefSeq:NP_789739 instance_of: HIV:00006 is_transcribed_and_translated_from: HIV:01001 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 is_transcribed_and_translated_from: HIV:00037 [Instance] id: HIV:01029 name: p66 namespace: HIV protein comment: Derived from Gag or Gag-Pol. synonym: "p66 RT+RNaseH" RELATED [] synonym: "Reverse Transcriptase + RNaseH" RELATED [] synonym: "RT+RNaseH" RELATED [] xref: RefSeq:NP_705927 instance_of: HIV:00006 is_transcribed_and_translated_from: HIV:01001 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 is_transcribed_and_translated_from: HIV:00037 [Instance] id: HIV:01030 name: Integrase namespace: HIV protein comment: Derived from Gag or Gag-Pol. synonym: "IN" RELATED [] synonym: "p31" RELATED [] synonym: "p31 integrase" RELATED [] xref: RefSeq:NP_705928 instance_of: HIV:00006 is_transcribed_and_translated_from: HIV:01001 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 is_transcribed_and_translated_from: HIV:00037 [Instance] id: HIV:01031 name: Matrix namespace: HIV protein comment: Derived from gag or gag-pol. synonym: "MA" RELATED [] synonym: "Matrix protein" RELATED [] synonym: "p17" RELATED [] xref: RefSeq:NP_579876 instance_of: HIV:00006 is_transcribed_and_translated_from: HIV:01000 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 is_transcribed_and_translated_from: HIV:00037 [Instance] id: HIV:01032 name: rev responsive element comment: A high affinity site for Rev protein binding. synonym: "RRE" RELATED [] instance_of: HIV:00039 part_of: HIV:00042 part_of: HIV:00038 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 binds_to: HIV:01016 [Instance] id: HIV:01033 name: psi element comment: Regions recognized by HIV NC protein binding. synonym: "encapsidation signal" RELATED [] synonym: "packaging signal" RELATED [] synonym: "PE" RELATED [] instance_of: HIV:00039 part_of: HIV:00042 part_of: HIV:00038 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 [Instance] id: HIV:01034 name: slippery sequence comment: A TTTTTT slippery site followed by a stem-loop structure, responsible for regulating the -1 ribosomal frameshift out of the Gag reading frame into the Pol reading frame. synonym: "SLIP" RELATED [] instance_of: HIV:00039 part_of: HIV:00042 part_of: HIV:00038 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 [Instance] id: HIV:01035 name: primer binding site comment: Site to which tRNA binds to initiate reverse transcription. synonym: "PBS" RELATED [] instance_of: HIV:00039 part_of: HIV:00042 part_of: HIV:00038 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 [Instance] id: HIV:01036 name: polyadenylation site synonym: "Poly A addition signal" RELATED [] synonym: "Poly A site" RELATED [] instance_of: HIV:00039 part_of: HIV:00042 part_of: HIV:00038 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 [Instance] id: HIV:01037 name: dimer linkage structure comment: Partial structures within DLS, such as SL1, 2, 3 and 4, have been solved. synonym: "dimer initiation site" RELATED [PMID:22328732] synonym: "DIS" RELATED [PMID:22328732] synonym: "DIS/DLS" RELATED [PMID:22328732] synonym: "DLS" RELATED [PMID:22328732] instance_of: HIV:00039 Definition: "The 5′ region of both viral RNAs contains a primary contact point and is referred to as the dimer linkage structures (DLS)." [PMID:22328732] part_of: HIV:00042 part_of: HIV:00038 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 [Instance] id: HIV:01038 name: stem loop 4 comment: Involved in dimerization of HIV genomic RNAs. synonym: "SL1" RELATED [PMID:22328732] synonym: "SL2" RELATED [PMID:22328732] synonym: "SL4" RELATED [PMID:22328732] instance_of: HIV:00039 part_of: HIV:00042 part_of: HIV:00038 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 part_of: HIV:01037 part_of: HIV:00042 part_of: HIV:00038 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 part_of: HIV:01037 part_of: HIV:00042 part_of: HIV:00038 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 part_of: HIV:01037 part_of: HIV:00042 part_of: HIV:00038 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104 part_of: HIV:01037 [Instance] id: HIV:01039 name: transactivation response element comment: Binding site for Tat protein and other cellular proteins. synonym: "TAR" RELATED [] instance_of: HIV:00039 part_of: HIV:00042 part_of: HIV:00010 part_of: HIV:00038 part_of: HIV:00000 part_of: HIV:00101 part_of: HIV:00102 part_of: HIV:00103 part_of: HIV:00104