Viral genome integration

Many viruses are able to insert their genetic material into host chromosomes. Three kind of integration exist:

Mandatory integration

Viruses for which this is an obligatory event during viral replication. This is the cases for the retroviridae, pseudoviridae, metaviridae, some myoviridae and siphoviridae. Integration of the viral DNA results in permanent insertion of the viral genome into the host chromosomal DNA, referred as a provirus in the case of retroviruses or prophage in the case of prokaryotic viruses.

Occasional integration

This kind of integration is not necessary for virus replication, but confers some advantages to the host/virus couple. It can facilitate long term asymptomatic infection of cells (latency),and also provide an advantage to the host cell. Many bacterial toxines are carried out by prophages for example.

Endogenous viral elements (EVE)

Viruses integrated long time ago and “fossilized” into a host genome, through a rare and sometimes accidental process. There are two kinds of endogenous viruses: endogenous retroviruses, and rare RNA virus integration.

Endogenous retro-viruses: Integrated viral genome can remain latent and be passively replicated along with the host genome and passed on to the cell’s offspring. Host’s environmental condition changes can however reactivate the virus leading to viral transcription and production of new infectious viruses (productive infection).
Retrovirus genomes that become integrated in the germline are referred as endogenous retroviruses (ERV) to distinguish them from horizontally transmitted, not passed on to host progeny, termed “exogenous” retroviruses. Hepadnaviridae have ben found also integrated inhost genome, notably in plants

Endogenous ssDNA viruses: SsDNA viruses like circoviridae which don’t encode for an integrase have been found integrated in many genomes. It can happen also in plants: Geminivirus genome have been found in the tobacco genome.

Rare RNA virus integration:dsRNA, ssRNA(+) and ssRNA(-) viruses do not get reverse transcribed and are unable to integrate in host genome. Still Arenavirus reverse-transcribed genome has been detected in mice. Also Bornaviridae, filoviridae and Totiviridae sequences have been found integrated into several mammalian genome, and Rhabdoviridae in insect genomes indicating tat this event can occur although it’s very rare.

Matching UniProtKB/Swiss-Prot entries

135 entries grouped by protein (browse by keywords)

All proteins are shown (view only 83 complete proteome entries)

Putative integrase


INTG_BPPF1Pseudomonas phage Pf1 (Bacteriophage Pf1) reference strain

Gag-Pol polyprotein (Pr160Gag-Pol)

Select_all Deselect_all  
POL_RSVSAAvian leukosis virus RSA (RSV-SRA) (Rous sarcoma virus (strain Schmidt-Ruppin ... reference strain

Gag-Pro-Pol polyprotein

POL_FFVFeline foamy virus (FFV) (Feline syncytial virus) reference strain

Pro-Pol polyprotein (Pr125Pol)

POL_HV1MAHuman immunodeficiency virus type 1 group M subtype A (isolate MAL) (HIV-1) reference strain
POL_HV1B1Human immunodeficiency virus type 1 group M subtype B (isolate BH10) (HIV-1) reference strain

pdb 1A9M  1AJV  1AJX  1AXA  1BQM  1BQN  1D4H  1D4I  1D4J  1DLO  1DW6  1EBK  1EBW  1EBY  1EBZ  1EC0  1EC1  1EC2  1EC3  1EET  1G35  1GNM  1GNN  1GNO  1HAR  1HBV  1HEF  1HEG  1HIH  1HMV  1HNI  1HNV  1HOS  1HPS  1HPZ  1HQE  1HQU  1HRH  1HTE  1HTF  1HTG  1HVI  1HVK  1HVP  1HVU  1HYS  1IKV  1IKW  1IKX  1IKY  1J5O  1KJH  1MER  1MES  1MET  1MEU  1N5Y  1N6Q  1NPA  1NPV  1NPW  1QE1  1QMC  1R0A  1RDH  1RTD  1RVL  1RVM  1RVN  1RVO  1RVP  1RVQ  1RVR  1S6P  1S6Q  1S9E  1S9G  1SBG  1SUQ  1SV5  1T03  1T05  1T7K  1TV6  1TVR  1UWB  1W5V  1W5W  1W5X  1W5Y  1YT9  1ZP8  1ZPA  1ZSF  1ZSR  2AQU  2B5J  2B6A  2BAN  2BBB  2BE2  2EXF  2G69  2HB3  2HMI  2HNZ  2HS1  2HS2  2I4D  2I4U  2I4V  2I4W  2I4X  2I5J  2IAJ  2IC3  2IDW  2IEO  2JZW  2L45  2L46  2L4L  2UXZ  2UY0  2VG5  2VG6  2VG7  2X4U  2YKM  2YKN  2ZD1  2ZE2  3AVI  3BGR  3DLK  3GGA  3GGV  3GGX  3HVT  3IG1  3IRX  3IS9  3ISN  3ITH  3JSM  3JYT  3K2P  3K4V  3KLE  3KLF  3KLG  3KLH  3KLI  3NDT  3NU3  3NU4  3NU5  3NU6  3NU9  3NUJ  3NUO  3OK9  3PSU  3QAA  3QLH  3QO9  3TKG  3TKW  3TL9  3TLH  3V4I  3V6D  3V81  3ZPS  3ZPT  3ZPU  4COE  4CP7  4CPQ  4CPR  4CPS  4CPT  4CPU  4CPW  4CPX  4DG1  4G1Q  4G8G  4G8I  4G9D  4G9F  4H4M  4H4O  4I2P  4I2Q  4ICL  4ID5  4IDK  4IFV  4IFY  4IG0  4IG3  4KFB  4KKO  4KO0  4LSL  4LSN  4MFB  4O44  4O4G  4OJR  4PQU  4PUO  4PWD  4Q0B  4QAG  4R5P  4RW4  4RW6  4RW7  4RW8  4RW9  4U8W  4WE1  4YE3  4YHQ  4ZIP  4ZLS  5AGZ  5AH6  5AH7  5AH8  5AH9  5AHA  5AHB  5AHC  5BRY  5BS4  5C24  5C25  5C42  5CYM  5CYQ  5D3G  5FDL  5HBM  5HLF  5HP1  5HRO  5I3U  5I42  5J1E  5JFP  5JFU  5JG1  5TEP  5TER 

POL_HV1BRHuman immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI) (HIV-1) reference strain
POL_HV1H2Human immunodeficiency virus type 1 group M subtype B (isolate HXB2) (HIV-1) reference strain
POL_HV193Human immunodeficiency virus type 1 group M subtype F1 (isolate 93BR020) (HIV-1) reference strain
POL_HV1VIHuman immunodeficiency virus type 1 group M subtype F1 (isolate VI850) (HIV-1) reference strain
POL_HV1ANHuman immunodeficiency virus type 1 group O (isolate ANT70) (HIV-1) reference strain
POL_HV1MVHuman immunodeficiency virus type 1 group O (isolate MVP5180) (HIV-1) reference strain
POL_HV2BEHuman immunodeficiency virus type 2 subtype A (isolate BEN) (HIV-2) reference strain
POL_FOAMVHuman spumaretrovirus (SFVcpz(hu)) (Human foamy virus) reference strain

Pro-Pol polyprotein (Pr125Pol)

POL_HTL1CHuman T-cell leukemia virus 1 (isolate Caribbea HS-35 subtype A) (HTLV-1) reference strain

Gag-Pro-Pol polyprotein (Pr160Gag-Pro-Pol)

POL_HTLV2Human T-cell leukemia virus 2 (HTLV-2) reference strain

Gag-Pro-Pol polyprotein (Pr160Gag-Pro-Pol)

POL_HTL32Human T-cell leukemia virus 3 (strain 2026ND) (HTLV-3) reference strain

Gag-Pro-Pol polyprotein (Pr160Gag-Pro-Pol)

POL_MLVMSMoloney murine leukemia virus (isolate Shinnick) (MoMLV) reference strain

Gag-Pol polyprotein (Pr180gag-pol)

POL_MMTVCMouse mammary tumor virus (strain C3H) (MMTV) reference strain

Gag-Pro-Pol polyprotein

POL_SFVCPSimian foamy virus (isolate chimpanzee) (SFVcpz) reference strain

Pro-Pol polyprotein (Pr125Pol)

POL_SFV1Simian foamy virus type 1 (SFVmac) (SFV-1) reference strain

Pro-Pol polyprotein (Pr125Pol)

POL_SIVEKSimian immunodeficiency virus (isolate EK505) (SIV-cpz) (Chimpanzee ... reference strain
POL_SIVMBSimian immunodeficiency virus (isolate MB66) (SIV-cpz) (Chimpanzee ... reference strain
POL_SIVTNSimian immunodeficiency virus (isolate TAN1) (SIV-cpz) (Chimpanzee ... reference strain
POL_XMRV6Xenotropic MuLV-related virus (isolate VP62) (XMRV) reference strain

Gag-Pol polyprotein (Pr180gag-pol)

POL_MLVAVAKV murine leukemia virus (AKR (endogenous) murine leukemia virus)

Pol polyprotein

POL_ALVAvian leukosis virus (ALV)

Pol polyprotein

POL_BAEVMBaboon endogenous virus (strain M7)

Pol polyprotein

POL_BIV29Bovine immunodeficiency virus (strain R29) (BIV) (Bovine immunodeficiency-like ...

Gag-Pol polyprotein (Pr170Gag-Pol)

POL_BLVAUBovine leukemia virus (isolate Australian) (BLV)

Pol polyprotein

POL_BLVJBovine leukemia virus (isolate Japanese BLV-1) (BLV)

Pol polyprotein

POL_CAEVCCaprine arthritis encephalitis virus (strain Cork) (CAEV-Co)

Pol polyprotein

POL_EIAV9Equine infectious anemia virus (isolate 1369) (EIAV)

Pol polyprotein

POL_EIAVCEquine infectious anemia virus (isolate CL22) (EIAV)

Pol polyprotein

POL_EIAVYEquine infectious anemia virus (strain Wyoming) (EIAV)

Pol polyprotein

POL_FIVPEFeline immunodeficiency virus (isolate Petaluma) (FIV)

Pol polyprotein

POL_FIVT2Feline immunodeficiency virus (isolate TM2) (FIV)

Pol polyprotein

POL_FIVSDFeline immunodeficiency virus (strain San Diego) (FIV)

Pol polyprotein

POL_MLVF5Friend murine leukemia virus (isolate 57) (FrMLV)

Pol polyprotein

POL_MLVFFFriend murine leukemia virus (isolate FB29) (FrMLV)

Pol polyprotein

POL_MLVFPFriend murine leukemia virus (isolate PVC-211) (FrMLV)

Pol polyprotein

POL_GALVGibbon ape leukemia virus (GALV)

Pol polyprotein

POL_IPHAHamster intracisternal a-particle H18 (IAP-H18)

Putative Pol polyprotein

POL_HV1U4Human immunodeficiency virus type 1 group M subtype A (isolate U455) (HIV-1)
POL_HV1A2Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2) (HIV-1)
POL_HV1B5Human immunodeficiency virus type 1 group M subtype B (isolate BH5) (HIV-1)
POL_HV1JRHuman immunodeficiency virus type 1 group M subtype B (isolate JRCSF) (HIV-1)
POL_HV1LWHuman immunodeficiency virus type 1 group M subtype B (isolate LW123) (HIV-1)
POL_HV1MNHuman immunodeficiency virus type 1 group M subtype B (isolate MN) (HIV-1)
POL_HV1N5Human immunodeficiency virus type 1 group M subtype B (isolate NY5) (HIV-1)
POL_HV1OYHuman immunodeficiency virus type 1 group M subtype B (isolate OYI) (HIV-1)
POL_HV1RHHuman immunodeficiency virus type 1 group M subtype B (isolate RF/HAT3) (HIV-1)
POL_HV1Y2Human immunodeficiency virus type 1 group M subtype B (isolate YU-2) (HIV-1)
POL_HV1B9Human immunodeficiency virus type 1 group M subtype B (strain 89.6) (HIV-1)
POL_HV192Human immunodeficiency virus type 1 group M subtype C (isolate 92BR025) (HIV-1)
POL_HV1ETHuman immunodeficiency virus type 1 group M subtype C (isolate ETH2220) (HIV-1)
POL_HV1ELHuman immunodeficiency virus type 1 group M subtype D (isolate ELI) (HIV-1)
POL_HV1NDHuman immunodeficiency virus type 1 group M subtype D (isolate NDK) (HIV-1)
POL_HV1Z2Human immunodeficiency virus type 1 group M subtype D (isolate Z2/CDC-Z34) ...
POL_HV1MPHuman immunodeficiency virus type 1 group M subtype F2 (isolate MP255) (HIV-1)
POL_HV1M2Human immunodeficiency virus type 1 group M subtype F2 (isolate MP257) (HIV-1)
POL_HV19NHuman immunodeficiency virus type 1 group M subtype G (isolate 92NG083) (HIV-1)
POL_HV1SEHuman immunodeficiency virus type 1 group M subtype G (isolate SE6165) (HIV-1)
POL_HV190Human immunodeficiency virus type 1 group M subtype H (isolate 90CF056) (HIV-1)
POL_HV1V9Human immunodeficiency virus type 1 group M subtype H (isolate VI991) (HIV-1)
POL_HV1S9Human immunodeficiency virus type 1 group M subtype J (isolate SE9173) (HIV-1)
POL_HV1S2Human immunodeficiency virus type 1 group M subtype J (isolate SE9280) (HIV-1)
POL_HV196Human immunodeficiency virus type 1 group M subtype K (isolate 96CM-MP535) ...
POL_HV197Human immunodeficiency virus type 1 group M subtype K (isolate 97ZR-EQTB11) ...
POL_HV1YBHuman immunodeficiency virus type 1 group N (isolate YBF106) (HIV-1)
POL_HV1YFHuman immunodeficiency virus type 1 group N (isolate YBF30) (HIV-1)
POL_HV2CAHuman immunodeficiency virus type 2 subtype A (isolate CAM2) (HIV-2)
POL_HV2D1Human immunodeficiency virus type 2 subtype A (isolate D194) (HIV-2)
POL_HV2G1Human immunodeficiency virus type 2 subtype A (isolate Ghana-1) (HIV-2)
POL_HV2KRHuman immunodeficiency virus type 2 subtype A (isolate KR) (HIV-2)
POL_HV2NZHuman immunodeficiency virus type 2 subtype A (isolate NIH-Z) (HIV-2)
POL_HV2ROHuman immunodeficiency virus type 2 subtype A (isolate ROD) (HIV-2)
POL_HV2SBHuman immunodeficiency virus type 2 subtype A (isolate SBLISY) (HIV-2)
POL_HV2STHuman immunodeficiency virus type 2 subtype A (isolate ST) (HIV-2)
POL_HV2D2Human immunodeficiency virus type 2 subtype B (isolate D205) (HIV-2)
POL_HV2EHHuman immunodeficiency virus type 2 subtype B (isolate EHO) (HIV-2)
POL_HV2UCHuman immunodeficiency virus type 2 subtype B (isolate UC1) (HIV-2)
POL_HTL1LHuman T-cell leukemia virus 1 (isolate Melanesia mel5 subtype C) (HTLV-1)

Gag-Pro-Pol polyprotein (Pr160Gag-Pro-Pol)

POL_HTL1AHuman T-cell leukemia virus 1 (strain Japan ATK-1 subtype A) (HTLV-1)

Gag-Pro-Pol polyprotein (Pr160Gag-Pro-Pol)

POL_HTL3PHuman T-cell leukemia virus 3 (strain Pyl43) (HTLV-3)

Gag-Pro-Pol polyprotein (Pr160Gag-Pro-Pol)

POL_JEMBRJembrana disease virus (JDV)

Gag-Pol polyprotein (Pr170Gag-Pol)

POL_KORVKoala retrovirus (KoRV)

Pro-Pol polyprotein (Pr125Pol)

POL_VILV1Maedi visna virus (strain 1514 / clone LV1-1KS1) (MVV) (Visna lentivirus)

Pol polyprotein

POL_VILV2Maedi visna virus (strain 1514 / clone LV1-1KS2) (MVV) (Visna lentivirus)

Pol polyprotein

POL_VILVMaedi visna virus (strain 1514) (MVV) (Visna lentivirus)

Pol polyprotein

POL_VILVKMaedi visna virus (strain KV1772) (MVV) (Visna lentivirus)

Pol polyprotein

POL_MPMVMason-Pfizer monkey virus (MPMV) (Simian Mason-Pfizer virus)

Pol polyprotein

POL_IPMAIMouse intracisternal a-particle IL3 (IAP-IL3)

Probable Pol polyprotein

POL_IPMAMouse intracisternal a-particle MIA14 (IAP-MIA14)

Putative Pol polyprotein

POL_MMTVBMouse mammary tumor virus (strain BR6) (MMTV)

Pol polyprotein

POL_OMVVSOvine maedi visna related virus (strain South Africa) (SA-OMVV) (Ovine ...

Pol polyprotein

POL_MLVRDRadiation murine leukemia virus

Pol polyprotein

POL_RSVPRous sarcoma virus (strain Prague C) (RSV-PrC)

Gag-Pro-Pol polyprotein

POL_RSVSBRous sarcoma virus (strain Schmidt-Ruppin B) (RSV-SRB)

Gag-Pro-Pol polyprotein

POL_JSRVSheep pulmonary adenomatosis virus (Jaagsiekte sheep retrovirus) (JSRV)

Pol polyprotein

POL_SFV3LSimian foamy virus type 3 (strain LK3) (SFVagm) (SFV-3)

Pro-Pol polyprotein (Pr125Pol)

POL_SIVCZSimian immunodeficiency virus (isolate CPZ GAB1) (SIV-cpz) (Chimpanzee ...
POL_SIVS4Simian immunodeficiency virus (isolate F236/smH4) (SIV-sm) (Simian ...
POL_SIVGBSimian immunodeficiency virus (isolate GB1) (SIV-mnd) (Simian immunodeficiency ...
POL_SIVMKSimian immunodeficiency virus (isolate K6W) (SIV-mac) (Simian immunodeficiency ...
POL_SIVM1Simian immunodeficiency virus (isolate Mm142-83) (SIV-mac) (Simian ...
POL_SIVSPSimian immunodeficiency virus (isolate PBj14/BCL-3) (SIV-sm) (Simian ...
POL_SIVG1Simian immunodeficiency virus agm.grivet (isolate AGM gr-1) (SIV-agm.gri) ...
POL_SIVVTSimian immunodeficiency virus agm.vervet (isolate AGM TYO-1) (SIV-agm.ver) ...
POL_SIVV1Simian immunodeficiency virus agm.vervet (isolate AGM155) (SIV-agm.ver) (Simian ...
POL_SIVVGSimian immunodeficiency virus agm.vervet (isolate AGM3) (SIV-agm.ver) (Simian ...
POL_SRV1Simian retrovirus SRV-1

Pol polyprotein

POL_SRV2Simian retrovirus SRV-2

Pol polyprotein

POL_SMRVHSquirrel monkey retrovirus (SMRV-H) (SMRV-HLB)

Pol polyprotein

POL_XMRV3Xenotropic MuLV-related virus (isolate VP35) (XMRV)

Gag-Pol polyprotein (Pr180gag-pol)

POL_XMRV4Xenotropic MuLV-related virus (isolate VP42) (XMRV)

Gag-Pol polyprotein (Pr180gag-pol)

Putative integrase V10


V10_SPTNKSputnik virophage reference strain

Integrase (EC 2.7.7.-) (EC 3.1.-.-)

Select_all Deselect_all  
VINT_BPL2Acholeplasma phage L2 (Bacteriophage L2) reference strain

Probable integrase/recombinase (EC 2.7.7.-) (EC 3.1.-.-) (ORF5)

VINT_BPP4Enterobacteria phage P4 (Bacteriophage P4) reference strain
VINT_BP186Escherichia phage 186 (Bacteriophage 186) reference strain
VINT_LAMBDEscherichia phage lambda (Bacteriophage lambda) reference strain
VINT_BPP2Escherichia phage P2 (Bacteriophage P2) reference strain
VINT_FRG3GFrog virus 3 (isolate Goorha) (FV-3) reference strain

Integrase homolog

VINT_BPHC1Haemophilus phage HP1 (strain HP1c1) (Bacteriophage HP1) reference strain
VINT_BPMD2Mycobacterium phage D29 (Mycobacteriophage D29) reference strain
VINT_BPML5Mycobacterium phage L5 (Mycobacteriophage L5) reference strain
VINT_BPP22Salmonella phage P22 (Bacteriophage P22) reference strain
VINT_SSV1Sulfolobus spindle-shape virus 1 (SSV1) reference strain
VINT_BP434Enterobacteria phage 434 (Bacteriophage 434)
VINT_BPP21Enterobacteria phage P21 (Bacteriophage 21) (Bacteriophage P21)
VINT_BPPH8Enterobacteria phage phi80 (Bacteriophage phi-80)
VINT_BPHK0Escherichia phage HK022 (Bacteriophage HK022)
VINT_BPMFRMycobacterium phage FRAT1 (Mycobacteriophage FRAT1)
VINT_BPSFVShigella phage Sf6 (Shigella flexneri bacteriophage VI) (Bacteriophage SfVI)
VINT_BPL54Staphylococcus phage L54a (Bacteriophage L54a)

Putative integrase ORF241


Y241_ATVAcidianus two-tailed virus (ATV) reference strain