HERV-K-HML5 Reference Sequence and Metadata

Clade II > Betaretrovirus Group > Archaeobeta Subgroup

Description

ERV-2.Beta.K5 (HERV-K-HML5) is an ancient lineage of betaretroviruses belonging to the broader HERV-K radiation. Among the HERV-K groups identified in primate genomes, HML-5 is notable for its great evolutionary age and is thought to represent the oldest known betaretrovirus lineage preserved in the primate germ line.

Comparative analyses indicate that HML-5 became established in ancestral primates approximately 55 million years ago, before the evolutionary split between New World and Old World monkeys. Consistent with this antiquity, related elements have been identified in a wide range of simian primates but are absent from more distantly related prosimians. These observations suggest that the exogenous viruses that gave rise to HML-5 circulated during an early phase of primate evolution and subsequently became extinct.

Unlike the younger HML-2 lineage, which remained active during relatively recent stages of human evolution, HML-5 appears to have experienced a comparatively brief period of expansion followed by long-term evolutionary inactivity. Most HML-5 loci in the human genome are highly degraded and contain characteristic deletions affecting portions of the viral gag-pro and env genes. Nevertheless, reconstruction of a consensus sequence indicates that the ancestral virus possessed the canonical retroviral gag, pro, pol and env gene complement.

Phylogenetic analyses suggest that HML-5 forms a distinct branch within the HERV-K radiation. The lineage is associated with several related LTR families and displays evidence of internal diversification during its period of activity. Interestingly, studies of the primer binding site indicate that HML-5 may have utilised methionine tRNA rather than lysine tRNA to initiate reverse transcription, leading some authors to propose that the lineage should be designated "HERV-M". Despite this observation, the historical HML-5 designation remains the most widely used name in the literature.

The HML-5 lineage provides a rare glimpse into an early chapter of primate retrovirus evolution. As one of the oldest betaretroviral groups represented in the human genome, it helps illuminate the diversity of retroviruses that circulated in ancestral primates long before the emergence of the younger HERV-K lineages that dominate much of the modern literature.

Phylogenetic Classification

  • Classification: Clade II > Genus Betaretrovirus > Subgenus Archaeobeta
  • Lineage Age: Not Available

Alternative Classifications

  • Retrotector: hml5
  • Repbase: HERVK22

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Loci Associated with HERV-K-HML5

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Genes and Features

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Feature Sequences

TAACCAGGTGGGAAACTTCATGAGGGGCCGGCCCCAGGCCCCGCTCCAAACTGGGGCAATGCCAGCGGCTTTCCTCGGTCAGATGGAAAGCCCACAGTCCTCTCTCTCAGAGCAGCCACCACTGGGAGCGCAGGACTGGACTTACTCTGCCCCAACAAATTAGTGCTAAAAGAAGGAGAAGACCCTAAAAGGGTTGCAACTGGGATCTGGGGCCCACTGCCTCTGGGAACAGTGGGATTAGTCCTAGGGCGATCAAGCCTATCCAGTAAAGGAATTAATGTGCTCACTGGGGTAATTGATAGTGATTATCAAGGTGAGATATTAGTTATGATGGAATGTAAAGGTCTGCATATTCTTCCCCCTGGATCAAAGATAGCTCAGTTACTGCTTTTACCATACTGGGTCCCCAATGCCCATGGAAAGGAAAGGGGAAAGGGAAGTTTTGGAAGCACAGGAGCCACAGGAGTATATTGGAATCAATTAATCACTGATCAGAGACCCATGATTACCTTAAAAATTGGAAATAAGAATTTTACTGGCTTATTGGACACAGGGGTGGACATTTCAATCATTAGTGATCAAAACTGGCCAGAAAAAACAAAAAATTGTCAGCATCAGGGAAGCACACACAGCCAAGCAGAGCACACACCCCCTAACATGTTGTGATTCAGAGGGAAGAAAGGCAGTTATACAACCTCTAATCATGCCCATCCCTGTTAATCTTTGGGGATGGGACCTATTAGCCCAATGGGGGGTCACTCTGCAGACCCCTTTCTAATAATGGCCACTGTTATTATTCCTCCCCTACCCCTGACGTGGCTCTCTCAAGATCCAATTTGGGTAGAACAGTGGCCTTTAAAGGGAGAGAAATTACAAAGAGCCCATGAATTAGTTGAGGAGCAATTAAAAGCCGGCCATATAGAACCATCAAACAGCCCTTGGAATTCGCCCATTTTCGTCATTCCCAAAAAGTCTGGTAAATGGAGACTTTTGCATGACTTACATGCTATCAATGCTAATTTGCAACCTATGGGGCCCCTTCAACAGGGGCTCCCTTCCCCCACGGCGATTCCTCAAGATTGGCCTATAATCATTATTGACTTAAAAGACTGCTTTTATACTATTCCCCTTGCAGAACAGGACAGAGAAAAATTTGCATTTACAATACCAGCTATCAATAATGAAAGGCCAGCTTGCCGATTTCATTGGAAAGTGCTTCCTCAAGGAATGCTAAACAGTCCTACCATGTGTCAGTATCATGTAAATCAGGCTTTGCTCCCCAGTAGAAAAGAATTTCCTAATTGCAAGATTATTCATTTTATGGATGATATTTTACTAGCAGCCCCAACGGAGCCAGTACTTTTAAGTTTATATGCCTCTGTCATAAAGAATACACAGTTAAGAGGTTTAATCATAGCACCTGAAAAAGTACAAATGTCCTCTCCTTGGAAATATCTTGGATACATACTAACTTCCTGGTCAGTAAGACCTCAAAACACCTTAAATGATTATCAGAAATTACTAGGTGATATTAACTGGCTTCACCCCACCTTGGGCATAACTACTGATAAGTTACAAAACCTGTTTTCTATCTTAAAGGGCAATACAGCCCTAGACTCTCCCAGGTATTTAACCCCTGCAGCAAAAAGGGAAATTGAGGAAATAGAGCAAGCTATTTCTCAGAGGCAACTAGATCGCATAGATCCATGATATTCAGTTCAATTGTTTTTTCCTACTAAACACTCCCCTACAGGGTTAATAGGACAGATGGCCCCAGGGCTACGCTTCCTAGAATGGGTTTTTTGCTCACATACCGGGACTAAAACACTATCTCCCTATATCCAGTTAGTTAGTAAAGTCATCTATTCAGGCCGCAGACGATGCAATCAGTTGCTAGGTTATGACCCTGATGTCATCAGAATTCCTTTAAGTAAAAAGCAATTCGAAGCAGTATTGCCCTTATCTATAGATCTGCAAATAGCACTCTCTGATTACACAGGCCATATAGAGCATGCCCTTCCTGCTGACAAACTCCTTCAGTTCTTATCTCATACTCCTGTAGTTTTGCCTACAAAAATAGTTCACTCCCCCATACCTAATGCTTTAACACTGTTTACTGATGGCTCTGGTAAACATGGAAAAGCGGCTGTCTGGTGGAGACCACATAATTCCCTCACTCGTTCTGGATTTACTAGCACTCAGAGAGCTGAGGTTGGAGCCTTAATATTGGCCTTGGAAACTTTTTCCACTCAGCCCATCAATATTGTTAGTGACTCTGCTTACTCTGTTTATTTATTGCAGAACCTTGAGACAGCCCTCATTAAGTCCACTCTGGAGCCCACCCTGTGTGCACTTTTTCTTTGACTTCAGCAATTGCTAGATCAACGTACACATCCTATTTTTATCACACACATTCGAGCCCACAGCTCACTGCCTGGCCCATTGGCTTATGGCAATGATCAAGCAGACCTGCAGGTTATGACATCACTGCTTGACCAAGCCACCCAATCGCATCAATTTTTCCACCAAAATTGGAGAAACTTATCTAAACAATTTCAACTTACCCAAAGACTAGCTAAACAAATTATCCTGCAATGCCCAGATTGCCAGCTCACAGGCACATCCCCTCCTTCAACAGGTGTTAACCCTAGAGGACTAGAACCTAATCAGTTATGGCAAACAGATGTTACACACATCCCTGAATTTGGAAAACTAAGATATGTACATGTATCCATTGATACCAATTCTCACTTAATTAGTGCACATGCTCTTCCTGGAGAGTCCACCCAATATGTCATTAAACATCTTCTTTTAACTTTTGCATTTATGGGGCGGCCCACAAAAATTAAAACTGATAATGGTCCGGCTTATGCCAGCTCACAATTTCAACAATTTTGTCACACGTGGAACATCCAACATTCCACAGGCATCCCGTATAACCCCCAAGGACAGGCCATAGTAGAACGTGCCCACTCCACCCTTAAAAATATGCTCAGAAAACAAAAAAGGGGGAATATGAGTAAGGACCCTGCAACACTACTGGCACAAGCCTTATTTACCCTTAATTTTTAAAATTTAGATGATAAATTTCAATCAGCTATAGAAAAGCACTTTGCTAAAACCTCTCAAGACATAAAACCTGCAGTTTTATGGAAAGATGTAAACAGTAATGTATGGTGTGGTCCAAATGAATTGTTAACATGGGGAAGAGGATATGCTTGTGTTCACACCCCCTCAGGTCCTCTTTGGATTCCAGCATGATGCATCAAACCATACCATGGCATGGCTAGGACCCAACCCGGTACCAGAAATGAAGGAAATGACCCTGCAGGACCCACAGCCCCAGACGATGCGGCTTCCTCGGATGACACAAGCCCCAGACATTACCTGGGGGATGCTGAAGAAGACAACTCAGGAGGC

ATGGGACAACAGTTATCAGCTCAACAGAAACAGTATATAAAAGTATTGAAACAGCTGCTTAAAGCTAGTGGAGCCTCAGTTTCGCAGGCTCAATTAAGGGACCTAATGCAAACTGTTGTTTCCCATAACCCATGGTTCCCAGAAGAAGGTACGCTAGACGTAGAGCTCTGGGAACAAGTGGGGAGAAATCTTAAACAACATCATGCACAAGGGCAACGGGTCCCAGTAACATCTCTAACGTTATGGGCTTTAGTTAGGGCTGCTTTGGTCCCACTCTACACAGAAGAGCCTAAAAAGGGAAGGGAGGAGGAACCGTCACCTACCTTACCGCCTCCTTCTCCCTCAGCCCCGCTATCACCGGGCCAAAATAACAAAGAGGAAACGGAGGTTTTGCCTGAGCCCCCTCCTCCAATAAATTGGAAAAAAGACAAGGGATATGCTACAGCTATGGGACCCTGTCTTAGGCAAGCGGCATTAGAAGGGGAGCTCTTAGCCTGCCCGGTAATGCAAGATCAACAAGGCAATCAGGTACATGAACCCATTTCTTTTAACGCTTATAAAGAGATAAGAAAAAGCATTAAAGAAAATGGAGCCGCTAGCCCATTTATGAAAGGAATGATTGAAGCCATAGCAGACAACTTCCATATGACCCCATGGGACTGGTCAGTGCTAGCTAAAACAACTTTGGAGCCCAGCCAATACCTCCTCTGGAAGGCAGAATATGATGAGTTGTGTGAACAACAAGCCAACCAGAATCAGGTGGCCAGGCAAGACATAACAGCTGCTATGCTCCAGGGGAGGGGTCCCCATGCCGATGTACAACAACAACTAAATTTTGATCCCCAGGCCTATGCACAAGTGTCTTTGTGTGCTCTCAGGGCTTGGGACTGAATTCCCAAAAGCGGAGTTCAACAGGGATCTTTTATAAATGTTCGACAAGGGCCTCAGGAGCCATTTGTTGAGTTTATCAATCGGTTAACCCAGGCAATTAAGAGACAAATTAGTCATGCCCAGGCCGCTGATATCTTATTGTTGCAATTGGCTTATGAAAATGCTAATGTGGATTGCCAGCAAGCAATGCAGGCAATCAGAGGAAAGGCAGCCACAGTCGGGGAACTTATATGAGCATGTCAACTGGTGGGGACTGAAACACACAAAGCCAAAATATTGGCTATGGCATTAAGGCCTCCTAAAGTGAAAAGGGAGAGAAACCCAAATTGTTTTCTATGTGGAGAGCCAGGTCATATGAAGAGGGAATGCCCCAATAGTAGAGACCAAGGTAACTCAGGAAAAGAACCCCCTTCTATATGCCCCCAATGTAAAAAGGGGAAACATTGGGCAAATCAATGCAGGTCCAAATTTGATAAAAACGGCAACCCCATAAGT

GAATCCTGCTCCAGACACAGACACCATTCACTCCAGATAATTTGTTCCTTGCTATGCTTTCTGTTGTACATTGCAACTCACATAGGGTATTGATCCTTTTTATGCTCTCGCTTTGTCTGCAACCTGTACCTGCTACACTCTATTGGGCTCATATCTTAGATCCGCCTTTCTTTCGCCGTCACCTGGGCAGACACCCCCTTCCCAGCCTCTAATAACATAACTGCTTGGCTAGGAGGGATAGATTTACCCCCAGTGGGGTCCCTCATTAATGGCACACATTGGACTAAGGTGCCAGGTAACACTACATATCACTCCACTATCCTCCCACTGTGTGTAAGTTATAAAAGTTCTAACCCTTACTGTGTACCTGCCCAAACACAATTATGGCTACATCATGGCAAAGGAAATGCCTTAACAGTCTTAGCTGCAGGTAGCCTCAAACCGGGCAATGCAATCAATGCCACTTTCCCAAACATTCCTTCCTGTGCTAAAGAACAAAGCCAGGAAAGTAATGGATTCCACTTTAGCTGGGAGGTCTGTCACGGGGGACAAGCCCATAGCCTCCAGTTAGGCAATTATAACATCTTAGACTGGAGCCCCCACAGCCATTTGCAGGGCAACCATACTGATGTCCTCATCCATCATGGCATCAATCACAGTTTCATAGCCACGTCCCATTCCCCTATAATTTGGGCCGATGGGGGGATGGGATATCCCAGACCCCAAGTAAAGTCCATGCCACCCCAAGACACTTTATGGTGCCTGGGACATCTTAGCACCTCCCTTAACACCTGGCATGGGACATATCATAATTCCAGTCACAACTATACTATGACCTTTATTCATAATCACACTGATCAGTGCCTGATTTGCACTACCCATCCATATGTTTTCCTTATGGGAACCAATATTTCCATTACACCCCAAAACTCCACGTTTGTGACCCGGGTGCAGGGACAGGCTTGGTTTGCCTCATGTATCACTAATTACAATATATCTAATTTAAATATTACTAGTGTCATGGTATTAAGGAGACAATCTGAGGCATTCCTACCAGTCAATTTGACATGCGATTGGCAAGGTTCCTCTGCCCTTGCCACCTTAGAACGTGCCCTGTCCCAGGTCAGACACAAAAGATTCATAGTTACACTTATAGCCTTTATAGTCTCAGCCATAGTCATCCTAGCAACTGCTAGTGTTGCTGTAGCATCTATTACTGAATCAGTACAAACAGCTACTTTTGTAGATAATTTGGCCAGAAATGTGTCTAATGAACTTCTCTTACAGCAGGGTATAGATCAAAAGATTCTTGCATGTCTGCAAGCCCTCGAGGCTGCCTTGGAATATGTGGGGGAGCGACAAGATGCACTGGCATTCTGACAGCAATTAAACTGTGACTGGGAGCATAAACATATCTGTGTCACTTCTCTACCATGGAATCAATCAATACATAGTTGGGATGAGGTGAAACAACACCTCTGGGGAACCTTTCATGACAATTTAACAGCAGACGTAAAGCAACTTAAAACTAAAATTTTAGAATCCCTAAACACCATAGATCTACACACCCAACAAACAGCCATATGGAAGGGTGTGCAAGATCATCTCTCCTGGATAGACCCCCACTCCTGGGGGTCACTCCTTGATTGGAAAAGAATGTTGCTAATTATACTCATGTTTGTCTTATGTTATTTACTAATTCTAGGATGCAAAGCCGGAATAAGAGCAATGACCGCCACGCCTGACAAACCTGTTGCTGCACACATCTGTACTCTTCAATCAACAAAACCTGATGCAAAAAACAGAAAAAGGGGGAGA

Translated Sequences

*PGGKLHEGPAPGPAPNWGNASGFPRSDGKPTVLSLRAATTGSAGLDLLCPNKLVLKEGEDPKRVATGIWGPLPLGTVGLVLGRSSLSSKGINVLTGVIDSDYQGEILVMMECKGLHILPPGSKIAQLLLLPYWVPNAHGKERGKGSFGSTGATGVYWNQLITDQRPMITLKIGNKNFTGLLDTGVDISIISDQNWPEKTKNCQHQGSTHSQAEHTPPNML*FRGKKGSYTTSNHAHPC*SLGMGPISPMGGHSADPFLIMATVIIPPLPLTWLSQDPIWVEQWPLKGEKLQRAHELVEEQLKAGHIEPSNSPWNSPIFVIPKKSGKWRLLHDLHAINANLQPMGPLQQGLPSPTAIPQDWPIIIIDLKDCFYTIPLAEQDREKFAFTIPAINNERPACRFHWKVLPQGMLNSPTMCQYHVNQALLPSRKEFPNCKIIHFMDDILLAAPTEPVLLSLYASVIKNTQLRGLIIAPEKVQMSSPWKYLGYILTSWSVRPQNTLNDYQKLLGDINWLHPTLGITTDKLQNLFSILKGNTALDSPRYLTPAAKREIEEIEQAISQRQLDRIDP*YSVQLFFPTKHSPTGLIGQMAPGLRFLEWVFCSHTGTKTLSPYIQLVSKVIYSGRRRCNQLLGYDPDVIRIPLSKKQFEAVLPLSIDLQIALSDYTGHIEHALPADKLLQFLSHTPVVLPTKIVHSPIPNALTLFTDGSGKHGKAAVWWRPHNSLTRSGFTSTQRAEVGALILALETFSTQPINIVSDSAYSVYLLQNLETALIKSTLEPTLCALFL*LQQLLDQRTHPIFITHIRAHSSLPGPLAYGNDQADLQVMTSLLDQATQSHQFFHQNWRNLSKQFQLTQRLAKQIILQCPDCQLTGTSPPSTGVNPRGLEPNQLWQTDVTHIPEFGKLRYVHVSIDTNSHLISAHALPGESTQYVIKHLLLTFAFMGRPTKIKTDNGPAYASSQFQQFCHTWNIQHSTGIPYNPQGQAIVERAHSTLKNMLRKQKRGNMSKDPATLLAQALFTLNF*NLDDKFQSAIEKHFAKTSQDIKPAVLWKDVNSNVWCGPNELLTWGRGYACVHTPSGPLWIPA*CIKPYHGMARTQPGTRNEGNDPAGPTAPDDAASSDDTSPRHYLGDAEEDNSGG

MGQQLSAQQKQYIKVLKQLLKASGASVSQAQLRDLMQTVVSHNPWFPEEGTLDVELWEQVGRNLKQHHAQGQRVPVTSLTLWALVRAALVPLYTEEPKKGREEEPSPTLPPPSPSAPLSPGQNNKEETEVLPEPPPPINWKKDKGYATAMGPCLRQAALEGELLACPVMQDQQGNQVHEPISFNAYKEIRKSIKENGAASPFMKGMIEAIADNFHMTPWDWSVLAKTTLEPSQYLLWKAEYDELCEQQANQNQVARQDITAAMLQGRGPHADVQQQLNFDPQAYAQVSLCALRAWD*IPKSGVQQGSFINVRQGPQEPFVEFINRLTQAIKRQISHAQAADILLLQLAYENANVDCQQAMQAIRGKAATVGELI*ACQLVGTETHKAKILAMALRPPKVKRERNPNCFLCGEPGHMKRECPNSRDQGNSGKEPPSICPQCKKGKHWANQCRSKFDKNGNPIS

ESCSRHRHHSLQIICSLLCFLLYIATHIGY*SFLCSRFVCNLYLLHSIGLIS*IRLSFAVTWADTPFPASNNITAWLGGIDLPPVGSLINGTHWTKVPGNTTYHSTILPLCVSYKSSNPYCVPAQTQLWLHHGKGNALTVLAAGSLKPGNAINATFPNIPSCAKEQSQESNGFHFSWEVCHGGQAHSLQLGNYNILDWSPHSHLQGNHTDVLIHHGINHSFIATSHSPIIWADGGMGYPRPQVKSMPPQDTLWCLGHLSTSLNTWHGTYHNSSHNYTMTFIHNHTDQCLICTTHPYVFLMGTNISITPQNSTFVTRVQGQAWFASCITNYNISNLNITSVMVLRRQSEAFLPVNLTCDWQGSSALATLERALSQVRHKRFIVTLIAFIVSAIVILATASVAVASITESVQTATFVDNLARNVSNELLLQQGIDQKILACLQALEAALEYVGERQDALAF*QQLNCDWEHKHICVTSLPWNQSIHSWDEVKQHLWGTFHDNLTADVKQLKTKILESLNTIDLHTQQTAIWKGVQDHLSWIDPHSWGSLLDWKRMLLIILMFVLCYLLILGCKAGIRAMTATPDKPVAAHICTLQSTKPDAKNRKRGR

Expression Graph

Data from https://rna.recount.bio/

Tree of loci