Type II


Cas9 is the most widely used gene editor of the CRISPR family and the first CRISPR nuclease with demonstrated programmable RNA-guided activity 1. The conventional classification divides type II CRISPR-Cas, or Cas9, systems into subtypes II-A, II-B, and II-C, and is based on multiple criteria. However, the basis of this classification is the presence of signature proteins in the CRISPR-Cas9 locus and the locus organization 2,3,4,5,6. A finer division of Type II proteins into clades I-X based on Cas9 phylogeny, which reproduces the subtypes II-A,B,C separation into groups of clades, was previously published 7. Finally, recent studies have reported functional characterization and gene editing ability of compact RNA-guided ancestors of Cas9 proteins, which are referred to as IscBs and HEAROs. In addition, a new subtype II-D that includes compact Cas9s homologous to these ancestors has been proposed 8,9,10.

For convenience, CasPEDIA phylogenetic tree integrates two classifications of Cas9 according to subtypes A,B,C, and to phylogenetic clades I-X, and in addition, includes clade U with type II-D, and IscB, HEARO RNA-guided nucleases.

The phylogenetic tree was generated with Cas9 sequences acquired from (Gasiunas et al. 2020) with minor modifications, sequences from public databases, from selected studies with in vivo editing data 11,12,13,14,15,16,17,18,19,8,9, and from the literature on published Cas9 and IscB structures 20,21,22,23,24,25,26,27,27,28,29.

Phylogeny Download

Download the phylogenetic reconstruction source of Type II members

Download the multiple sequence alignment source of the Type II phylogenetic reconstruction

IX VIII X VII VI V I II III IV Tree scale: 1 Colored ranges Type II-A Cas9 Type II-B Cas9 Type II-C Cas9 Type II-D Cas9 HEARO IscB U WP_001040085.1 KLL20707.1 Sag1 WP_112435821.1 WP_123957750.1 WP_112477766.1 WP_123947897.1 WP_001040087.1 WP_050881965.1 WP_088181599.1 WP_038406070.1 WP_001040110.1 WP_001040107.1 WP_001040108.1 WP_088881668.1 WP_017648376.1 WP_001040098.1 WP_001040096.1 WP_001040103.1 Sag2 WP_001040102.1 WP_014608595.1 WP_024703962.1 Sth3 WP_014727651.1 WP_111679672.1 WP_024703962.1 Sth3 WP_065972475.1 WP_111675746.1 WP_096753782.1 WP_060553428.1 WP_120770653.1 WP_061563899.1 WP_002280230.1 WP_012997688.1 WP_106006713.1 WP_002263549.1 WP_061046374.1 WP_014677909.1 WP_002279859.1 Smu WP_082312238.1 WP_126475526.1 WP_105184075.1 WP_024390729.1 WP_024405243.1 WP_003088697.1 Sra WP_126402616.1 WP_111698941.1 WP_020917064.1 WP_039691759.1 Seq1 WP_014334983.1 WP_077497300.1 WP_009854540.1 WP_067062573.1 WP_012962174.1 Sga WP_119877030.1 WP_003031511.1 WP_126408155.1 WP_003030002.1 WP_003079701.1 Sma1 WP_111674566.1 WP_011054416.1 WP_111686257.1 WP_030126706.1 WP_038431314.1 WP_032462936.1 WP_111704216.1 WP_014407541.1 WP_111713801.1 4ZT0_A Spy WP_049524935.1 WP_129304756.1 WP_010922251.1 Spy WP_002989955.1 WP_011527619.1 WP_111689242.1 WP_129846771.1 WP_011284745.1 WP_111690765.1 WP_020905136.1 WP_012560673.1 WP_111703313.1 WP_038434062.1 WP_031488318.1 WP_111705078.1 WP_111694788.1 WP_030125963.1 WP_111704663.1 WP_023610282.1 WP_023080005.1 WP_038432938.1 WP_101248361.1 WP_111693164.1 WP_063631341.1 WP_111679121.1 WP_011528583.1 WP_015017095.1 WP_111681791.1 WP_015057649.1 Sdy WP_012767106.1 WP_014612333.1 WP_111716689.1 WP_129555603.1 WP_003043819.1 Sca WP_126426708.1 WP_111692589.1 WP_126436870.1 WP_012515931.1 Seq2 WP_111690263.1 WP_003099269.1 WP_111673267.1 WP_007896501.1 WP_014601172.1 WP_003723650.1 WP_058876445.1 WP_003730785.1 WP_003727705.1 WP_072238933.1 Lmo WP_010991369.1 WP_077287021.1 WP_023548323.1 WP_085392451.1 WP_033920898.1 WP_085400884.1 WP_031669209.1 WP_003733029.1 WP_038409211.1 WP_002413717.1 WP_002364836.1 WP_002378009.1 WP_096397536.1 WP_095803385.1 WP_063627610.1 WP_010737004.1 WP_095454139.1 WP_095443635.1 WP_023519017.1 WP_002335161.1 WP_119364770.1 WP_002320716.1 Efa WP_071456514.1 WP_077275696.1 WP_007209003.1 Eit KRM56765.1 Lan WP_116877370.1 WP_128735912.1 WP_108730630.1 WP_013252099.1 WP_013709575.1 Cgl WP_013980829.1 Esp1 WP_060684250.1 WP_128729551.1 WP_122036847.1 WP_106904639.1 WP_027821588.1 WP_064578474.1 WP_054519097.1 WP_064523476.1 WP_015379638.1 WP_065080293.1 WP_063722122.1 WP_074029542.1 WP_120769497.1 WP_050337970.1 WP_101872621.1 WP_065937575.1 WP_065902179.1 WP_087609243.1 WP_110139996.1 WP_065200954.1 WP_087741344.1 WP_081528804.1 WP_052916100.1 WP_003588546.1 WP_100908617.1 WP_012491871.1 WP_101512178.1 WP_109990335.1 WP_003659473.1 WP_094516034.1 WP_020751689.1 WP_077069534.1 WP_014569977.1 WP_047676366.1 Lsp1 WP_005713195.1 Lrh WP_005684674.1 WP_070652006.1 WP_089542143.1 WP_064777233.1 WP_069468140.1 BBE26067.1 WP_089556639.1 WP_116843570.1 WP_065825603.1 WP_126133368.1 WP_056965860.1 WP_099947667.1 WP_057890055.1 WP_010009270.1 WP_062913273.1 WP_062904505.1 WP_062903918.1 WP_057773983.1 WP_014567561.1 WP_127835850.1 WP_069168517.1 WP_117285354.1 WP_087712910.1 WP_020807054.1 WP_127345750.1 WP_080881730.1 WP_034978824.1 Lsp2 WP_109585852.1 WP_038521270.1 WP_109918023.1 WP_109715097.1 WP_060598264.1 WP_072547243.1 WP_114893867.1 WP_119906237.1 WP_077302299.1 WP_089119823.1 WP_075362504.1 WP_128737221.1 WP_128688323.1 WP_004166700.1 WP_075139705.1 WP_065124500.1 WP_002831105.1 Pac WP_128472058.1 WP_070366671.1 WP_115154636.1 WP_094104688.1 WP_023440039.1 WP_014940461.1 WP_013728652.1 WP_114806560.1 WP_082229465.1 WP_107760052.1 WP_080650625.1 WP_087908354.1 WP_128492537.1 WP_124891202.1 WP_127429586.1 WP_104878060.1 WP_039945658.1 WP_065533057.1 WP_054646658.1 WP_014082128.1 WP_050952303.1 WP_042996237.1 WP_013362995.1 WP_045920486.1 WP_010017027.1 WP_010018949.1 WP_041499991.1 WP_076614067.1 WP_118908584.1 WP_069125601.1 WP_119945366.1 WP_002681289.1 Tde WP_044978320.1 Tpu WP_106894870.1 WP_089612183.1 WP_069177230.1 WP_009016219.1 Ain WP_076779133.1 CCY92141.1 Esp2 WP_083799662.1 WP_106788657.1 WP_012290141.1 Fma WP_106084434.1 WP_099990583.1 WP_099986054.1 WP_100026503.1 WP_008799285.1 WP_008797465.1 ALF19895.1 WP_041954361.1 WP_068552050.1 Tba WP_083631498.1 WP_003145379.1 WP_111743047.1 WP_082729137.1 WP_114889507.1 WP_095064669.1 WP_035463602.1 Vpa WP_002681289.1 Lce WP_127504989.1 WP_014613259.1 WP_096598476.1 WP_103209613.1 WP_105977863.1 WP_107552556.1 WP_095105824.1 WP_029499861.1 Khu WP_081487811.1 WP_104928915.1 WP_071660307.1 WP_003038941.1 Fno WP_071304231.1 WP_014549645.1 WP_003036236.1 WP_003033603.1 WP_014548420.1 WP_066046523.1 WP_122951191.1 WP_065299424.1 WP_038837027.1 WP_011212792.1 Lpn WP_027223967.1 WP_028378712.1 WP_027228131.1 WP_062726656.1 WP_086315938.1 WP_086296884.1 WP_066592711.1 WP_011139431.1 WP_095559301.1 WP_101415585.1 WP_014608134.1 WP_128887992.1 WP_014621379.1 WP_023909534.1 WP_011680957.1 WP_011680957.1 Sth1 6RJD_0 Sth1 WP_014727388.1 WP_059257345.1 WP_011225725.1 Sth1A WP_011227028.1 WP_116920169.1 WP_113870396.1 WP_111679519.1 WP_087009798.1 WP_126429293.1 WP_014634195.1 Ssa WP_107372848.1 WP_084871438.1 WP_126407025.1 WP_021002704.1 WP_057489650.1 WP_021001655.1 WP_037618037.1 Ssi WP_012130469.1 Sgo WP_046165401.1 WP_023026749.1 WP_039671019.1 Sma2 WP_014294907.1 WP_069788897.1 WP_013852048.1 WP_012962169.1 WP_058621517.1 WP_111712910.1 WP_058814078.1 WP_126437961.1 WP_126440388.1 WP_002935602.1 WP_014637067.1 Ssu WP_024409212.1 WP_120171880.1 WP_037591994.1 WP_120141936.1 WP_010018698.1 WP_077276356.1 WP_016251609.1 Ece WP_006907934.1 Fho WP_087548596.1 WP_120771636.1 WP_068759260.1 Tsp WP_012742555.1 WP_060552032.1 WP_039643679.1 WP_085237539.1 WP_107392933.1 Sauri WP_050331073.1 WP_050345681.1 WP_060829977.1 WP_126510167.1 WP_058710220.1 WP_075777761.1 WP_104681501.1 WP_023374365.1 WP_002460848.1 Slu WP_053019794.1 WP_088922804.1 WP_096754380.1 WP_105977729.1 WP_096075831.1 WP_062197343.1 Mse WP_076767463.1 WP_077916261.1 WP_084781893.1 Bni WP_096550266.1 WP_125669251.1 WP_117347264.1 WP_119362967.1 WP_004800457.1 Edo WP_075048454.1 WP_075058359.1 WP_069117188.1 WP_115558502.1 WP_011113935.1 WP_027333323.1 WP_014886349.1 Mga WP_011883478.1 WP_014574789.1 WP_046643012.1 WP_004794730.1 WP_015287703.1 WP_117274954.1 WP_041352097.1 WP_044635168.1 WP_099451754.1 WP_129644562.1 WP_060823277.1 WP_129646764.1 WP_114191009.1 WP_129692608.1 WP_041362727.1 WP_025208688.1 WP_066390315.1 WP_125296444.1 WP_130234171.1 WP_012859073.1 WP_069972580.1 WP_002246410.1 WP_002235162.1 WP_012221298.1 WP_014574210.1 Nme1 WP_002256913.1 WP_015815286.1 WP_002249455.1 WP_002230835.1 Nme2 6JE3_A Nme2 WP_115436905.1 WP_002217928.1 WP_002238326.1 WP_002236121.1 WP_111726279.1 WP_114934979.1 WP_013449463.1 WP_107854655.1 WP_054618016.1 Nsp WP_126304706.1 WP_123795625.1 WP_002641950.1 WP_038329902.1 Kki WP_005751838.1 WP_010907033.1 WP_005754641.1 WP_108511526.1 WP_126372222.1 WP_126290512.1 WP_041834594.1 WP_014991277.1 WP_095176968.1 WP_014065572.1 WP_025236609.1 WP_015432202.1 WP_126598092.1 WP_066887219.1 Dde AMS32010.1 WP_126444802.1 WP_012655176.1 WP_046860449.1 Ga0078972_1010018 Ghy44 WP_095858800.1 WP_033016936.1 Geo WP_023633350 1 Gsp WP_041267823.1 WP_099233044.1 WP_087959824.1 WP_087094968.1 WP_048723014.1 WP_084138993.1 Bok WP_001105083.1 WP_065212529.1 WP_082918497.1 WP_010014406.1 WP_104964710.1 WP_120784844.1 WP_065928594.1 WP_065901900.1 WP_107196622.1 WP_003473526.1 Cpe WP_111744215.1 WP_060670422.1 WP_003452083.1 WP_013389026.1 WP_014748117.1 Tmo WP_041249387.1 WP_015458289.1 WP_011474892.1 WP_011501452.1 WP_003611034.1 OIO17574.1 Ghc2 WP_066045006.1 WP_015423233.1 WP_077538522.1 YP 002344900.1 WP_002864485.1 Cje WP_075867373.1 WP_052784881.1 WP_032586895.1 WP_002851159.1 WP_041160257.1 WP_002858341.1 WP_002895475.1 WP_126418076.1 WP_052834735.1 WP_002855697.1 WP_107128025.1 WP_069176623.1 WP_126655109.1 WP_115766867.1 WP_115794652.1 WP_038814334.1 WP_022552435.1 WP_042635940.1 WP_070300721.1 WP_069179465.1 WP_020836910.1 WP_002883590.1 WP_002799306.1 WP_038400688.1 WP_052805632.1 WP_069360684.1 WP_012006786.1 WP_052805507.1 WP_071319729.1 WP_002819067.1 WP_052802742.1 WP_021137704.1 WP_002855546.1 WP_057034899.1 WP_070306793.1 WP_002890122.1 WP_015016497.1 WP_002886998.1 WP_002780990.1 WP_044306279.1 WP_002916466.1 WP_039666904.1 WP_039625276.1 WP_044598268.1 WP_075489449.1 Cco WP_110581844.1 WP_015453612.1 WP_104717230.1 WP_014667007.1 WP_108911279.1 WP_034342349.1 WP_027305220.1 WP_104745660.1 WP_058914657.1 WP_071609185.1 WP_115784888.1 WP_107127902.1 WP_013022389.1 WP_011139289.1 KFL34573.1 Ga0078972_1020432 Ghy3 WP_148224960.1 Nsa BBG66273.1 WP_114842230.1 WP_086333498.1 WP_086315836.1 WP_095916790.1 WP_013997568.1 WP_126321326.1 WP_042346730.1 Cca1 WP_095893406.1 WP_095896902.1 WP_098029595.1 WP_095901370.1 WP_002678519.1 WP_095909429.1 WP_106096331.1 WP_015781852.1 WP_053581145.1 WP_008582100.1 WP_067760338.1 WP_068397880.1 Ga0079224_100045232 Cme1 WP_123901968.1 WP_123872731.1 VFB02498.1 WP_045502672.1 WP_123882753.1 WP_053329437.1 Cga WP_098193375.1 WP_038693822.1 WP_014938037.1 WP_079206934.1 WP_004918207.1 WP_013073784.1 WP_100945244.1 WP_070235793.1 WP_114902879.1 WP_102995112.1 WP_100021242.1 WP_014708934.1 WP_100023185.1 WP_100019439.1 WP_112199926.1 WP_100013851.1 WP_099983984.1 WP_100015610.1 WP_028906301.1 WP_036868838.1 Phi WP_005791619.1 WP_053874249.1 WP_009293010.1 WP_106069253.1 WP_005855543.1 Psp WP_108741992.1 WP_129538186.1 ID9 Ffr SHH94364.1 WP_011963637.1 WP_014773653.1 WP_107011025.1 WP_099841149.1 WP_099838520.1 WP_099896360.1 WP_077094666.1 WP_047033642.1 WP_045179909.1 WP_076351459.1 WP_088583860.1 WP_124803323.1 WP_038656028.1 WP_084546960.1 WP_095073413.1 WP_123856220.1 WP_126370911.1 WP_095898369.1 WP_095914261.1 WP_088593991.1 WP_106098546.1 WP_013598930.1 Wvi WP_079559033.1 WP_079465816.1 WP_076559079.1 WP_123844212.1 WP_104917102.1 WP_022546547.1 WP_076929686.1 WP_013687888.1 WP_060383764.1 WP_063743464.1 WP_014165808.1 WP_120175212.1 WP_050696304.1 WP_060831628.1 WP_012819984.1 WP_095911833.1 WP_014791819.1 Orh WP_066331514.1 WP_068481078.1 WP_015022951.1 WP_108879264.1 WP_128501545.1 WP_123941184.1 WP_076701793.1 WP_014561873.1 WP_095899957.1 WP_095918475.1 Ga0078972_1022257 Ghy2 WP_122933462.1 WP_014084151.1 WP_069797278.1 WP_014164458.1 WP_060381523.1 WP_106042830.1 WP_013063831.1 WP_035473639.1 Rsp WP_100996834.1 WP_114984028.1 WP_106053875.1 WP_116787333.1 WP_109567989.1 WP_103292747.1 WP_016200142.1 AMS26831.1 WP_118866786.1 WP_044112561.1 WP_057952188.1 WP_042249802.1 Jpa WP_124985915.1 WP_076615834.1 WP_068206408.1 WP_100211383.1 Ga0079224_100005449 Cme3 JGI11876J14442_10007391 Ghe WP_057952132.1 WP_024267366.1 Spa Ga0078972_1025093 Ghy1 WP_095415415.1 WP_082846128.1 WP_077026422.1 WP_011995013.1 WP_081371634.1 Ga0008837_100633 Ghh2 Ga0065720_1018820 Cme4 Ga0079224_100072790 Cme2 WP_085755463.1 AQT67652.1 WP_077972354.1 WP_078039855.1 WP_077993175.1 AQS41335.1 WP_058898100.1 WP_094463462.1 WP_064329368.1 WP_115377717.1 WP_025290702.1 WP_113667871.1 WP_120251735.1 WP_081536063.1 WP_048531597.1 WP_012177079.1 WP_025058256.1 Sdo WP_066816048.1 WP_066137387.1 WP_120219131.1 WP_104942053.1 Ga0008833_1001252 Ghh1 KQZ15465.1 WP_011505017.1 WP_012044026.1 WP_121730027.1 WP_011809011.1 WP_013592777.1 WP_013517127.1 WP_043213455.1 WP_050715031.1 WP_013648685.1 AJP48396.1 9 Ghc1 WP_114562700.1 WP_013263448.1 WP_126462099.1 WP_105885336.1 WP_118909446.1 WP_013047413.1 9 Msc WP_015469618.1 WP_008738269.1 WP_012414420.1 WP_013607849.1 WP_011388212.1 WP_009541330.1 Csa WP_014301099.1 WP_070794736.1 WP_085666229.1 WP_014317373.1 WP_014318431.1 WP_014316098.1 WP_014311133.1 WP_014319618.1 6JOO_A Cdi WP_025253428.1 WP_035106817.1 Cca2 WP_123930632.1 WP_053411199.1 WP_106110768.1 4OGE_A Ana WP_050695651.1 WP_072457083.1 WP_076389496.1 WP_007057059.1 WP_003839956.1 WP_095508358.1 WP_050752380.1 WP_052377369.1 Bbo WP_083760582.1 6WBR_A Ace WP_053961988.1 WP_102732593.1 WP_012421034.1 WP_102737403.1 WP_123052294.1 WP_067777314.1 WP_082083265.1 WP_052571014.1 MG33-34 MG33-31 MG33-2 MG33-29 MG33-28 MG33-1 MG33-33 MG33-30 MG33-27 MG102-19 MG102-3 MG102-6 MG102-13 MG102-5 MG102-11 MG102-9 MG102-15 MG102-10 MG102-42 MG102-47 MG102-43 MG102-45 MG102-14 MG102-35 MG102-36 MG102-48 MG102-2 MG102-32 MG102-1 MG102-38 MG102-39 MG102-44 MG145-1 MG34-20 MG34-14 MG34-16 MG34-17 MG34-1 MG34-9 MG144-4 MG144-3 MG144-2 MG144-1 MG143-1 MG35-1 HEARO OgeuIscB HEARO/IscB

Type V


Cas12 enzymes are RNA-guided nucleases and are the defining component of Type V CRISPR systems 30. These enzymes appear to have evolved from TnpB proteins encoded within IS200/IS605 family mobile genetic elements, potentially on multiple occasions 30,31,8. Of the Class 2 CRISPR enzymes, Cas12 proteins appear to be the most biochemically diverse by Cas enzymatic classification and thus suited for a wide variety of applications including, but also beyond, gene editing 32,33,34. With the notable exception of Cas12k which directs transposition of a Tn7 transposase, the activity of these enzymes tends to be self-contained and not reliant on additional proteins 34. In addition to being a biochemically diverse family, they exhibit great genetic diversity, with some subtypes forming polyphyletic clades (ex. Cas12f) 35. As within-subfamily clades continue to be characterized biochemically, researchers have (and will likely continue to) find divisions of enzymatic activity, such as recently reported with Cas12c2 and Cas12a2 36,37,38.

The above tree was produced using data from the most recent phylogenetic analysis of Cas12 proteins 30as well as recent reports of Cas12 enzymes since then including Cas12j (previously known as CasPhi), CasLambda and Cas12L 39,40,41and Cas12 ancestor, TnpB 31. In general Cas12 proteins are labeled a to n in order of discovery/characterization except for CasPhi and CasLambda owing to their viral origin 39,40. Some Cas12 proteins without known function appear widespread and have only recently been characterized: Cas12k (Cas12 U5), Cas12m (Cas12 U1), and Cas12n (Cas12 U4) 34,42,43. Two remaining Cas12 families are to-date uncharacterized, Cas12 U2 and Cas12 U3. Only complete Cas12 sequences (using non-truncated RuvC domains) were used. From these sequences, Cas12 proteins were aligned using MUSCLE, trees constructed with IQ-TREE, rooted against TnpB, and visualized with iTOL 44,45,46. Trees were manually curated by pruning errant Cas12 leaves.

Phylogeny Download

Download the phylogenetic reconstruction source of Type V members

Download the multiple sequence alignment source of the Type V phylogenetic reconstruction

set 1 4 Cas12a set 1 65 Cas12a set 1 24 Cas12a set 1 39 Cas12a set 1 15 Cas12a set 1 68 Cas12a set 1 67 Cas12a set 1 56 Cas12a set 1 1 Cas12a set 1 14 Cas12a set 1 13 Cas12a set 1 25 Cas12a set 1 53 Cas12a set 1 51 Cas12a set 1 69 Cas12a set 1 5 Cas12a set 1 22 Cas12a set 1 30 Cas12a set 1 44 Cas12a set 1 35 Cas12a set 1 59 Cas12a set 1 57 Cas12a set 1 50 Cas12a set 1 46 Cas12a set 1 17 Cas12a set 1 70 Cas12a set 1 60 Cas12a set 1 28 Cas12a set 1 21 Cas12a set 1 48 Cas12a set 1 66 Cas12a set 1 31 Cas12a set 1 8 Cas12a set 1 10 Cas12a set 1 37 Cas12a set 1 45 Cas12a set 1 47 Cas12a set 1 26 Cas12a set 1 16 Cas12a set 1 63 Cas12a set 1 36 Cas12a set 1 61 Cas12a set 1 54 Cas12a set 1 6 Cas12a set 1 38 Cas12a set 1 55 Cas12a set 1 11 Cas12a set 1 49 Cas12a set 1 29 Cas12a set 1 18 Cas12a set 1 23 Cas12a set 7 4 Cas12a set 1 71 Cas12a set 2 3 Cas12a var set 2 2 Cas12a var set 2 1 Cas12a var set 2 4 Cas12a var set 2 5 Cas12a var set 2 6 Cas12a var set 2 8 Cas12a var set 2 9 Cas12a var set 2 7 Cas12a var set 5 4 Cas12c P.2Z4XVH Cas12c arbor variant set 5 5 Cas12c set 5 3 Cas12c P.5PUA5Q Cas12c arbor variant P.2DIIQE Cas12c arbor variant P.4PBMFE Cas12c arbor variant P.5R3FNR Cas12c arbor variant P.3LWNW3 Cas12c arbor variant P.5KL5A2 Cas12c arbor variant P.3B0TNI Cas12c arbor variant P.3CP1Y8 Cas12c arbor variant P.5KC90I Cas12c arbor variant P.51P6N4 Cas12c arbor variant P.5OR2SY Cas12c arbor variant P.5FF447 Cas12c arbor variant set 5 2 Cas12c set 5 7 Cas12c P.3S1QBQ Cas12c arbor variant set 5 6 Cas12c KZX85786.1 Cas12c arbor variant set 6 4 Cas12d set 6 3 Cas12d set 6 1 Cas12d set 6 5 Cas12d set 6 11 Cas12d Cas12L 57 Cas12L 58 Cas12L 68 Cas12L 56 Cas12L 67 Cas12L 63 Cas12L 64 Cas12L 65 Cas12L 62 Cas12L 60 Cas12L 61 Cas12L 59 set 7 1 Cas12e var set 7 2 Cas12e var Cas14b.3 Cas14b Cas14b.8 Cas14b Cas14b.1 Cas14b Cas14b.2 Cas14b Cas14b.6 Cas14b Cas14b.9 Cas14b Cas14b.5 Cas14b Cas14b.4 Cas14b Cas14b.7 Cas14b Cas14b.12 Cas14b Cas14b.13 Cas14b Cas14b.14 Cas14b Cas14b.15 Cas14b Cas14b.10 Cas14b Cas14b.11 Cas14b Cas14b.16 Cas14b Cas14d.1 Cas14d Cas14d.3 Cas14d Cas14u.3 Cas14u Cas14d.2 Cas14d set 13 81 V U5 set 13 29 V U5 set 13 74 V U5 set 13 80 V U5 set 13 66 V U5 set 13 68 V U5 set 13 52 V U5 set 13 54 V U5 set 13 62 V U5 set 13 64 V U5 set 13 48 V U5 set 13 60 V U5 set 13 43 V U5 set 13 61 V U5 set 13 58 V U5 set 13 41 V U5 set 13 34 V U5 set 13 28 V U5 set 13 1 V U5 set 13 5 V U5 set 13 4 V U5 set 13 3 V U5 set 13 25 V U5 set 13 24 V U5 set 13 6 V U5 set 13 46 V U5 set 13 45 V U5 set 13 27 V U5 set 13 42 V U5 set 13 7 V U5 set 13 31 V U5 set 13 37 V U5 set 13 33 V U5 set 13 39 V U5 set 13 36 V U5 set 13 35 V U5 set 13 75 V U5 set 13 72 V U5 set 13 17 V U5 set 13 20 V U5 set 13 21 V U5 set 13 23 V U5 set 13 73 V U5 set 13 40 V U5 set 13 38 V U5 set 13 15 V U5 set 13 50 V U5 set 13 13 V U5 set 13 51 V U5 set 13 57 V U5 set 13 14 V U5 set 13 19 V U5 set 13 59 V U5 set 13 8 V U5 set 13 12 V U5 set 13 9 V U5 set 13 10 V U5 set 13 11 V U5 set 13 16 V U5 set 13 30 V U5 set 13 18 V U5 set 13 65 V U5 set 13 83 V U5 set 13 90 V U5 set 13 67 V U5 set 13 93 V U5 set 13 87 V U5 set 13 89 V U5 set 13 79 V U5 set 13 95 V U5 set 13 101 V U5 set 13 85 V U5 set 13 82 V U5 set 13 100 V U5 set 13 94 V U5 set 13 103 V U5 set 13 104 V U5 set 13 97 V U5 set 13 70 V U5 set 13 69 V U5 set 13 99 V U5 set 13 98 V U5 set 13 88 V U5 set 13 92 V U5 set 13 86 V U5 Asp2Cas12l Asp4Cas12l Asp1Cas12l Asp3Cas12l P.584LYY Cas12i P.6RA186 Cas12i P.4O9XYF Cas12i P.32WY90 Cas12i set 11 97 V U3 set 11 79 V U3 set 11 75 V U3 set 11 102 V U3 set 11 99 V U3 set 11 152 V U3 set 11 149 V U3 set 11 148 V U3 set 11 151 V U3 set 11 150 V U3 set 11 147 V U3 set 11 145 V U3 set 11 142 V U3 set 11 141 V U3 set 11 138 V U3 set 11 74 V U3 set 11 73 V U3 set 11 72 V U3 set 11 67 V U3 set 11 68 V U3 set 11 66 V U3 set 11 71 V U3 set 11 70 V U3 set 11 69 V U3 set 11 64 V U3 set 11 65 V U3 set 11 161 V U3 set 11 162 V U3 set 11 160 V U3 set 11 154 V U3 set 11 153 V U3 set 11 158 V U3 set 11 159 V U3 set 11 157 V U3 Cas14a.1 Cas14a Cas14a.2 Cas14a Cas14a.3 Cas14a Cas14a.4 Cas14a Cas14a.6 Cas14a set 11 15 V U3 set 11 16 V U3 set 11 14 V U3 set 11 36 V U3 set 11 37 V U3 set 11 18 V U3 set 11 19 V U3 set 11 24 V U3 set 11 27 V U3 set 11 22 V U3 set 11 30 V U3 set 11 35 V U3 set 11 5 V U3 set 11 7 V U3 set 11 6 V U3 set 11 10 V U3 set 11 60 V U3 set 11 50 V U3 set 11 38 V U3 set 11 53 V U3 set 11 48 V U3 set 11 40 V U3 set 11 44 V U3 set 11 39 V U3 set 11 4 V U3 set 11 3 V U3 set 11 1 V U3 set 11 2 V U3 set 3 16 Cas12b set 3 19 Cas12b set 3 10 Cas12b set 3 17 Cas12b set 3 6 Cas12b set 3 7 Cas12b set 3 15 Cas12b set 3 14 Cas12b set 3 9 Cas12b set 3 20 Cas12b set 3 5 Cas12b set 3 2 Cas12b set 3 1 Cas12b set 3 3 Cas12b set 3 4 Cas12b set 3 12 Cas12b set 3 21 Cas12b set 3 22 Cas12b set 3 23 Cas12b set 3 11 Cas12b set 4 2 Cas12b2 set 4 1 Cas12b2 P.4YGB0J Cas12g P.5OCL1S Cas12g P.5QHCBV Cas12g P.8LSBWZ Cas12g P.52N52T Cas12g P.2THOZ9 Cas12g P.3ABEIE Cas12h Cas14K8 Cas14u.4 Cas14u Cas14K1 Cas14K7 Cas14K2 Cas14K6 Cas14K4 Cas14K5 Cas14K3 Cas14u.2 Cas14u Cas14u.1 Cas14u Cas12j10 Cas12j2 Cas12j8 Cas12j5 Cas12j4 Cas12j3 Cas12j9 Cas12j1 Cas12j7 set 9 9 V U1 set 9 10 V U1 set 9 7 V U1 set 9 1 V U1 set 9 12 V U1 set 9 15 V U1 set 9 16 V U1 set 9 18 V U1 set 9 14 V U1 set 9 19 V U1 set 9 22 V U1 set 9 27 V U1 set 9 23 V U1 set 9 24 V U1 set 9 21 V U1 Cas14f.1 Cas14f Cas14f.2 Cas14f Cas14e.1 Cas14e Cas14e.3 Cas14e Cas14e.2 Cas14e set 10 18 V U2 set 10 15 V U2 set 10 14 V U2 set 10 9 V U2 set 10 2 V U2 set 10 13 V U2 set 10 11 V U2 set 10 12 V U2 set 10 10 V U2 set 10 3 V U2 set 10 17 V U2 set 10 4 V U2 set 12 39 V U4 set 12 38 V U4 set 12 43 V U4 set 12 44 V U4 set 12 42 V U4 set 12 41 V U4 set 12 45 V U4 set 12 40 V U4 set 12 34 V U4 set 12 36 V U4 set 12 35 V U4 set 12 33 V U4 set 12 32 V U4 set 12 31 V U4 set 12 26 V U4 set 12 24 V U4 set 12 21 V U4 set 12 29 V U4 set 12 28 V U4 set 12 19 V U4 set 12 25 V U4 set 12 27 V U4 set 12 23 V U4 set 12 22 V U4 set 12 20 V U4 set 12 30 V U4 set 12 46 V U4 set 12 15 V U4 set 12 16 V U4 set 12 14 V U4 set 12 13 V U4 set 12 12 V U4 set 12 11 V U4 set 12 10 V U4 set 12 9 V U4 set 12 7 V U4 set 12 8 V U4 set 12 49 V U4 set 12 17 V U4 set 12 47 V U4 set 12 37 V U4 set 12 18 V U4 set 12 4 V U4 set 12 5 V U4 set 12 2 V U4 set 12 1 V U4 set 12 6 V U4 set 12 48 V U4 Cas14i2 Cas14i3 Cas14i1 Cas14h.1 Cas14h Cas14h.2 Cas14h Cas14h.3 Cas14h Cas14u.6 Cas14u Cas14J6 Cas14J1 Cas14J7 Cas14c.2 Cas14c Cas14u.8 Cas14u Cas14J3 Cas14J2 Cas14c.1 Cas14c Cas14u.7 Cas14u Cas14J5 Cas14J4 IsDra2 TnpB Tree scale: 1 Colored ranges Cas12a Cas12a2 Cas12b Cas12c1 Cas12c2 Cas12d /CasX Cas12e /CasY Cas12f /Cas14 Cas12g Cas12h Cas12i Cas12j /CasΦ Cas12k /U5 Cas λ Cas12L Cas12m /U1 Cas12n /U4 Cas12U2 Cas12U3 TnpB TnpB a2 a c2 c1 d λ e f/14 f/14 f/14 f/14 f/14 n U2 m Φ/j h b g U3 U3 i L k

Type VI


All known Cas13 enzymes are RNA-guided RNA endonucleases and are the defining component of Type VI CRISPR systems 30. In contrast to Cas9 and Cas12, the primary activity of Cas13 proteins appears to be due to its trans-RNAse activity conferred by HEPN domains 47,48. These enzymes vary by the extent and bias of HEPN activity, having a strong influence on how they are used in diverse applications ranging from RNA-targeting to RNA diagnostics 49,50,51,52. Unlike Cas9 and Cas12 enzymes, the evolutionary origins of Cas13 enzymes remains unclear 30. These enzymes are organized into 4 subtypes, Cas13a-Cas13d, where characterization of Cas13c remains unknown (although assumed to target RNA). While these enzymes are generally capable of processing their own CRISPR array and function as standalone enzymes, they occasionally co-occur with additional proteins that appear co-functional 53,54,55.

The reported Cas13 tree was recreated from a recent report on Cas13 phylogeny 56. Briefly Cas13-annotated sequences from subtypes a-d were gathered from NCBI and GTDB r95 57using Hidden Markov Models. Sequences lacking two R/Q/N/K/H****H sequence motifs were assumed to be truncated proteins and removed. Sequences were clustered with CD-HIT v4.8.1 with length and sequence similarity cutoffs of 0.9 58. Sequences were aligned with MUSCLE v3.8.31, tree built with IQ-TREE v1.6.12, and visualized with iTOL 44,45,46. Trees were manually curated by pruning errant Cas13 leaves.

Phylogeny Download

Download the phylogenetic reconstruction source of Type VI members

Download the multiple sequence alignment source of the Type VI phylogenetic reconstruction

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