Genome Property Definition Page
Accession | GenProp0021 | |
Name | CRISPR region | |
Type | GUILD | |
Description | CRISPR repeats are by definition Clustered Regularly Interspaced Short Palindromic Repeats, described by Jansen [3]. Certain proteins, including Cas1 to Cas4, are found only in genomes with CRISPR repeats, and are near these repeats. Jansen, et al. describe CRISPR loci as having direct repeats, varying in size from 21 to 37 bp, interspaced by similarly sized non-repetitive sequences. We (Haft, et al.) described subtypes in which certain groups of subtype-specific genes are found in addition to characteristic sets of the more widely distributed cas genes [2]. A number of strictly CRISPR-associated genes with narrow species distributions have not yet been assigned to subtypes and have been collected into an _other_category. A recent review of CRISPR families [3] has identified broader categories of CRISPR systems. Apern is I-A, Tneap/Hmari is I-B, Dvulg is I-C, Cyano is I-D, Ecoli is I-E, Ypest is I-F, Nmeni is type II, Mtube is type III-A, and the RAMP module is type III-B. | |
JCVI Role | Other | |
Parent Property | GenProp1067: Defense systems | |
Literature References |
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Gene Ontology Term | GO:0043571: maintenance of CRISPR repeat elements (biological_process) |
Components
Step Name | Step Num | Required | Evidence (Method) | Evidence Go Terms |
---|---|---|---|---|
Aferr subtype specific proteins | Aferr | NO | TIGR03114 (HMM): CRISPR type AFERR-associated protein Csf1 TIGR03115 (HMM): CRISPR type IV/AFERR-associated protein Csf2 TIGR03116 (HMM): CRISPR type IV/AFERR-associated protein Csf3 TIGR03117 (HMM): CRISPR type AFERR-associated DEAD/DEAH-box helicase Csf4 | GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements |
Apern subtype specific proteins | Apern | NO | TIGR01874 (HMM): CRISPR-associated protein Cas5, subtype I-A/APERN TIGR01878 (HMM): CRISPR type I-A/APERN-associated protein Csa5 TIGR01884 (HMM): CRISPR locus-related DNA-binding protein TIGR01896 (HMM): CRISPR-associated protein Cas4/Csa1, subtype I-A/APERN TIGR01914 (HMM): CRISPR-associated protein Cas8a2/Csa4, subtype I-A/APERN TIGR02583 (HMM): CRISPR-associated protein Cas7/Csa2, subtype I-A/APERN TIGR02671 (HMM): CRISPR-associated protein Cas8a2/Csx9, subtype I-A/APERN TIGR03876 (HMM): CRISPR type I-A/APERN-associated protein CsaX | GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements |
Cas1 | Cas1 | YES | TIGR00287 (HMM): CRISPR-associated endonuclease Cas1 | GO:0043571: maintenance of CRISPR repeat elements |
Cas2 | Cas2 | NO | TIGR01573 (HMM): CRISPR-associated endonuclease Cas2 TIGR01873 (HMM): CRISPR-associated endoribonuclease Cas2, subtype I-E/ECOLI | GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements |
Cas3 (core, HD domain, Ypest-specific) | Cas3 | NO | TIGR01587 (HMM): CRISPR-associated helicase Cas3 TIGR01596 (HMM): CRISPR-associated endonuclease Cas3-HD TIGR02562 (HMM): CRISPR-associated helicase Cas3, subtype I-F/YPEST TIGR02621 (HMM): CRISPR-associated helicase Cas3, subtype Dpsyc | GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements |
Cas4 | Cas4 | NO | TIGR00372 (HMM): CRISPR-associated protein Cas4 | GO:0043571: maintenance of CRISPR repeat elements |
Cas5 | Cas5 | NO | TIGR02593 (HMM): CRISPR-associated protein Cas5 | GO:0043571: maintenance of CRISPR repeat elements |
Cas6 | Cas6 | NO | TIGR01877 (HMM): CRISPR-associated endoribonuclease Cas6 | GO:0043571: maintenance of CRISPR repeat elements |
Dpsyc subtype specific proteins | Dpsyc | NO | TIGR02165 (HMM): CRISPR-associated protein GSU0054/csb2, Dpsyc system TIGR02570 (HMM): CRISPR-associated protein GSU0053/csb1, Dpsyc system TIGR04106 (HMM): CRISPR-associated protein GSU0052/csb3, Dpsyc system TIGR04113 (HMM): CRISPR-associated protein Csx17, subtype Dpsyc | GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements |
Dvulg subtype specific proteins | Dvulg | NO | TIGR01863 (HMM): CRISPR-associated protein Cas8c/Csd1, subtype I-C/DVULG TIGR01876 (HMM): CRISPR-associated protein Cas5, subtype I-C/DVULG TIGR02589 (HMM): CRISPR-associated protein Cas7/Csd2, subtype I-C/DVULG | GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements |
Ecoli subtype specific proteins | Ecoli | NO | TIGR01868 (HMM): CRISPR-associated protein Cas5/CasD, subtype I-E/ECOLI TIGR01869 (HMM): CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI TIGR01907 (HMM): CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI TIGR02547 (HMM): CRISPR type I-E/ECOLI-associated protein CasA/Cse1 TIGR02548 (HMM): CRISPR type I-E/ECOLI-associated protein CasB/Cse2 | GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements |
Hmari subtype specific proteins | Hmari | NO | TIGR02591 (HMM): CRISPR-associated protein Cas8b/Csh1, subtype I-B/HMARI TIGR02590 (HMM): CRISPR-associated protein Cas7/Csh2, subtype I-B/HMARI TIGR02592 (HMM): CRISPR-associated protein Cas5, subtype I-B/HMARI | GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements |
Mtube subtype specific proteins | Mtube | NO | TIGR01870 (HMM): CRISPR type III-A/MTUBE-associated protein Csm2 TIGR02578 (HMM): CRISPR-associated protein Cas10/Csm1, subtype III-A/MTUBE TIGR02582 (HMM): CRISPR type III-A/MTUBE-associated RAMP protein Csm3 TIGR01903 (HMM): CRISPR type III-A/MTUBE-associated RAMP protein Csm4 TIGR01899 (HMM): CRISPR type III-A/MTUBE-associated RAMP protein Csm5 TIGR02672 (HMM): CRISPR type III-A/MTUBE-associated protein Csm6 | GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements |
Myxan subtype specific proteins | Myxan | NO | TIGR03485 (HMM): CRISPR-associated protein Cas8a1/Csx13, MYXAN subtype TIGR03486 (HMM): CRISPR-associated protein Cas8a1/Csx13, MYXAN subtype, C-terminal region TIGR02586 (HMM): CRISPR-associated protein Cas5/DevS, subtype MYXAN | GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements |
Nmeni subtype specific proteins | Nmeni | NO | TIGR01865 (HMM): CRISPR subtype II RNA-guided endonuclease Cas9 TIGR01866 (HMM): CRISPR type II-A/NMEMI-associated protein Csn2 | GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements |
Pging subtype specific proteins | Pging | NO | TIGR03489 (HMM): CRISPR-associated protein Cas7/Csp1, subtype PGING TIGR03487 (HMM): CRISPR-associated protein Cas8c/Csp2, subtype PGING | GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements |
PreFran subtype specific proteins | PreFran | NO | TIGR04330 (HMM): CRISPR-associated protein Cpf1, subtype PREFRAN | GO:0043571: maintenance of CRISPR repeat elements |
RAMP module proteins | R-module | NO | TIGR01881 (HMM): CRISPR type III-B/RAMP module-associated protein Cmr5 TIGR02577 (HMM): CRISPR-associated protein Cas10/Cmr2, subtype III-B TIGR01894 (HMM): CRISPR type III-B/RAMP module RAMP protein Cmr1 TIGR01888 (HMM): CRISPR type III-B/RAMP module-associated protein Cmr3 TIGR02580 (HMM): CRISPR type III-B/RAMP module RAMP protein Cmr4 TIGR01898 (HMM): CRISPR type III-B/RAMP module RAMP protein Cmr6 | GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements |
RAMPs not otherwise accounted for | RAMP-new | NO | TIGR02581 (HMM): CRISPR-associated RAMP protein, SSO1426 family TIGR02674 (HMM): CRISPR-associated RAMP protein, Csx10 family | GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements |
Tneap subtype specific proteins | Tneap | NO | TIGR01908 (HMM): CRISPR-associated protein Cas8b1/Cst1, subtype I-B/TNEAP TIGR01895 (HMM): CRISPR-associated protein Cas5, subtype I-B/TNEAP TIGR02585 (HMM): CRISPR-associated protein Cas7/Cst2/DevR, subtype I-B/TNEAP | GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements |
Ypest subtype specific proteins | Ypest | NO | TIGR02563 (HMM): CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST TIGR02566 (HMM): CRISPR type I-F/YPEST-associated protein Csy3 TIGR02565 (HMM): CRISPR type I-F/YPEST-associated protein Csy2 TIGR02564 (HMM): CRISPR type I-F/YPEST-associated protein Csy1 | GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements |
other CRISPR-associated families | other | NO | TIGR01897 (HMM): CRISPR-associated protein, MJ1666 family TIGR02221 (HMM): CRISPR-associated protein, TM1812 family TIGR02579 (HMM): CRISPR-associated protein, Csx3 family TIGR02584 (HMM): CRISPR-associated protein, NE0113 family TIGR02620 (HMM): putative CRISPR-associated protein, VVA1548 family TIGR02670 (HMM): CRISPR-associated protein Cas8a1/Csx8, subtype I TIGR03031 (HMM): CRISPR system subtype II-B RNA-guided endonuclease Cas9/Csx12 TIGR02619 (HMM): putative CRISPR-associated protein, APE2256 family TIGR02682 (HMM): CRISPR-associated protein, Csx11 family TIGR03984 (HMM): CRISPR-associated protein, TIGR03984 family TIGR03985 (HMM): CRISPR-associated protein, TIGR03985 family TIGR03986 (HMM): CRISPR-associated protein TIGR02710 (HMM): CRISPR-associated protein, TIGR02710 family TIGR03642 (HMM): CRISPR-associated protein, Csx14 family TIGR02556 (HMM): CRISPR-associated protein, TM1802 family | GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements GO:0043571: maintenance of CRISPR repeat elements |
CRISPR | rpt | NO | CRISPR (FEATURE_TYPE) | GO:0043571: maintenance of CRISPR repeat elements |
Parent Properties
Accession | Name |
---|---|
GenProp1067 | Defense systems |
Child Properties
Accession | Name |
---|---|
GenProp0310 | CRISPR system, I-F/Ypest subtype |
GenProp0313 | CRISPR system, I-C/Dvulg subtype |
GenProp0314 | CRISPR system, II/Nmeni subtype |
GenProp0315 | CRISPR system, I-E/Ecoli subtype |
GenProp0316 | CRISPR system, III-B/RAMP module subtype |
GenProp0317 | CRISPR system, I-B subtype, Tneap branch |
GenProp0318 | CRISPR system, III-A/Mtube subtype |
GenProp0319 | CRISPR system, I-A/Apern subtype |
GenProp0320 | CRISPR system, I-B subtype, Hmari branch |
GenProp0469 | CRISPR system, Dpsyc subtype |
GenProp0670 | CRISPR system, Aferr subtype |
GenProp0685 | CRISPR system, I-D/Cyano subtype |
GenProp0768 | CRISPR system, Pging subtype |
GenProp0922 | CRISPR system, Myxan subtype |
GenProp1061 | CRISPR system, PreFran subtype |
Sibling Properties
Accession | Name |
---|---|
GenProp0455 | restriction enzyme system, type I |
GenProp0650 | type II restriction system, Alw26I/Eco31I/Esp3I family |
GenProp0701 | DNA sulfur modification system dnd |