Genome Property Definition Page

AccessionGenProp0021
NameCRISPR region
TypeGUILD
DescriptionCRISPR 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 RoleOther
Parent PropertyGenProp1067: Defense systems
Literature References
[ 1 ]Haft DH, Selengut J, Mongodin EF, Nelson KE  A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes.  PLoS Comput Biol. 2005 Nov;1(6):e60. Epub 2005 Nov 11.  PMID 16292354
[ 2 ]Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, Moineau S, Mojica FJ, Wolf YI, Yakunin AF, van der Oost J, Koonin EV  Evolution and classification of the CRISPR-Cas systems.  Nat Rev Microbiol. 2011 Jun;9(6):467-77. Epub 2011 May 9.  PMID 21552286
[ 3 ]Jansen R, Embden JD, Gaastra W, Schouls LM  Identification of genes that are associated with DNA repeats in prokaryotes.  Mol Microbiol. 2002 Mar;43(6):1565-75.  PMID 11952905
Gene Ontology TermGO:0043571: maintenance of CRISPR repeat elements (biological_process)

Components
Step NameStep NumRequiredEvidence (Method)Evidence Go Terms
Aferr subtype specific proteinsAferrNOTIGR03114 (HMM): CRISPR type AFERR-associated protein Csf1
TIGR03115 (HMM): CRISPR type AFERR-associated protein Csf2
TIGR03116 (HMM): CRISPR type 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 proteinsApernNOTIGR01874 (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
Cas1Cas1YESTIGR00287 (HMM): CRISPR-associated endonuclease Cas1GO:0043571: maintenance of CRISPR repeat elements
Cas2Cas2NOTIGR01573 (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)Cas3NOTIGR01587 (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
Cas4Cas4NOTIGR00372 (HMM): CRISPR-associated protein Cas4GO:0043571: maintenance of CRISPR repeat elements
Cas5Cas5NOTIGR02593 (HMM): CRISPR-associated protein Cas5GO:0043571: maintenance of CRISPR repeat elements
Cas6Cas6NOTIGR01877 (HMM): CRISPR-associated endoribonuclease Cas6GO:0043571: maintenance of CRISPR repeat elements
Dpsyc subtype specific proteinsDpsycNOTIGR02165 (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 proteinsDvulgNOTIGR01863 (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 proteinsEcoliNOTIGR01868 (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 proteinsHmariNOTIGR02591 (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 proteinsMtubeNOTIGR01870 (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 proteinsMyxanNOTIGR03485 (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 proteinsNmeniNOTIGR01865 (HMM): CRISPR-associated protein Cas9/Csn1, subtype II/NMEMI
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 proteinsPgingNOTIGR03489 (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 proteinsPreFranNOTIGR04330 (HMM): CRISPR-associated protein Cpf1, subtype PREFRANGO:0043571: maintenance of CRISPR repeat elements
RAMP module proteinsR-moduleNOTIGR01881 (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 forRAMP-newNOTIGR02581 (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 proteinsTneapNOTIGR01908 (HMM): CRISPR-associated protein Cas8a1/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 proteinsYpestNOTIGR02563 (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 familiesotherNOTIGR01897 (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-associated protein Cas9/Csx12, subtype II-B/NMENI
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
CRISPRrptNOCRISPR (FEATURE_TYPE)
GO:0043571: maintenance of CRISPR repeat elements

Parent Properties
AccessionName
GenProp1067Defense systems

Child Properties
AccessionName
GenProp0310CRISPR system, I-F/Ypest subtype
GenProp0313CRISPR system, I-C/Dvulg subtype
GenProp0314CRISPR system, II/Nmeni subtype
GenProp0315CRISPR system, I-E/Ecoli subtype
GenProp0316CRISPR system, III-B/RAMP module subtype
GenProp0317CRISPR system, I-B subtype, Tneap branch
GenProp0318CRISPR system, III-A/Mtube subtype
GenProp0319CRISPR system, I-A/Apern subtype
GenProp0320CRISPR system, I-B subtype, Hmari branch
GenProp0469CRISPR system, Dpsyc subtype
GenProp0670CRISPR system, Aferr subtype
GenProp0685CRISPR system, I-D/Cyano subtype
GenProp0768CRISPR system, Pging subtype
GenProp0922CRISPR system, Myxan subtype
GenProp1061CRISPR system, PreFran subtype

Sibling Properties
AccessionName
GenProp0455restriction enzyme system, type I
GenProp0650type II restriction system, Alw26I/Eco31I/Esp3I family
GenProp0701DNA sulfur modification system dnd