转座子分类表 – 转座子实验室

Copy-out–Paste-in IS elements identifed in prokaryotes

Families	groups	Size-range	DR	Ends	IRs	Nb ORF	Frameshift	Chemistry

IS1	IS1	740-1180	8-9	GGnnnTG	Y	2	ORFAB	DDE
	ISMhu11	900-4600	0-10		Y	2	ORFAB
IS3	IS911	1250			Y	2	ORFAB
	IS150	1200-1600	3-4	TG	Y	2	ORFAB	DDE
	IS407	1100-1400	4	TG
	IS51	1000-1400	3-4	TG
	IS3	1150-1750	3-4	TGa/g
	IS2	1300-1400	5	TG
IS481	–	950-1300	4-15	TGT	Y	1
IS30	–	1000-1700	2-3		Y	1		DDE
IS110	IS110	1200-1550	0		N			DEDD
	IS1111				Y *			DEDD
IS256	–	1200-1500	8-9	Ga/g	Y	1		DDE
ISL3	–	1300-2300	8	GG	Y	1
IS21	–	1750-2600	4-8	TG	Y	2 *		DDE
ISLre2

Based on reference: Copy-out–paste-in transposition of IS911: a major transposition pathway. Microbiol Spectrum 3(4):MDNA3-0031-2014 Reference

Classification, terminal features, TSD features and the number of entries of DNA transposons in Repbase

Group	Superfamily	Termini	Mechanism	TSD	Entries
IS630/Mariner	Mariner/Tc1	YR..YR	Cut-and-paste	TA	2,539
	Zator	GG..CC	Cut-and-paste	3	54
IS481/Ginger	Ginger1	TGT..ACA	Cut-and-paste	4	39
	Ginger2/TDD	TGT..ACA	Cut-and-paste	4–5	20
IS3/IS3EU	IS3EU	TAY..RTA	Copy-out–Paste-in?	6	23
IS1016/Merlin	Merlin	GG..CC	Cut-and-paste	8–9	75
IS256/DxxH	hAT	YA..TR	Cut-and-paste	5–8	2,955
	MuDR	GR..YC	Cut-and-paste	8–9	1,345
	P	CA..TG	Cut-and-paste	7–8	189
	Kolobok	RR..YY	Cut-and-paste	TTAA	286
	Dada	?		6–7	36
IS1380/piggyBac	piggyBac	YY..RR	Cut-and-paste	TTAA	377
IS5/PHIS	Harbinger	RR..YY	Cut-and-paste	3	1,097
	ISL2EU	RR..YY	Cut-and-paste?	2	88
	Spy		Cut-and-paste	no
	NuwaI
	NuwaII
	Pangu
CCHH	EnSpm/CACTA	CAC..GTG	Cut-and-paste	2–4	715
	Transib	CAC..GTG	Cut-and-paste	5	123
KDZP	Zisupton	?	?	8	18
Sola	Sola		Cut-and-paste
	Sola1	?	Cut-and-paste	4	100
	Sola2	GRG..CYC	Cut-and-paste	4	90
	Sola3	GAG..CTC	Cut-and-paste	TTAA	28
	Unclassified Sola		Cut-and-paste		1
?	Academ	YR..YR	Cut-and-paste	3–4	90
?	Novosib	CA..TG	Cut-and-paste	8	9
Crypton	Crypton		Copy-out–Paste-in
	CryptonF		Copy-out–Paste-in	0	23
	CryptonA	TTA..	Copy-out–Paste-in	0	17
	CryptonI	?	Copy-out–Paste-in	0	9
	CryptonS	TATGG..	Copy-out–Paste-in	0	59
	CryptonV	?	Copy-out–Paste-in	0	46
	Unclassified Crypton		Copy-out–Paste-in		80
Helitron	Helitron	TC..CTRR	Rolling circle	0	955
Polinton	Polinton	AG..CT	Self-synthesizing	6	108
	Unclassified DNA transposon				2,357
	Total				13,960

Eukaryotic cut-and-paste transposase superfamilies

Fig. 2. An unrooted consensus tree of the transposase superfamilies inferred from the presence or absence of the highly conserved residues in the signature strings. Bootstrap values are at the nodes. The arrows with labels indicate superfamily clusters merged in our revised classification. Shown on the right is a schematic representation of the DDE/D domain and the signature string for each superfamily. Conserved blocks are highlighted in blue, variable regions are in gray. White gaps are regions not drawn to scale. The DDE triads are highlighted in red. Alternative residues are marked by slashes; lowercase indicates that a residue occurs in <10% of the sequences in the alignment profile. The C/DH motif is highlighted in orange; the C(2)C, [M/L]H, and H(3-4)H motifs are highlighted in green.

DDE-domain-sequences (fasta): The-catalytic-domain-of-all-eukaryotic-cut-and-paste-transposase-superfamilies-dataset1 下载

List of Copy-out–Paste-in IS elements

List of mobile elements whose transposases have been examined by secondary structure prediction programs

Family	Element (or protein) analyzed	Active or # copies in genome1	From secondary structure, type of DDE/D motif2	Relevant references3
IS1	IS1NISSto9	>40*5	DD(24)EDD(20)E	* Nyman et al., 1981; Ohta et al., 2002, 2004; Siguier et al., 2009
IS1595	1. ISPna2	?,DD(36)N”	Siguier et al., 2009
	2. ISH4	?,DD(36)E”	Siguier et al., 2009
	3. IS1016C	?,DD(34)E”	Siguier et al., 2009
	4. IS1595	?,DD(35)N”	Siguier et al., 2009
	5. ISSod11	13	DD(34)H	Siguier et al., 2009
	6. ISNWi1	?,DD(35)E”	Siguier et al., 2009
	7. ISNha5	?,DD(33)E”	Siguier et al., 2009
	Merlin: MERLIN1_SM	Consensus	DD(36)E	Feschotte, 2004
IS3	IS911	Active	DD(35)E	Polard and Chandler, 1995; Rousseau et al., 2002
IS481	IS481	?00*	DD(35)E	*Glare et al., 1990; Chandler and Mahillon, 2002
IS4	IS50R	Active	PDB ID: 1muhDD(-strand)E	Rezshazy et al., 1993; Davies et al., 2000
IS701	IS701ISRso17	Active (15*)7	DD(-strand)E	*Mazel et al., 1991
ISH3	ISC1359ISC1439A	513	DD(-strand)E
IS1634	IS1634ISMac5ISPlu4	Active (?0*)77	DD(-strand)E	*Vilei et al., 1999
IS5	IS903	Active	DD(65)E	Derbyshire et al., 1987; Rezshazy et al., 1993; Tavakoli et al., 1997
	PIF/Harbinger: PIFa (Z. mays)	Active	DD(59)E	Zhang et al., 2001; Kapitonov and Jurka, 2004; Sinzelle et al., 2008
IS1182	IS660ISPsy6	314	DD(-strand)E	Takami et al., 2001
IS6	IS6100	Active	DD(34)E	Martin et al., 1990; Mahillon and Chandler, 1998
IS21	IS21	Active	DD(45)E	Mahillon and Chandler, 1998; Berger and Haas, 2001
IS30	IS30	Active	DD(33)E	Caspers et al., 1984; Mahillon and Chandler, 1998
IS66	IS679ISPsy5ISMac8	Active333	DD(-helical?)E	Han et al., 2001
IS110	IS492IS1111	Active20	DEDDDEDD	Perkins-Balding et al., 1999; Buchner et al., 2005
IS256	IS256	Active	DD(-helical)E	Mahillon and Chandler, 1998; Prudhomme et al., 2002
	MuDr/Foldback (Mutator)	Active	DD(-helical)E	Eisen et al., 1994; Babu et al., 2006; Hua-Van and Capy, 2008
IS630	ISY100	Active	DD(34)E	Doak et al., 1994; Feng and Colloms, 2007
	Tc1/mariner: Mos1 (D. mauritiana)	Active	PDB ID: 2f7tDD(34)D	Plasterk et al., 1999; Richardson et al., 2006
	Zator: Zator-1_HM	36*	DD(43)E	*Bao et al., 2009
IS982	ISPfu3	5	DD(47)E	Mahillon and Chandler, 1998
IS1380	IS1380A	?00*	DD(-strand)E	*Takemura et al., 1991; Chandler and Mahillon, 2002
	piggyBac (T. ni)	Active	DD(-strand)D	Cary et al., 1989; Sarkar et al., 2003; Mitra et al., 2008
ISAs1	ISAzo3	7	DD(-strand)E/D?
ISL3	IS31831IS651	Active22	DD(-helical)E	Suzuki et al., 2006
Tn3	Tn3 (E. coli)	Active	DD(-helical?)E	Grindley, 2002
hAT	Hermes (M. domestica)	Active	PDB ID: 2bw3 DD(-helical)E insertion	Warren et al., 1994; Rubin et al., 2001; Hickman et al., 2005
CACTA	CACTA1 (A. thaliana) En/Spm ZM	Active	DD(-helical?)E/D?	Miura et al., 2001; DeMarco et al., 2006
P	Drosophila	Active	?	Rio, 2002
Transib	Transib1_AG	Consensus	DD(-helical)E	Kapitonov and Jurka, 2005; Chen and Li, 2008
	RAG1 (M. musculus)	Active	DD(-helical)E	Kim et al., 1999; Landree et al., 1999; Lu et al., 2006
Sola	Sola3-3_HM	Multiple copies*	DD(40)E	*Bao et al., 2009

Hickman AB, Chandler M, Dyda F. Integrating prokaryotes and eukaryotes: DNA transposases in light of structure. Crit Rev Biochem Mol Biol. 2010 Feb;45(1):50-69. doi: 10.3109/10409230903505596.

Classification, distribution and the number of entries of LTR retrotransposons in Repbase

Superfamily	Total
Copia	10,595
Gypsy	6,694
BEL	1,855
ERV
ERV1	1,967
ERV2	1,266
ERV3	657
ERV4	187
Lentivirus	4
Unclassified ERV	325
Unclassified LTR	719
DIRS	418

Classification, and the number of entries of non-LTR retrotransposons in Repbase

Group	Clade	Total
CRE	CRE	43
R2	R4	46
	Hero	23
	NeSL	106
	R2	159
Dualen	RandI/Dualen	13
L1	Proto1	6
	L1	1,690
	Tx1	273
RTE	RTETP	1
	Proto2	47
	RTEX	138
	RTE	487
I	Outcast	23
	Ingi	17
	Vingi	141
	I	195
	Nimb	108
	Tad1	141
	Loa	74
	R1	237
	Jockey	243
CR1	Rex1	95
	CR1	803
	Kiri	91
	L2	285
	L2A	5
	L2B	27
	Crack	140
	Daphne	227
Ambal	Ambal	8
Penelope	Penelope	477
SINE	SINE1/7SL	95
	SINE2/tRNA	539
	SINE3/5S	30
	SINEU	17
	Unclassified SINE	112
	Unclassified non-LTR retrotransposon	179
	Total	7,341

Reference: Kenji K. Kojima, Structural and sequence diversity of eukaryotic transposable elements, Genes & Genetic Systems, 2019, Volume 94, Issue 6, Pages 233-252

Proposal of TE classes with some members having a DNA transposon phenotype

Reference: Benoît Piégu, Solenne Bire, Peter Arensburger, Yves Bigot, A survey of transposable element classification systems – A call for a fundamental update to meet the challenge of their diversity and complexity,
Molecular Phylogenetics and Evolution, Volume 86, 2015, Pages 90-109,
ISSN 1055-7903, https://doi.org/10.1016/j.ympev.2015.03.009.

Major Features of Prokaryotes IS families (ISfinder)

Overview of common transposon annotation tools

	Approach			Class I			Class II
Name		Novo.	Struc.	Simil.	LTR	LINE	SINE	TIR	HEL	MITE
RepeatMasker		x		x	x	x	x	x	x	x
RepeatModeler		x			x	x	x	x	x	x
CLARI_TE	(107)	x	x	x	x	x	x	x	x	x
TESeeker	(41)			x	x	x	x	x	x	x
PILER	(40)	x			x	x	x	x	x	x
Censor	(108)	x			x	x	x	x	x	x
RepLong	(109)	x			x	x	x	x	x	x
EDTA	(44)	x	x	x	x	x	x	x	x	x
MGEScan	(110)	x	x	x	x	x	x
LTR_Finder	(111)		x		x
LtrDetector	(112)		x		x
LTRpred	(73)	x	x	x	x
LTRharvest	(66)	x	x	x	x
LTRdigest	(113)		x		x
SINE-Finder	(68)	x	x				x
SINE-Scan	(69)	x	x				x
TIRvish	(67)		x					x
HelitronScanner	(42)		x						x
MUSTv2	(70)		x							x
MiteFinderII	(71)		x							x
MITE-Tracker	(72)		x							x
detectMITE	(45)		x							x
MITE-Hunter	(47)		x							x
TransposonUltimate

Refernce