ISfinder Mirror Site

IS1248A

Family IS5
Group IS427

MGE type ISRelated element(s) :
Isoform Synonym(s) IS1248, ISBm4

Accession number	Transposition	Origin	Host
U08864	Y	Paracoccus denitrificans	Paracoccus pantotrophus LMD 82.5 Paracoccus denitrificans PdX13 Paracoccus denitrificans Pd1235 Thiosphaera pantotropha

DNA section

IS Length : 832 bp

Ends

IR Length : 13/14

IRL : GGGTCAGGATGCATTGATTTTCAGTGTGCTACGTGATTCACGGCTCGGAA
IRR : GGGTCAGGATTCATAACCAATAAATGACGGTTGCCGCGAGCGCGATGGCC

Insertion site

Left flank	Direct repeat	Right flank	DR Length
TAGAGAAAGC	TA	AGACCGGCAA	2
TCCGCATTTT	TA	GGATCTCCGG	2

DNA sequence

GGGTCAGGATGCATTGATTTTCAGTGTGCTACGTGATTCACGGCTCGGAAAACGGAGCGGTGACATGAGCGACCTGTACTGGCTGACCGACGAGCAGATG
GCCAAGCTTGCCCCTTTCTTCCCGAAGTCGCACGGCAAGCCACGCGTCGATGACAAGCGTGTTCTAAGCGGGATTATCTTCATCAATCGCAATGGTTTGC
GCTGGCGAGATGCCCCCAGGGAGTATGGGCCGCACAAGACGCTCTACAGCCGGTGGAAGCGTTGGAGCGAGAAAGGCATTTTCGCCAGGATGATGATCGG
GCTGGCCGCCGACCACGGCGAGGAAAAGACCGTGATGATCGACGCGACCTATCTGAAAGCGCACCGCACCGCGACCAGCATGGCCGCGAAAAAGGGGGGC
GTGGACGCCTCGTCGGCCGGACCAAGGGCGGCATGAACACGAAGCTGCATGCCATCTGTGACAGCCAGGGCCGACCGCTCGACCTGTTCGTCACCGCAGG
GCAGGTCAGCGACTACATCGGGGCGCGGGCGTTGCTCAGCAGCCTCCCAAAGGTCGATTGGCTGCTCGGGGATCGCGGCTATGACGCCGACTGGTTCCGG
GAAGCCTTGCAGGACAAGGGGATACGAGCCTGCATCCCCGGTCGAAAGCAGCGCAAGACACCGGTCAAATACGACAAGCGCCGATACAAGCGGCGCAACC
GCATCGAGATCATGTTTGGCAGGCTCAAGGACTGGCGGCGCGTGGCAACCCGATACGACAGATGCCCGAAGGTCTTCCTCTCGGCCATCGCGCTCGCGGC
AACCGTCATTTATTGGTTATGAATCCTGACCC

Recoding section

Recoding by frameshift
Frame
Type
Experimentally demonstrated

Stimulators :

Shine-Dalgarno sequence :
Secondary structure :

Recoding motif :

Protein section

ORF number : 3

ORF 1

Length		Begin	End	Strand	Fusion ORF
372 bp	123 aa	65	436	+	No

ORF function : Transposase
Description : First part of the transposase

ORF sequence :

MSDLYWLTDEQMAKLAPFFPKSHGKPRVDDKRVLSGIIFINRNGLRWRDAPREYGPHKTLYSRWKRWSEKGIFARMMIGLAADHGEEKTVMIDATYLKAH
RTATSMAAKKGGVDASSAGPRAA

Blast result :

ORF 2

Length		Begin	End	Strand	Fusion ORF
570 bp	189 aa	253	822	+	No

ORF function : Transposase
Description : Second part of the transposase

ORF sequence :

MEALERERHFRQDDDRAGRRPRRGKDRDDRRDLSESAPHRDQHGREKGGRGRLVGRTKGGMNTKLHAICDSQGRPLDLFVTAGQVSDYIGARALLSSLPK
VDWLLGDRGYDADWFREALQDKGIRACIPGRKQRKTPVKYDKRRYKRRNRIEIMFGRLKDWRRVATRYDRCPKVFLSAIALAATVIYWL

Blast result :

ORF 3

Length		Begin	End	Strand	Fusion ORF
758 bp	252 aa	65	822	+	Yes

ORF function : Transposase
Chemistry : DDE

ORF sequence :

MSDLYWLTDEQMAKLAPFFPKSHGKPRVDDKRVLSGIIFINRNGLRWRDAPREYGPHKTLYSRWKRWSEKGIFARMMIGLAADHGEEKTVMIDATYLKAH
RTATSMAAKKGGRGRLVGRTKGGMNTKLHAICDSQGRPLDLFVTAGQVSDYIGARALLSSLPKVDWLLGDRGYDADWFREALQDKGIRACIPGRKQRKTP
VKYDKRRYKRRNRIEIMFGRLKDWRRVATRYDRCPKVFLSAIALAATVIYWL

Blast result :

Comments

Paracoccus denitrificans is a Gram-negative aerobic bacterium. At least four IS1248 copies reside in the Paracoccus denitrificans genome. At position 388, IS1248a harbours the sequence 5'-GAAAAAGGGGGGC-3' that might function as a -1 translational frameshifting site. The ORF proposed here is the fusion between the two IS1248a ORFs, as follows: (65-391) and (391-822). IS1248a allows non-replicative vector to be integrated into Paracoccus denitrificans genome. Several IS1248a variants have been isolated: IS1248b, c, d and e. IS1248b has one nt different with IS1248a.

References

1] Van Spanning, R.J.M., De Boer, A.P.N., Slotboom, D.-J., Reijnders, W.N.M., and Stouthamer, A.H. (1995) Plasmid 34, 11-21.
2] Van Spanning, R.J.M., Reijnders, W.N.M., and Stouthamer, A.H. (1995) J.Bacteriol. 177, 4772-4778.