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Status
Public on Aug 31, 2013
Title
Lactococcus lactis IL1403 and lactococcal plasmids 2.5K
Technology type
in situ oligonucleotide
Distribution
custom-commercial
Organism
Lactococcus lactis Manufacturer
NimbleGen
Manufacture protocol
High-density DNA array prepared with Maskless Array Synthesizer (MAS) technology. See manufacturer's website at http://www.nimblegen.com/.
Description
The genome sequences and ORF predictions for the chromosome of L. lactis IL1403 and several lactococcal plasmids were obtained from GenBank (accession numbers J05748, AF247159, X99798, AF409136, AF242367, AF036485, AF243383, AF207855, J04962, and AE005176). The genome sequences encoded a total of 2533 predicted ORFs (2425 genes from IL1403 and 108 genes from plasmids). The custom oligonucleotide microarrays contained 111,452 probe pairs, with each pair containing a perfect-match 24-mer oligonucleotide probe. Microarray hybridization experiments were performed at the GeneFrontier Corporation (Tokyo, Japan).
Submission date
Jun 20, 2013
Last update date
Aug 31, 2013
Contact name
Miho Kobayashi
E-mail(s)
mihokoba@affrc.go.jp Phone
+81-29-838-8685
Organization name
National Institute of Livestock and Grassland Science
Department
Animal Products Research
Street address
2 Ikenodai
City
Tsukuba
ZIP/Postal code
300-0901
Country
Japan
Samples (2)
GSM1169700 , GSM1169701 Series (1)
GSE48143 Expression analysis of Lactococcus lactis NIAI712 and its plasmid cured variant
Data table header descriptions ID GB_ACC GenBank accession number
secondary_name GI Gene Bank identification number of the sequence used to design oligonucleotide probe
FUNCTION POSITION position of the probe within the parent sequence
DESCRIPTION Gene description
Data table ID GB_ACC secondary_name GI FUNCTION POSITION DESCRIPTION LLAC030500000001
AF036485 GI:5230679
5123513
hypothetical protein
1-42810
Orf-100
LLAC030500000002
AF036485 GI:2895543
5123513
unknown
183-1115
OrfD1; similar to HsdS of pIL2614
LLAC030500000003
AF036485 GI:2895542
5123513
unknown
1103-1711
OrfC1
LLAC030500000004
AF036485 GI:2895541
5123513
replication protein
1704-2903
RepB1
LLAC030500000005
AF036485 GI:5123514
5123513
hypothetical protein
3621-3989
Orf-122
LLAC030500000006
AF036485 GI:5123515
5123513
hypothetical protein
4737-5015
Orf-92
LLAC030500000007
AF036485 GI:5123516
5123513
hypothetical protein
5127-5729
Orf-200; similar to CbiM of Archaeglobus fulgidus
LLAC030500000008
AF036485 GI:5123517
5123513
hypothetical protein
5729-6520
Orf-263; similar to CbiQ of Methanobacterium thermoautotrophicum; putative cobalt transporter
LLAC030500000009
AF036485 GI:5123518
5123513
hypothetical protein
6496-7332
Orf-278; similar to CbiO; putative cobalt transporter
LLAC030500000010
AF036485 GI:5123519
5123513
hypothetical protein
7319-8119
Orf-266; similar to CbiO; putative cobalt transporter
LLAC030500000011
AF036485 GI:5123520
5123513
unknown
8334-8495
OrfD2
LLAC030500000012
AF036485 GI:2895539
5123513
unknown
8483-9070
OrfC2
LLAC030500000013
AF036485 GI:2895538
5123513
replication protein
9063-10268
RepB2
LLAC030500000014
AF036485 GI:5123521
5123513
hypothetical protein
11812-12276
Orf-154
LLAC030500000015
AF036485 GI:5123522
5123513
hypothetical protein
12305-12601
Orf-98
LLAC030500000016
AF036485 GI:2072450
5123513
unknown
13400-14302
OrfY; similar to LytR-type regulators
LLAC030500000017
AF036485 GI:2072449
5123513
EpsL
14327-15226
LLAC030500000018
AF036485 GI:2072448
5123513
EpsK
15324-16742
similar to O-antigen exporter of Enterobacteriaceae
LLAC030500000019
AF036485 GI:2072447
5123513
EpsJ
16729-17919
LLAC030500000020
AF036485 GI:2072446
5123513
EpsI
17906-19096
similar to O-antigen polymerase of Enterobacteriaceae
2533 352 Kbytes .Supplementary file Size Download File type/resource GPL17320_2004-12-08_GFC034_Llactis.ndf.gz
5.9 Mb
(ftp) (http) NDF
GPL17320_2004-12-08_GFC034_Llactis.ngd.gz
104.0 Kb
(ftp) (http) NGD
