GABI Primary Database ( GabiPD ) - Genomanalyse im biologischen System Pflanze

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Clone: HA01F20

Genotype (Genotype)

	species:	Hordeum vulgare
	type:	wildtype
	common name:	barley
	cultivar:	Barke

Library:

	lib name:	IPKc 2018
	tissue:	embryosac
	stage/tissue:	0-7 DAP (days after pollination)
	cloning vector:	pBluescript SK+ site_1: EcoRI (5'-end of cDNA); site_2: XhoI (3'-end of cDNA)
	host:	XL10-Gold
	antibiotic:	Ampicillin
	library description:
	0-7 DAP(days after pollination) Due to a cloning artefact caused by the kit, in most cases the EcoRI site is NOT present, as well as the EcoRIadapter used for cloning. To excise the insert, restriction sites upstream EcoRI should be used (e.g. BamHI, SalI,PstI). NOTE: Also due to the cloning system used Blue/white selection for recombinats is not 100% reliable. Average insert size is 1 kb

Related with

LOC_Os09g39400.2	annotated gene (TIGR5)
LOC_Os09g39400.1	annotated gene (TIGR5)
Hv.8009	unigene cluster
Sof.14315	unigene cluster
Os.4702	unigene cluster
Hv.13426	unigene cluster
Hv.23678	unigene cluster
LOC_Os09g39400.2	annotated gene (MSU 6.1)
LOC_Os09g39400.1	annotated gene (MSU 6.1)

Sequence: HA01F20r

submitter of sequence:	Dr. Nils Stein
length:	263
priming:	5-prime
GenBankAc:	BQ459352
IPK CR-EST:	HA01F20r

HA01F20r
CGGCACGAGG CCAGCAGCTG CAGTCGCTGG AGGAGGGGGG CAGCGCGTCG GGCTTCGTCG         60
CCGAGGTCGC CACCCTCTTC ATCGAAGACG CCGACCGGAT CATCGCCGAC ATCGCCGCCC        120
TGCTGGACCA GCCCGCCGTG GACTTCGACA AGGTGGACGC GCACGTGCAC CAGCTCAAGG        180
GGAGCAGCTC CAGTGTTGGC GCTCAGAAAG TGAAGCTCGC CTGCATGCAC TTCCGCCAGT        240
TCTATGAGGC AAAAAGTAAA GAT                                                263

Type	Position	Orientation
ORF	1 - 210:	forward
ORF	2 - 244:	forward
ORF	112 - 2:	reverse
ORF	261 - 178:	reverse

Cluster Info:
Contig3529.1	(9 members)
Representative for Uniset

view Blast Searches

Oryza sativa pep on 09-MAR-07
E-val	simil.	overlap	accno	description
03e-20	57	149	TIGR:LOC_Os09g39400.1	LOC_Os09g39400.1\|11979.m06878\|protein Histidine-containing phosphotransfer protein 1, putative, expressed
06e-16	50	147	TIGR:LOC_Os08g44350.1	LOC_Os08g44350.1\|11978.m08408\|protein Hpt domain containing protein, expressed
non redundant GenBank CDS translations \+ PDB \+ SwissProt \+ PIR on 09-MAR-07
E-val	simil.	overlap	accno	description
01e-18	57	149	GenBankAc:1YVI	pdb\|1YVI\|B Chain B, X-Ray Structure Of Putative Histidine-Containing Phosphotransfer Protein From Rice, Ak104879 pdb\|1YVI\|A Chain A, X-Ray Structure Of Putative Histidine-Containing Phosphotransfer Protein From Rice, Ak104879
01e-18	57	149	GenBankAc:AAQ24029.1	gb\|AAQ24029.1\| two-component phosphorelay mediator HP1 [Oryza sativa (japonica cultivar-group)] dbj\|BAD46253.1\| putative histidine-containing phosphotransfer protein [Oryza sativa (japonica cultivar-group)]
02e-14	50	147	GenBankAc:XP_483752.1	ref\|XP_483752.1\| two-component phosphorelay mediator HP2 [Oryza sativa (japonica cultivar-group)] gb\|AAQ24030.1\| two-component phosphorelay mediator HP2 [Oryza sativa (japonica cultivar-group)] dbj\|BAD09087.1\| two-component phosphorelay mediator HP2 [Oryza sativa (japonica cultivar-group)] gb\|AAV31128.1\| histidine-containing phosphotransfer protein [Oryza sativa (japonica cultivar-group)]
06e-19	58	145	GenBankAc:1WN0	pdb\|1WN0\|D Chain D, Crystal Structure Of Histidine-Containing Phosphotransfer Protein, Zmhp2, From Maize pdb\|1WN0\|C Chain C, Crystal Structure Of Histidine-Containing Phosphotransfer Protein, Zmhp2, From Maize pdb\|1WN0\|B Chain B, Crystal Structure Of Histidine-Containing Phosphotransfer Protein, Zmhp2, From Maize pdb\|1WN0\|A Chain A, Crystal Structure Of Histidine-Containing Phosphotransfer Protein, Zmhp2, From Maize dbj\|BAA82874.1\| histidine-containing phosphotransfer protein [Zea mays]
03e-14	51	144	GenBankAc:BAA84993.1	dbj\|BAA84993.1\| histidine-containing phosphotransfer protein [Zea mays]
All nt+env_nt+patnt+pdbnt on 31-MAR-10
E-val	simil.	overlap	accno	description
06e-78	91.1	257	GenBankAc:EA153178.1	Sequence 17493 from patent US 7214786
01e-105	94.5	255	GenBankAc:AY342358.1	Triticum aestivum histidine-containing phosphotransfer protein mRNA, complete cds
01e-114	96	252	GenBankAc:BK005644.1	TPA_inf: Triticum aestivum histidine-containing phosphotransfer protein 2 (HP) mRNA, complete cds
01e-105	94.8	249	GenBankAc:GP685097.1	Sequence 36006 from patent US 7569389
01e-105	94.8	249	GenBankAc:BK005645.1	TPA_inf: Triticum aestivum histidine-containing phosphotransfer protein 3 (HP) mRNA, complete cds
01e-32	84.6	195	GenBankAc:CT832141.1	Oryza sativa (indica cultivar-group) cDNA clone:OSIGCEA040M21, full insert sequence
01e-32	84.6	195	GenBankAc:AK072521.1	Oryza sativa Japonica Group cDNA clone:J023131B06, full insert sequence
01e-32	84.6	195	GenBankAc:AY345241.1	Oryza sativa (japonica cultivar-group) two-component phosphorelay mediator HP1 mRNA, complete cds
01e-32	84.6	195	GenBankAc:NM_001070496.1	Oryza sativa (japonica cultivar-group) Os09g0567400 (Os09g0567400) mRNA, complete cds
01e-32	84.6	195	GenBankAc:AK104879.1	Oryza sativa Japonica Group cDNA clone:001-044-F01, full insert sequence
03e-30	84.1	195	GenBankAc:AX654330.1	Sequence 4200 from Patent WO03000898
09e-46	87.6	193	GenBankAc:EA150185.1	Sequence 14500 from patent US 7214786
02e-43	87	193	GenBankAc:GP686133.1	Sequence 39951 from patent US 7569389
02e-43	87	193	GenBankAc:XM_002459786.1	Sorghum bicolor hypothetical protein, mRNA
02e-43	87	193	GenBankAc:EZ054445.1	TSA: Zea mays contig55567, mRNA sequence
02e-43	87	193	GenBankAc:BT064302.1	Zea mays full-length cDNA clone ZM_BFc0157M04 mRNA, complete cds
02e-43	87	193	GenBankAc:EU963994.1	Zea mays clone 274899 histidine-containing phosphotransfer protein 1 mRNA, complete cds
02e-43	87	193	GenBankAc:AY109580.1	Zea mays CL1301_1 mRNA sequence
02e-43	87	193	GenBankAc:NM_001111380.1	Zea mays histidine-containing phosphotransfer protein2 (hp2), mRNAdbj\|AB024292.1\| Zea mays ZmHP2 mRNA for histidine-containing phosphotransfer protein, complete cds
02e-43	87	193	GenBankAc:BT037916.1	Zea mays full-length cDNA clone ZM_BFb0202M22 mRNA, complete cds
08e-28	85	167	GenBankAc:FP099014.1	Phyllostachys edulis cDNA clone: bphyst333z60, full insert sequence
03e-18	82.8	163	GenBankAc:FP096691.1	Phyllostachys edulis cDNA clone: bphyst026d11, full insert sequence
UniProt 15.12 UniRef100 on 28-DEC-09
E-val	simil.	overlap	accno	description
02e-26	76.5	85	UniProt_UniRef:UniRef100_Q4VWF0	Histidine-containing phosphotransfer protein n=1 Tax=Triticum aestivum RepID=Q4VWF0_WHEAT
02e-18	58.3	84	UniProt_UniRef:UniRef100_Q9SLX1	Histidine-containing phosphotransfer protein 1 n=1 Tax=Zea mays RepID=Q9SLX1_MAIZE
02e-18	58.3	84	UniProt_UniRef:UniRef100_C5X5X2	Putative uncharacterized protein Sb02g011910 n=1 Tax=Sorghum bicolor RepID=C5X5X2_SORBI
01e-15	57.1	84	UniProt_UniRef:UniRef100_B3TLT2	Histidine-containing phosphotransfer protein Zmhp2 chain D n=1 Tax=Elaeis guineensis RepID=B3TLT2_ELAGV
07e-17	57.1	84	UniProt_UniRef:UniRef100_B8BEM5	Putative uncharacterized protein n=1 Tax=Oryza sativa Indica Group RepID=B8BEM5_ORYSI
04e-18	57.1	84	UniProt_UniRef:UniRef100_Q6VAK4	Histidine-containing phosphotransfer protein 1 n=2 Tax=Oryza sativa Japonica Group RepID=HP1_ORYSJ
03e-14	53.6	84	UniProt_UniRef:UniRef100_C5YN90	Putative uncharacterized protein Sb07g024310 n=1 Tax=Sorghum bicolor RepID=C5YN90_SORBI
07e-14	50	84	UniProt_UniRef:UniRef100_Q6VAK3	Os08g0557700 protein n=1 Tax=Oryza sativa Japonica Group RepID=Q6VAK3_ORYSJ
07e-14	50	84	UniProt_UniRef:UniRef100_B8B9H1	Putative uncharacterized protein n=1 Tax=Oryza sativa Indica Group RepID=B8B9H1_ORYSI
05e-16	55.7	79	UniProt_UniRef:UniRef100_B7EKW5	cDNA clone:001-044-F01, full insert sequence n=1 Tax=Oryza sativa Japonica Group RepID=B7EKW5_ORYSJ
Oryza sativa japonica annotation TIGR 6.1 (cDNA)20091211 on 14-DEC-09
E-val	simil.	overlap	accno	description
03e-35	84.6	195	GabiPD:LOC_Os09g39400.2 TIGR:LOC_Os09g39400.2	LOC_Os09g39400.2\|protein histidine-containing phosphotransfer protein, putative, expressed (TIGR 6.1)
03e-35	84.6	195	GabiPD:LOC_Os09g39400.1 TIGR:LOC_Os09g39400.1	LOC_Os09g39400.1\|protein histidine-containing phosphotransfer protein, putative, expressed (TIGR 6.1)
UniGeneDec2009.fasta on 14-DEC-09
E-val	simil.	overlap	accno	description
01e-133	98.8	253	GabiPD:Hv.8009 unigene:Hv.8009	Hv.8009
02e-34	84.6	195	GabiPD:Os.4702 unigene:Os.4702	Os.4702
03e-45	87	193	GabiPD:Sof.14315 unigene:Sof.14315	Sof.14315
06e-19	81.6	185	GabiPD:Hv.23678 unigene:Hv.23678	Hv.23678
06e-28	85.3	156	GabiPD:Hv.13426 unigene:Hv.13426	Hv.13426

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