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

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Clone: HP07D15

Genotype (Genotype)

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

Library:

	lib name:	IPKc 2028
	tissue:	epidermis
	stage/tissue:	seedlings grown in greenhouse for 6 days
	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:
	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 850 bp

Related with

Hv.23072	unigene cluster
Sbi.12403	unigene cluster

Sequence: HP07D15T

submitter of sequence:	Dr. Nils Stein
length:	548
priming:	5-prime
GenBankAc:	CB878068
IPK CR-EST:	HP07D15T

Sequence features and Clone alignments (BLAST):

	X

Gene structure	UTR	start codon	stop codon	exon-exon border
Clone alignments	forward	reverse	start	stop
Protein domains	domain

Click on sequence features to obtain additional information.

HP07D15T
GATCAAGGAC TCGCGGCGCA GTTGGTCCCT GTAGCACCCA CCCACCCACA CAGCTCCAGC         60
TCCGAAGGAG GAGTGAGGAC CATGGCCACC TCCACCGCCG CCGTGCTGTC CCCGCCCGCC        120
GTGGCCGGGC TCCGCCTAGC GCCGTCCCCG CGCGCGGCGG CCTCGTTCCG GGGGGTCTCA        180
CCGCCGGCGC GGCGGTCCGT GGCGGCGCGG GCCGCGCTGG AGCCGTCGGT GGTGATCAGC        240
CTCAGCACGG GGCTGTCGCT CGTGATGGGC CGCTTCGTCT TCTTCAACTT CCAGCGGGAG        300
AACGTGGCGA AGCAGGTCCC CGAGCAGAAC GGTAAGACCC ACTTCGAGGC CGGTGACGAG        360
CGCGCCAAGG AGTTCGCCGG GATCCTCAAG TCCAACGATC CCGTCGGCTT CAATCTCGTC        420
GACGTCCTCG CATGGGGCTC CATCGGCCAC ATCGTCGCCT ACTACATCCT CGCCACCACC        480
AGCTATGGAT ACGACCCTCC CTTCTTCGGC TGATCCGTCC GTCTCCCCTG CCTGCCTGCG        540
TGCCGGCC                                                                 548

Type	Position	Orientation
ORF	1 - 510:	forward
ORF	3 - 332:	forward
ORF	432 - 548:	forward
ORF	452 - 6:	reverse
ORF	485 - 547:	forward
ORF	546 - 181:	reverse
ORF	547 - 413:	reverse
ORF	548 - 486:	reverse

Cluster Info:
Contig40620.1	(29 members)

view Blast Searches

Oryza sativa pep on 09-MAR-07
E-val	simil.	overlap	accno	description
01e-50	72	141	TIGR:LOC_Os09g30340.1	LOC_Os09g30340.1\|11979.m06185\|protein Photosystem I reaction center subunit V, chloroplast precursor, putative, expressed
non redundant GenBank CDS translations \+ PDB \+ SwissProt \+ PIR on 09-MAR-07
E-val	simil.	overlap	accno	description
02e-42	83	160	GenBankAc:NP_175963.1	ref\|NP_175963.1\| unknown protein [Arabidopsis thaliana] gb\|AAK00374.1\| putative photosystem I subunit V precursor [Arabidopsis thaliana] gb\|AAG41452.1\| putative photosystem I subunit V precursor [Arabidopsis thaliana] gb\|AAK91476.1\| At1g55670/F20N2_3 [Arabidopsis thaliana] gb\|AAK55662.1\| At1g55670/F20N2_3 [Arabidopsis thaliana] gb\|AAG40061.1\| At1g55670 [Arabidopsis thaliana] emb\|CAB52748.1\| photosystem I subunit V precursor [Arabidopsis thaliana] sp\|Q9S7N7\|PSAG_ARATH Photosystem I reaction center subunit V, chloroplast precursor (PSI-G)
03e-65	89	143	GenBankAc:CAA42727.1	emb\|CAA42727.1\| photosystem I polypeptide PSI-G precursor [Hordeum vulgare] sp\|Q00327\|PSAG_HORVU Photosystem I reaction center subunit V, chloroplast precursor (PSI-G) (Photosystem I 9 kDa protein)
03e-63	87	143	GenBankAc:CAJ75642.1	emb\|CAJ75642.1\| photosystem 1 subunit 5 [Triticum aestivum]
01e-60	83	143	GenBankAc:CAJ26374.1	emb\|CAJ26374.1\| photosystem 1 subunit 5 [Brachypodium sylvaticum]
03e-49	72	141	GenBankAc:BAD46343.1	dbj\|BAD46343.1\| putative Photosystem I reaction center subunit V [Oryza sativa (japonica cultivar-group)] dbj\|BAD33396.1\| putative Photosystem I reaction center subunit V [Oryza sativa (japonica cultivar-group)]
All nt+env_nt+patnt+pdbnt on 31-MAR-10
E-val	simil.	overlap	accno	description
01e-168	97.9	331	GenBankAc:X60158.1	H.vulgare PsaG mRNA
01e-147	96	322	GenBankAc:EA162478.1	Sequence 26793 from patent US 7214786
01e-139	95	320	GenBankAc:EA162476.1	Sequence 26791 from patent US 7214786
01e-139	96.3	299	GenBankAc:EA162479.1	Sequence 26794 from patent US 7214786
01e-139	96.3	299	GenBankAc:AK332626.1	Triticum aestivum cDNA, clone: WT004_H11, cultivar: Chinese Spring
04e-99	92	275	GenBankAc:FP091369.1	Phyllostachys edulis cDNA clone: bphyst009d16, full insert sequence
01e-89	90.5	275	GenBankAc:GP612115.1	Sequence 20119 from patent US 7560542
01e-89	90.5	275	GenBankAc:GP662183.1	Sequence 70187 from patent US 7560542
01e-89	90.5	275	GenBankAc:DQ245899.1	Zea mays clone 22121 mRNA sequence
03e-87	90.2	275	GenBankAc:NM_001157742.1	Zea mays photosystem I reaction center subunit V (LOC100284847), mRNAgb\|EU969877.1\| Zea mays clone 336735 photosystem I reaction center subunit V mRNA, complete cds
03e-87	90.2	275	GenBankAc:EU958643.1	Zea mays clone 1707142 photosystem I reaction center subunit V mRNA, complete cds
03e-87	90.2	275	GenBankAc:GP677639.1	Sequence 7883 from patent US 7569389
03e-87	90.2	275	GenBankAc:BT043247.1	Zea mays full-length cDNA clone ZM_BFc0132C01 mRNA, complete cds
03e-87	90.2	275	GenBankAc:GP617552.1	Sequence 25556 from patent US 7560542
03e-87	90.2	275	GenBankAc:EU957381.1	Zea mays clone 1590298 photosystem I reaction center subunit V mRNA, complete cds
03e-87	90.2	275	GenBankAc:EU957293.1	Zea mays clone 1588044 photosystem I reaction center subunit V mRNA, complete cds
09e-94	91.2	274	GenBankAc:FP099694.1	Phyllostachys edulis cDNA clone: bbasst002l21, full insert sequence
09e-94	91.2	274	GenBankAc:FP096717.1	Phyllostachys edulis cDNA clone: bbasst002h12, full insert sequence
03e-84	89.8	274	GenBankAc:XM_002460382.1	Sorghum bicolor hypothetical protein, mRNA
UniProt 15.12 UniRef100 on 28-DEC-09
E-val	simil.	overlap	accno	description
01e-41	57.2	166	UniProt_UniRef:UniRef100_C6SWM2	Putative uncharacterized protein n=1 Tax=Glycine max RepID=C6SWM2_SOYBN
09e-65	89.5	143	UniProt_UniRef:UniRef100_Q00327	Photosystem I reaction center subunit V, chloroplastic n=1 Tax=Hordeum vulgare RepID=PSAG_HORVU
09e-63	87.4	143	UniProt_UniRef:UniRef100_Q2L3V4	Photosystem 1 subunit 5 n=1 Tax=Triticum aestivum RepID=Q2L3V4_WHEAT
04e-60	83.2	143	UniProt_UniRef:UniRef100_Q2L3E3	Photosystem 1 subunit 5 n=1 Tax=Brachypodium sylvaticum RepID=Q2L3E3_BRASY
02e-51	75.5	143	UniProt_UniRef:UniRef100_B6U534	Photosystem I reaction center subunit V n=1 Tax=Zea mays RepID=B6U534_MAIZE
04e-53	76.1	142	UniProt_UniRef:UniRef100_C5X3S4	Putative uncharacterized protein Sb02g027900 n=1 Tax=Sorghum bicolor RepID=C5X3S4_SORBI
01e-53	75.9	141	UniProt_UniRef:UniRef100_B4G1K9	Photosystem I reaction center subunit V n=1 Tax=Zea mays RepID=B4G1K9_MAIZE
07e-49	72.9	140	UniProt_UniRef:UniRef100_Q69QR6	Os09g0481200 protein n=2 Tax=Oryza sativa RepID=Q69QR6_ORYSJ
05e-42	83.8	99	UniProt_UniRef:UniRef100_Q9S7N7	Photosystem I reaction center subunit V, chloroplastic n=1 Tax=Arabidopsis thaliana RepID=PSAG_ARATH
09e-42	84.7	98	UniProt_UniRef:UniRef100_Q646H3	Chloroplast photosystem I reaction center V (Fragment) n=1 Tax=Camellia sinensis RepID=Q646H3_CAMSI
Oryza sativa japonica annotation TIGR 6.1 (cDNA)20091211 on 14-DEC-09 gave no results
UniGeneDec2009.fasta on 14-DEC-09
E-val	simil.	overlap	accno	description
01e-130	96.7	276	GabiPD:Hv.23072 unigene:Hv.23072	Hv.23072
05e-86	89.8	274	GabiPD:Sbi.12403 unigene:Sbi.12403	Sbi.12403

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