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

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Clone: HP06A13

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

Sequence: HP06A13T

submitter of sequence:	Dr. Nils Stein
length:	558
priming:	5-prime
GenBankAc:	CB877747
IPK CR-EST:	HP06A13T

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.

HP06A13T
CGGCGCGTTG GTCCCTGTAG CACCCACCCA CCCACACAGC TCCAGCTCCG AAGGAGGAGT         60
GAGGACCATG GCCACCTCCA CCGCCGCCGT GCTGTCCCCG CCCGCCGTGG CCGGGCTCCG        120
CCTAGCGCCG TCCCCGCGCG CGGCGGCCTC GTTCCGGGGG GTCTCACCGC CGGCGCGGCG        180
GTCCGTGGCG GCGCGGGCCG CGCTGGAGCC GTCGGTGGTG ATCAGCCTCA GCACGGGGCT        240
GTCGCTCGTG ATGGGCCGCT TCGTCTTCTT CAACTTCCAG CGGGAGAACG TGGCGAAGCA        300
GGTCCCCGAG CAGAACGGCA AGACCCACTT CGAGGCCGGC GACGAGCGCG CCAAGGAGTT        360
CGCCGGGATC CTCAAGTCCA ACGACCCCGT CGGCTTCAAC CTCGTCGACG TCCTCGCATG        420
GGGCTCCATC GGCCACATCG TCGCCTACTA CATCCTCGCC ACCACCAGCA ACGGATACGA        480
CCCTCCCTTC TTCGGCTGAT CCGTCCGTCT CCCCTGCCTG CCTGCGTGCC GGCCGGAGCG        540
GCTTTGCTGT TGTAATCC                                                      558

Type	Position	Orientation
ORF	1 - 552:	forward
ORF	2 - 496:	forward
ORF	438 - 1:	reverse
ORF	556 - 167:	reverse
ORF	557 - 399:	reverse
ORF	558 - 451:	reverse

Cluster Info:
Contig40620.1	(29 members)

view Blast Searches

Oryza sativa pep on 09-MAR-07
E-val	simil.	overlap	accno	description
01e-51	73	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-43	84	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)
04e-66	90	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)
04e-64	88	143	GenBankAc:CAJ75642.1	emb\|CAJ75642.1\| photosystem 1 subunit 5 [Triticum aestivum]
02e-61	83	143	GenBankAc:CAJ26374.1	emb\|CAJ26374.1\| photosystem 1 subunit 5 [Brachypodium sylvaticum]
03e-50	73	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-170	96.7	361	GenBankAc:EA162478.1	Sequence 26793 from patent US 7214786
01e-158	95.5	357	GenBankAc:EA162476.1	Sequence 26791 from patent US 7214786
00e1	99.4	355	GenBankAc:X60158.1	H.vulgare PsaG mRNA
01e-159	95.8	355	GenBankAc:AK332626.1	Triticum aestivum cDNA, clone: WT004_H11, cultivar: Chinese Spring
01e-159	95.8	355	GenBankAc:EA162479.1	Sequence 26794 from patent US 7214786
UniProt 15.12 UniRef100 on 28-DEC-09
E-val	simil.	overlap	accno	description
05e-43	58.1	167	UniProt_UniRef:UniRef100_C6SWM2	Putative uncharacterized protein n=1 Tax=Glycine max RepID=C6SWM2_SOYBN
01e-65	90.2	143	UniProt_UniRef:UniRef100_Q00327	Photosystem I reaction center subunit V, chloroplastic n=1 Tax=Hordeum vulgare RepID=PSAG_HORVU
01e-63	88.1	143	UniProt_UniRef:UniRef100_Q2L3V4	Photosystem 1 subunit 5 n=1 Tax=Triticum aestivum RepID=Q2L3V4_WHEAT
05e-61	83.9	143	UniProt_UniRef:UniRef100_Q2L3E3	Photosystem 1 subunit 5 n=1 Tax=Brachypodium sylvaticum RepID=Q2L3E3_BRASY
03e-52	76.2	143	UniProt_UniRef:UniRef100_B6U534	Photosystem I reaction center subunit V n=1 Tax=Zea mays RepID=B6U534_MAIZE
05e-54	76.8	142	UniProt_UniRef:UniRef100_C5X3S4	Putative uncharacterized protein Sb02g027900 n=1 Tax=Sorghum bicolor RepID=C5X3S4_SORBI
02e-54	76.6	141	UniProt_UniRef:UniRef100_B4G1K9	Photosystem I reaction center subunit V n=1 Tax=Zea mays RepID=B4G1K9_MAIZE
09e-50	73.6	140	UniProt_UniRef:UniRef100_Q69QR6	Os09g0481200 protein n=2 Tax=Oryza sativa RepID=Q69QR6_ORYSJ
06e-43	84.8	99	UniProt_UniRef:UniRef100_Q9S7N7	Photosystem I reaction center subunit V, chloroplastic n=1 Tax=Arabidopsis thaliana RepID=PSAG_ARATH
01e-42	85.7	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-159	99	300	GabiPD:Hv.23072 unigene:Hv.23072	Hv.23072

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