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

•Home •Contact •FAQs •Imprint •Login

Help us improve the primary database. What do you think and where should we go in the future: https://www.surveymonkey.com/s/RK3GMPC?

search
for

Help

Clone: HX10H05

Genotype (Genotype)

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

Library:

	lib name:	IPKc 2034
	tissue:	apex
	stage/tissue:	apex (3-5 mm in size)
	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.

Related with

LOC_Os01g55830.1	annotated gene (TIGR5)
LOC_Os01g55830.2	annotated gene (TIGR5)
LOC_Os01g54590.1	annotated gene (TIGR5)
Hv.932	unigene cluster
Hv.3134	unigene cluster
Zm.81924	unigene cluster
Os.97997	unigene cluster
Sbi.17905	unigene cluster
Sbi.17875	unigene cluster
Zm.9	unigene cluster
Sof.20462	unigene cluster
Sbi.18265	unigene cluster
Sbi.14146	unigene cluster
Hv.23217	unigene cluster
Os.35653	unigene cluster
Sof.10728	unigene cluster
Sbi.11521	unigene cluster
LOC_Os01g54590.1	annotated gene (MSU 6.1)
LOC_Os01g55830.1	annotated gene (MSU 6.1)

Sequence: HX10H05r

submitter of sequence:	Dr. Nils Stein
length:	627
priming:	5-prime
GenBankAc:	CA031566
IPK CR-EST:	HX10H05r

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.

HX10H05r
GAAGAAGAGA TAGAAAAAAA AAGGTTCGAG GGCGTTGCGG AGTGAGAAGA GACGAGATGG         60
CTCCGGTGAA GCTGTACGGC GCGACCCTGT CGTGGAACGT CACCAGGTGC GTGGCGGCGC        120
TGGAGGAGGC CGGCGTCGAG TACGAGCTCG TCCCCATCAA CTTCAGCACC GGCGAGCACA        180
AGAGCCCCGA CCACCTCGCC AGGAACCCCT TTGGGCAGGT GCCAGCTTTG CAGGATGGTG        240
ACTTGTATGT CTTCGAATCA CGTGCTATTT GCAAGTATGC GTGCCGCAAG AACAAGCCAG        300
AGCTGTTGAA GGAGGGCGAC ATCAAGGAGT CAGCAATGGT GGATGTGTGG CTCGAGGTGG        360
AGGCCCATCA GTACACCGCC GCTCTGAGCC CCATTCTCTT CGAGTGCCTT ATCCATCCTA        420
TGCTTGGGGG AGCCACTGAC CAGAAGGTCA TCGACGACAA CCTTGTTAAG ATCAAGAACG        480
TGCTGGCGGT GTACGAGGCG CGGCTCACCA AGTCCAAGTA CCTGGCTGGA GACTTCCTCA        540
GCCTTGCGGA CCTTAANCCA TGCGTCTGTC ACCCTGTGCT TGGCGGCCAC ACCCTATGCA        600
TCTCTGTTTG ACGCTTACCC GCATGTG                                            627

Type	Position	Orientation
ORF	3 - 608:	forward
ORF	235 - 306:	forward
ORF	322 - 2:	reverse
ORF	416 - 333:	reverse
ORF	451 - 371:	reverse
ORF	560 - 625:	forward
ORF	627 - 556:	reverse

Cluster Info:
Contig168.1	(88 members)

view Blast Searches

Sequence: HX10H05w

submitter of sequence:	Dr. Nils Stein
length:	619
priming:	3-prime
GenBankAc:	CB876152
IPK CR-EST:	HX10H05w

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.

HX10H05w
ACTGTAAACA AATTACTTGC AGAATATCAT AATCAATCTG ACATACCAGT TTCAGGTGAA         60
AGCTGAACCA ACCTAACCAT CACCATAACC GCAGCAAAAT GAGAGAATCA GTAAATCTGT        120
TTTGTTGCAA TACAAGATAC ACCAACTGGT AGAAAACGTA ACAAATAATA ATGCATCTAT        180
ACCCTAACTT GAGCAGCAGC CGGCTCTCTT CAGCGAAGAC ACGTCGTCTT TCACATTTAT        240
ATTCTCCCCT TTGCTTGGGG CAGATGAGCC GTCGTCTCCT GCATCAACCG TCTTCCTGCT        300
CGCAATACGG TATATCTGAG TCAAAACTTC TGAGAAAGCG TTGTCTACAT TTGTCGCGTC        360
TAATGCAGAT GTTTCCATGA AGTACAGTGA CTCCGCCTCA GCATATTCCT GCCCATCTTC        420
AGTTGAAACA GCCACCAAGT GGCGAAGGTC AGATTTGTTG CCAACTAGCA TGACAACAAT        480
GCTAGGGTCA GTATGATCTC TTAGCTCTTT TAGCCAGCGC GCCACATTGT CGAATGTAGC        540
ACGGCGAGTG ACATCATACA CCAGCAACGC ACCTACTGCT CCTCTATAAT AGGCACTCGT        600
AATAGCACGG TATCTCTCC                                                     619

Type	Position	Orientation
ORF	1 - 63:	forward
ORF	171 - 377:	forward
ORF	176 - 111:	reverse
ORF	377 - 493:	forward
ORF	618 - 187:	reverse

Cluster Info:
Contig2332.1	(12 members)

view Blast Searches

Oryza sativa pep on 09-MAR-07
E-val	simil.	overlap	accno	description
01e-69	89	221	TIGR:LOC_Os01g54590.1	LOC_Os01g54590.1\|11971.m11622\|protein Ras-related protein RIC2, putative, expressed
02e-66	83	220	TIGR:LOC_Os05g44070.1	LOC_Os05g44070.1\|11975.m08533\|protein Ras-related protein RIC2, putative, expressed
01e-62	78	217	TIGR:LOC_Os06g35814.1	LOC_Os06g35814.1\|11976.m08118\|protein Ras-related protein RIC2, putative, expressed
03e-53	68	217	TIGR:LOC_Os05g48980.1	LOC_Os05g48980.1\|11975.m08969\|protein Ras-related protein Rab11B, putative, expressed
04e-54	70	216	TIGR:LOC_Os09g15790.1	LOC_Os09g15790.1\|11979.m04840\|protein Ras-related protein Rab11B, putative, expressed
non redundant GenBank CDS translations \+ PDB \+ SwissProt \+ PIR on 09-MAR-07
E-val	simil.	overlap	accno	description
02e-68	89	221	GenBankAc:NP_916116.1	ref\|NP_916116.1\| putative GTP-binding protein [Oryza sativa (japonica cultivar-group)] gb\|AAP92129.1\| GTP-binding protein GTP1 [Oryza sativa (japonica cultivar-group)] dbj\|BAB56054.1\| GTP-binding protein GTP1 [Oryza sativa (japonica cultivar-group)]
01e-61	80	218	GenBankAc:CAA98180.1	emb\|CAA98180.1\| RAB11D [Lotus corniculatus var. japonicus] sp\|Q40194\|RB11D_LOTJA Ras-related protein Rab11D
04e-60	79	218	GenBankAc:ABE80757.1	gb\|ABE80757.1\| Sigma-54 factor, interaction region; Ras small GTPase, Rab type [Medicago truncatula]
03e-61	78	217	GenBankAc:BAA02904.1	dbj\|BAA02904.1\| ras-related GTP binding protein [Oryza sativa] sp\|P40393\|RIC2_ORYSA Ras-related protein RIC2
03e-61	78	217	GenBankAc:AAK15703.1	gb\|AAK15703.1\| GTP-binding protein [Oryza sativa] dbj\|BAD53715.1\| GTP-binding protein [Oryza sativa (japonica cultivar-group)]
All nt+env_nt+patnt+pdbnt on 31-MAR-10
E-val	simil.	overlap	accno	description
00e1	99.8	619	GenBankAc:AK248771.1	Hordeum vulgare subsp. vulgare cDNA clone: FLbaf5j14, mRNA sequence
00e1	95.5	619	GenBankAc:AK335920.1	Triticum aestivum cDNA, clone: SET1_C19, cultivar: Chinese Spring
00e1	95.6	614	GenBankAc:EA163551.1	Sequence 27866 from patent US 7214786
01e-117	87.1	450	GenBankAc:AK060095.1	Oryza sativa Japonica Group cDNA clone:006-307-F01, full insert sequence
01e-117	87.1	450	GenBankAc:NM_001050785.1	Oryza sativa (japonica cultivar-group) Os01g0750000 (Os01g0750000) mRNA, complete cds
01e-117	87.1	450	GenBankAc:AY327044.1	Oryza sativa (japonica cultivar-group) GTP-binding protein GTP1 mRNA, complete cds
01e-115	87	446	GenBankAc:EA701623.1	Sequence 80502 from patent US 7365185
01e-115	87	446	GenBankAc:AK066450.1	Oryza sativa Japonica Group cDNA clone:J013061B07, full insert sequence
01e-115	87	446	GenBankAc:AP003076.3	Oryza sativa Japonica Group genomic DNA, chromosome 1, PAC clone:P0481E12
01e-114	87.2	436	GenBankAc:AX654120.1	Sequence 3990 from Patent WO03000898
04e-44	80.5	431	GenBankAc:XM_002441337.1	Sorghum bicolor hypothetical protein, mRNA
01e-156	95.6	343	GenBankAc:EA163452.1	Sequence 27767 from patent US 7214786
01e-56	83.8	328	GenBankAc:FP100464.1	Phyllostachys edulis cDNA clone: bphyem105d20, full insert sequence
UniProt 15.12 UniRef100 on 28-DEC-09
E-val	simil.	overlap	accno	description
04e-61	80.8	146	UniProt_UniRef:UniRef100_Q40194	Ras-related protein Rab11D n=1 Tax=Lotus japonicus RepID=RB11D_LOTJA
01e-60	79.5	146	UniProt_UniRef:UniRef100_A7QDG9	Chromosome chr10 scaffold_81, whole genome shotgun sequence n=1 Tax=Vitis vinifera RepID=A7QDG9_VITVI
05e-62	82.8	145	UniProt_UniRef:UniRef100_A5BUD1	Chromosome chr19 scaffold_4, whole genome shotgun sequence n=1 Tax=Vitis vinifera RepID=A5BUD1_VITVI
07e-68	89.6	144	UniProt_UniRef:UniRef100_Q94J09	Os01g0750000 protein n=2 Tax=Oryza sativa RepID=Q94J09_ORYSJ
01e-64	83.3	144	UniProt_UniRef:UniRef100_Q75II9	Os05g0516800 protein n=1 Tax=Oryza sativa Japonica Group RepID=Q75II9_ORYSJ
05e-64	83.3	144	UniProt_UniRef:UniRef100_C5Z0Z5	Putative uncharacterized protein Sb09g025640 n=1 Tax=Sorghum bicolor RepID=C5Z0Z5_SORBI
01e-64	83.3	144	UniProt_UniRef:UniRef100_A2Y6J2	Putative uncharacterized protein n=1 Tax=Oryza sativa Indica Group RepID=A2Y6J2_ORYSI
04e-62	81.2	144	UniProt_UniRef:UniRef100_B6T0Y1	Ras-related protein RIC2 n=1 Tax=Zea mays RepID=B6T0Y1_MAIZE
09e-61	77.8	144	UniProt_UniRef:UniRef100_C5Z487	Putative uncharacterized protein Sb10g021730 n=2 Tax=Andropogoneae RepID=C5Z487_SORBI
09e-61	78.3	143	UniProt_UniRef:UniRef100_P40393	Ras-related protein RIC2 n=3 Tax=Oryza sativa RepID=RIC2_ORYSJ
Oryza sativa japonica annotation TIGR 6.1 (cDNA)20091211 on 14-DEC-09
E-val	simil.	overlap	accno	description
01e-120	87.1	450	GabiPD:LOC_Os01g54590.1 TIGR:LOC_Os01g54590.1	LOC_Os01g54590.1\|protein ras-related protein, putative, expressed (TIGR 6.1)
UniGeneDec2009.fasta on 14-DEC-09
E-val	simil.	overlap	accno	description
00e1	99.8	619	GabiPD:Hv.23217 unigene:Hv.23217	Hv.23217
01e-117	87	446	GabiPD:Os.35653 unigene:Os.35653	Os.35653
01e-37	80.1	396	GabiPD:Sbi.11521 unigene:Sbi.11521	Sbi.11521
01e-43	82.3	311	GabiPD:Sof.10728 unigene:Sof.10728	Sof.10728

GabiPD Webmaster