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: HA01N04

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

Hv.30839

unigene cluster

Sequence: HA01N04r

submitter of sequence:	Dr. Nils Stein
length:	485
priming:	5-prime
GenBankAc:	BQ459262
IPK CR-EST:	HA01N04r

HA01N04r
CGGCACGAGG CTCTCTCTCT ACACACTCCT CACCTGCCGC CGGAGTTCGG CTGATGGAGA         60
CCTCCCTGCG GCTTCGCGGC GCCGACTCCA CCGCCGGCCA GCAGCTCGGC CTCCGCATCC        120
ACGCCAAGCA GAAGTTGCCC ATCGCCTACA ACGCACTCCT ACAGGCTCAC GCGGAGATCG        180
ACACCTCAAC CAGGAAGCCC TGCCTCCTCG CCGTCCTCGC AAGGCACTTC TTCCCACAGC        240
TATCGGCCAA CGTCGGGGCG GGGGTCCAGC TGGAGAGGGG CAACATCTTC AGGTACGCCT        300
TCCGGGGCAA GAAGGCCGTC TCCTTCACCG ACGACGGCCT CCTCGGCCTC AACATCAAGG        360
GACGCCTCCT CGCCGACAAG AACTTCAAGC CGAGGAGGAA GAGCGGCGCC GTCGAGTTGG        420
CCTGGACCAT ACTCGACTTC AGAAAGGGCC AGGACGTCAG GATCAAGGCC GGCTACGAGC        480
TATAC                                                                    485

Type	Position	Orientation
ORF	54 - 485:	forward
ORF	142 - 2:	reverse
ORF	430 - 170:	reverse

Cluster Info:
Contig6869.1	(4 members)
Representative for Uniset

view Blast Searches

Oryza sativa pep on 09-MAR-07
E-val	simil.	overlap	accno	description
03e-38	55	185	TIGR:LOC_Os02g58550.2	LOC_Os02g58550.2\|11972.m33961\|protein chloroplast channel forming outer membrane protein, putative, expressed
03e-38	55	185	TIGR:LOC_Os02g58550.1	LOC_Os02g58550.1\|11972.m10875\|protein chloroplast channel forming outer membrane protein, putative, expressed
non redundant GenBank CDS translations \+ PDB \+ SwissProt \+ PIR on 09-MAR-07
E-val	simil.	overlap	accno	description
03e-15	30	203	GenBankAc:AAF80623.1	gb\|AAF80623.1\| F2D10.33 [Arabidopsis thaliana]
06e-37	55	185	GenBankAc:XP_468554.1	ref\|XP_468554.1\| putative chloroplast channel forming outer membrane protein [Oryza sativa (japonica cultivar-group)] dbj\|BAD23013.1\| putative chloroplast channel forming outer membrane protein [Oryza sativa (japonica cultivar-group)]
02e-25	42	178	GenBankAc:ABE83242.1	gb\|ABE83242.1\| chloroplast channel forming outer membrane protein [Medicago truncatula]
04e-22	38	177	GenBankAc:CAB58442.1	emb\|CAB58442.1\| chloroplast channel forming outer membrane protein [Pisum sativum]
All nt+env_nt+patnt+pdbnt on 31-MAR-10
E-val	simil.	overlap	accno	description
01e-167	92.4	433	GenBankAc:AK335899.1	Triticum aestivum cDNA, clone: SET2_L20, cultivar: Chinese Spring
01e-179	93.7	429	GenBankAc:EA141059.1	Sequence 5374 from patent US 7214786
UniProt 15.12 UniRef100 on 28-DEC-09
E-val	simil.	overlap	accno	description
02e-36	55.5	155	UniProt_UniRef:UniRef100_Q6K965	Os02g0832200 protein n=1 Tax=Oryza sativa Japonica Group RepID=Q6K965_ORYSJ
02e-36	55.5	155	UniProt_UniRef:UniRef100_B8AFI8	Putative uncharacterized protein n=1 Tax=Oryza sativa Indica Group RepID=B8AFI8_ORYSI
01e-39	59.1	149	UniProt_UniRef:UniRef100_C0P320	Putative uncharacterized protein n=1 Tax=Zea mays RepID=C0P320_MAIZE
01e-39	59.1	149	UniProt_UniRef:UniRef100_B6TGW0	Chloroplast channel forming outer membrane protein n=1 Tax=Zea mays RepID=B6TGW0_MAIZE
01e-29	58	119	UniProt_UniRef:UniRef100_C5XWT0	Putative uncharacterized protein Sb04g038500 n=1 Tax=Sorghum bicolor RepID=C5XWT0_SORBI
Oryza sativa japonica annotation TIGR 6.1 (cDNA)20091211 on 14-DEC-09 gave no results
UniGeneDec2009.fasta on 14-DEC-09 gave no results

Sequence: HA01N04u

submitter of sequence:	Dr. Nils Stein
length:	518
priming:	3-prime
GenBankAc:	BQ656849
IPK CR-EST:	HA01N04u

HA01N04u
GCATCTTTCC AGAGCAAGCA CCAGGTTTCT ACTTCTACAT ACGGCCTTTT CTCCATAAAA         60
CTGGTGCTTG CTGGTGAATG GCATCTTTCC AGAGCAATAC AATGAAATGA AATGGAATGG        120
TGGCCTCTAA AAGAGGGACA ACACCAGCAA GCACCAGGTT TCTACTTCTA CATACGGCCT        180
TTTCTCCATA AAACTGGTGC TTGCTGGTGA ATGGCATCTT TCCAGAGCAA TACAATGAAA        240
TGAAATGGAA TGGTGGCCTC TAAAAGAGGG ACAACACAAC TAGAGCGCTA ACTGATCGCC        300
AGAGAAGTCT CTCCTCCACA AACAGGTTCC AAGTCGATCA CATATCGAAT CTCACATCCC        360
ATTTTCCATC CATGTAACCA TTAAGAGTCC AGTTGCTCTC CCTCAACTGG AAATAAGGCA        420
TCTTGCGGTA TAGCTCGTAT CCGGCCTTGA TCCTGACGTC CTGGCCCTTT CTGAAGTCGA        480
GTATGGTCCA GGCCAACTCG ACGGCGCCGC TCTTCCTC                                518

Type	Position	Orientation
ORF	1 - 102:	forward
ORF	3 - 74:	forward
ORF	84 - 1:	reverse
ORF	112 - 207:	forward
ORF	117 - 188:	forward
ORF	217 - 38:	reverse
ORF	362 - 291:	reverse
ORF	516 - 406:	reverse
ORF	517 - 341:	reverse
ORF	518 - 384:	reverse

Cluster Info:
Contig6869.1	(4 members)

view Blast Searches

Sequence: RUS01H01w

submitter of sequence:	Dr. Nese Sreenivasulu
length:	643
priming:	3-prime
GenBankAc:	FD521494
IPK CR-EST:	RUS01H01w

RUS01H01w
AGGTTTCTAC TTCTACATAC GGCTTTTCTC CATAAAACTG GTGCTTGCTG GTGAATGGCA         60
TCTTTCCAGA GCAATACAAT GAAATGAAAT GGAATGGTGG CCTCTAAAAG AGGGACAACA        120
CCAGCAAGCA CCAGGTTTCT ACTTCTACAT ACGGCTTTTC TCCATAAAAC TGGTGCTTGC        180
TGGTGAATGG CATCTTTCCA GAGCAATACA ATGAAATGAA ATGGAATGGT GGCCTCTAAA        240
AGAGGGACAA CACAACTAGA GCGCTAACTG ATCGCCAGAG AAGTCTCTCC TCCACAAACA        300
GGTTCCAAGT CGATCACATA TCGAATCTCA CATCCCATTT TCCATCCATG TAACCATTAA        360
GAGTCCAGTT GTTCTCCCTC AACTGGAAAT AAGGCATCTT GCGGTATAGC TCGTAGCCGG        420
CCTTGATCCT GACGTCCTGG CCCTTTCTGA AGTCGAGTAT GGTCCAGGCC AACTCGACGG        480
CGCCGCTCTT CCTCCTCGGC TTGAAGTTCT TGTCGGCGAG GAGGCGTCCC TTGATGTTGA        540
GGCCGAGGAG GCCGTCGTCG GTGAAGGAGA CGGCCTTCTT GCCCCGGAAG GCGTACCTGA        600
AGATGTTGCC CCTCTCCAGC TGGACCCCCG CCCCGACGTT GGC                          643

Type	Position	Orientation
ORF	2 - 79:	forward
ORF	89 - 211:	forward
ORF	94 - 183:	forward
ORF	193 - 107:	reverse
ORF	338 - 267:	reverse
ORF	459 - 641:	forward
ORF	641 - 360:	reverse
ORF	642 - 382:	reverse
ORF	643 - 317:	reverse

Cluster Info:
Contig6869.1	(4 members)

view Blast Searches

Oryza sativa pep on 09-MAR-07
E-val	simil.	overlap	accno	description
06e-34	57	185	TIGR:LOC_Os02g58550.2	LOC_Os02g58550.2\|11972.m33961\|protein chloroplast channel forming outer membrane protein, putative, expressed
06e-34	57	185	TIGR:LOC_Os02g58550.1	LOC_Os02g58550.1\|11972.m10875\|protein chloroplast channel forming outer membrane protein, putative, expressed
non redundant GenBank CDS translations \+ PDB \+ SwissProt \+ PIR on 09-MAR-07
E-val	simil.	overlap	accno	description
05e-21	42	203	GenBankAc:AAF80623.1	gb\|AAF80623.1\| F2D10.33 [Arabidopsis thaliana]
01e-32	57	185	GenBankAc:XP_468554.1	ref\|XP_468554.1\| putative chloroplast channel forming outer membrane protein [Oryza sativa (japonica cultivar-group)] dbj\|BAD23013.1\| putative chloroplast channel forming outer membrane protein [Oryza sativa (japonica cultivar-group)]
08e-22	40	178	GenBankAc:ABE83242.1	gb\|ABE83242.1\| chloroplast channel forming outer membrane protein [Medicago truncatula]
07e-21	41	177	GenBankAc:CAB58442.1	emb\|CAB58442.1\| chloroplast channel forming outer membrane protein [Pisum sativum]
All nt+env_nt+patnt+pdbnt on 31-MAR-10
E-val	simil.	overlap	accno	description
01e-172	92.8	473	GenBankAc:DJ023307.1	Detection method of Triticeae alien chromosome in wheat
01e-139	92.2	370	GenBankAc:EA141059.1	Sequence 5374 from patent US 7214786
01e-136	93.7	333	GenBankAc:AK335899.1	Triticum aestivum cDNA, clone: SET2_L20, cultivar: Chinese Spring
UniProt 15.12 UniRef100 on 28-DEC-09
E-val	simil.	overlap	accno	description
04e-32	58	119	UniProt_UniRef:UniRef100_B8AFI8	Putative uncharacterized protein n=1 Tax=Oryza sativa Indica Group RepID=B8AFI8_ORYSI
04e-32	58	119	UniProt_UniRef:UniRef100_Q6K965	Os02g0832200 protein n=1 Tax=Oryza sativa Japonica Group RepID=Q6K965_ORYSJ
05e-38	69.1	110	UniProt_UniRef:UniRef100_B6TGW0	Chloroplast channel forming outer membrane protein n=1 Tax=Zea mays RepID=B6TGW0_MAIZE
03e-28	50.5	109	UniProt_UniRef:UniRef100_A7QPF2	Chromosome chr18 scaffold_137, whole genome shotgun sequence n=1 Tax=Vitis vinifera RepID=A7QPF2_VITVI
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
00e1	100	643	GabiPD:Hv.30839 unigene:Hv.30839	Hv.30839

GabiPD Webmaster