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: HE01G21

Genotype (Genotype)

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

Library:

	lib name:	IPKc 2021
	tissue:	etiolated leaves
	stage/tissue:	grown for 6 days in growth chamber (harvested at daylight conditions)
	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 900 bp

Related with

Hv.23072	unigene cluster
Zm.80765	unigene cluster
Sbi.12403	unigene cluster
Sof.11976	unigene cluster
Vvi.6924	unigene cluster

Sequence: HE01G21r

submitter of sequence:	Dr. Nils Stein
length:	459
priming:	5-prime
GenBankAc:	BQ461031
IPK CR-EST:	HE01G21r

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.

HE01G21r
GGCGCGGGCC GCGCTGGAGC CGTCGGTGGT GATCAGCCTC AGCACGGGGC TGTCGCTCGT         60
GATGGGCCGC TTCGTCTTCT TCAACTTCCA GCGGGAGAAC GTGGCGAAGC AGGTCCCCGA        120
GCAGAACGGC AAGACCCACT TCGAGGCCGG CGACGAGCGC GCCAAGGAGT TCGCCGGGAT        180
CCTCAAGTCC AACGACCCCG TCGGCTTCAA CCTCGTCGAC GTCCTCGCAT GGGGCTCCAT        240
CGGCCACATC GTCGCCTACT ACATCCTCGC CACCACCAGC AACGGATACG ACCCTCCCTT        300
CTTCGGCTGA TCCGTCCGTC TCCCCTGCCT GCCTGCGTGC CGGCCGGAGC GGCTTTGCTG        360
TTGTAATCCG CCGAGTTTTC ATTAGTTCTG TATACGCTGA TGATGTACCA TCATGAGTAT        420
GTATGTATGT ATGTGAGATG GTGAAAGATT GATCTGGAC                               459

Type	Position	Orientation
ORF	1 - 363:	forward
ORF	2 - 307:	forward
ORF	249 - 1:	reverse
ORF	382 - 2:	reverse
ORF	459 - 385:	reverse

Cluster Info:
Contig40620.1	(29 members)

view Blast Searches

Oryza sativa pep on 09-MAR-07
E-val	simil.	overlap	accno	description
04e-47	87	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
01e-44	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)
09e-53	100	143	GenBankAc:CAJ75642.1	emb\|CAJ75642.1\| photosystem 1 subunit 5 [Triticum aestivum]
09e-53	100	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)
01e-49	94	143	GenBankAc:CAJ26374.1	emb\|CAJ26374.1\| photosystem 1 subunit 5 [Brachypodium sylvaticum]
08e-46	87	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
00e1	93.5	463	GenBankAc:EA162478.1	Sequence 26793 from patent US 7214786
00e1	94.1	459	GenBankAc:AK332626.1	Triticum aestivum cDNA, clone: WT004_H11, cultivar: Chinese Spring
00e1	94.1	459	GenBankAc:EA162479.1	Sequence 26794 from patent US 7214786
00e1	99.1	458	GenBankAc:X60158.1	H.vulgare PsaG mRNA
01e-174	95.4	392	GenBankAc:EA162476.1	Sequence 26791 from patent US 7214786
01e-115	93.2	294	GenBankAc:FP091369.1	Phyllostachys edulis cDNA clone: bphyst009d16, full insert sequence
01e-104	92.7	275	GenBankAc:DQ245899.1	Zea mays clone 22121 mRNA sequence
01e-104	92.7	275	GenBankAc:GP662183.1	Sequence 70187 from patent US 7560542
01e-104	92.7	275	GenBankAc:GP612115.1	Sequence 20119 from patent US 7560542
01e-101	92.4	275	GenBankAc:BT043247.1	Zea mays full-length cDNA clone ZM_BFc0132C01 mRNA, complete cds
01e-101	92.4	275	GenBankAc:EU957293.1	Zea mays clone 1588044 photosystem I reaction center subunit V mRNA, complete cds
01e-101	92.4	275	GenBankAc:EU957381.1	Zea mays clone 1590298 photosystem I reaction center subunit V mRNA, complete cds
01e-101	92.4	275	GenBankAc:EU958643.1	Zea mays clone 1707142 photosystem I reaction center subunit V mRNA, complete cds
01e-101	92.4	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
01e-101	92.4	275	GenBankAc:GP617552.1	Sequence 25556 from patent US 7560542
01e-101	92.4	275	GenBankAc:GP677639.1	Sequence 7883 from patent US 7569389
01e-108	93.4	274	GenBankAc:FP099694.1	Phyllostachys edulis cDNA clone: bbasst002l21, full insert sequence
01e-108	93.4	274	GenBankAc:FP096717.1	Phyllostachys edulis cDNA clone: bbasst002h12, full insert sequence
01e-98	92	274	GenBankAc:XM_002460382.1	Sorghum bicolor hypothetical protein, mRNA
01e-95	92.2	269	GenBankAc:GP677542.1	Sequence 7510 from patent US 7569389
01e-83	90.3	269	GenBankAc:GP617158.1	Sequence 25162 from patent US 7560542
01e-100	92.5	268	GenBankAc:GP678125.1	Sequence 9712 from patent US 7569389
01e-100	92.5	268	GenBankAc:GP665468.1	Sequence 73472 from patent US 7560542
01e-100	92.5	268	GenBankAc:HB788109.1	Sequence 137323 from Patent EP2090662
01e-100	92.5	268	GenBankAc:FB918050.1	Sequence 137323 from Patent WO2008034648
01e-100	92.5	268	GenBankAc:BT083797.1	Zea mays full-length cDNA clone ZM_BFb0041D20 mRNA, complete cds
01e-100	92.5	268	GenBankAc:EZ108995.1	TSA: Zea mays contig44654, mRNA sequence
01e-100	92.5	268	GenBankAc:NM_001158351.1	Zea mays photosystem I reaction center subunit V (LOC100285458), mRNAgb\|EU972349.1\| Zea mays clone 380048 photosystem I reaction center subunit V mRNA, complete cds
01e-100	92.5	268	GenBankAc:AY110144.1	Zea mays CL7431_1 mRNA sequence
01e-100	92.5	268	GenBankAc:GP665469.1	Sequence 73473 from patent US 7560542
05e-95	91.8	268	GenBankAc:GP661261.1	Sequence 69265 from patent US 7560542
05e-95	91.8	268	GenBankAc:GP663334.1	Sequence 71338 from patent US 7560542
02e-85	91.8	244	GenBankAc:GP664088.1	Sequence 72092 from patent US 7560542
06e-76	90.2	244	GenBankAc:GP661222.1	Sequence 69226 from patent US 7560542
01e-40	84.2	241	GenBankAc:AM464448.1	Vitis vinifera contig VV78X273139.15, whole genome shotgun sequence
02e-38	83.8	241	GenBankAc:XM_002264197.1	PREDICTED: Vitis vinifera hypothetical protein LOC100244683 (LOC100244683), mRNA
03e-84	92	238	GenBankAc:GP645259.1	Sequence 53263 from patent US 7560542
01e-67	89	237	GenBankAc:GP629980.1	Sequence 37984 from patent US 7560542
03e-53	87.5	232	GenBankAc:GP646667.1	Sequence 54671 from patent US 7560542
UniProt 15.12 UniRef100 on 28-DEC-09
E-val	simil.	overlap	accno	description
03e-52	100	102	UniProt_UniRef:UniRef100_Q00327	Photosystem I reaction center subunit V, chloroplastic n=1 Tax=Hordeum vulgare RepID=PSAG_HORVU
03e-52	100	102	UniProt_UniRef:UniRef100_Q2L3V4	Photosystem 1 subunit 5 n=1 Tax=Triticum aestivum RepID=Q2L3V4_WHEAT
04e-49	94.1	102	UniProt_UniRef:UniRef100_Q2L3E3	Photosystem 1 subunit 5 n=1 Tax=Brachypodium sylvaticum RepID=Q2L3E3_BRASY
05e-44	84.3	102	UniProt_UniRef:UniRef100_Q9S7N7	Photosystem I reaction center subunit V, chloroplastic n=1 Tax=Arabidopsis thaliana RepID=PSAG_ARATH
04e-46	88.1	101	UniProt_UniRef:UniRef100_B4G1K9	Photosystem I reaction center subunit V n=1 Tax=Zea mays RepID=B4G1K9_MAIZE
03e-45	87.1	101	UniProt_UniRef:UniRef100_Q69QR6	Os09g0481200 protein n=2 Tax=Oryza sativa RepID=Q69QR6_ORYSJ
04e-44	86.1	101	UniProt_UniRef:UniRef100_C5X3S4	Putative uncharacterized protein Sb02g027900 n=1 Tax=Sorghum bicolor RepID=C5X3S4_SORBI
09e-44	85.1	101	UniProt_UniRef:UniRef100_B6U534	Photosystem I reaction center subunit V n=1 Tax=Zea mays RepID=B6U534_MAIZE
01e-43	84.2	101	UniProt_UniRef:UniRef100_C6SWM2	Putative uncharacterized protein n=1 Tax=Glycine max RepID=C6SWM2_SOYBN
01e-43	84.2	101	UniProt_UniRef:UniRef100_C6SVU4	Putative uncharacterized protein n=1 Tax=Glycine max RepID=C6SVU4_SOYBN
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	99	388	GabiPD:Hv.23072 unigene:Hv.23072	Hv.23072
01e-100	92	274	GabiPD:Sbi.12403 unigene:Sbi.12403	Sbi.12403
01e-101	92.5	268	GabiPD:Zm.80765 unigene:Zm.80765	Zm.80765
01e-76	90	250	GabiPD:Sof.11976 unigene:Sof.11976	Sof.11976
01e-42	84.2	241	GabiPD:Vvi.6924 unigene:Vvi.6924	Vvi.6924

GabiPD Webmaster