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

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Marker (SNP): GBS0712

Related with

HA12D17

cDNA clone

Mapping Info
map	species	chr.	mapped as	position	submitter
Dom x Rec	Barley	5	GBS0712	145 cm	Dr. Nils Stein
Consensus Stein2006	Barley	5	GBS0712	124.4 cm	Dr. Nils Stein

Related to Sequence, correspondig to BioObject: HA12D17

Sequence: HA12D17r

submitter of sequence:	Dr. Nils Stein
length:	612
priming:	5-prime
GenBankAc:	BU977893
IPK CR-EST:	HA12D17r

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.

HA12D17r
CGGCACGAGG TACCTACGAA ACTCTTGCTC GGGCTGCTTC AAACATCCAT GATTCTGAAG         60
ACCAGCTCCA CTTGCATTGC CAACTTAGAG AAACGTGTTG GCATGCAGCT TGACCAGGCC        120
AGTCTGGAAG ATCTACTGCT GCCAAATTAC TCTTACACCA TGGAAACACT GTACAACGTC        180
GAGTGCATGC ACAGGATTGT TGAGCACTTT TTGGCAATGG ACCAAGCCAA CGGTGGTTGC        240
TCCCCGTGCA TCGATGATAT GATGGCGTCC CCTTCTATGA TACCAATCAC TGCTGTTGCC        300
AAGTTACTTG ATGGCTATCT TGCAGAGGTT GCACCGGATG TCAATCTGAA ACCTCCGAAA        360
TTCCAAGCTC TGGCATCTGC TTTGCCTGAG TATGCCCGGC CACTGGATGA TGGCCTCTAC        420
CGTGCCATCG ATGTGTACTT GAAGGCACAT TCCTGGCTAT CAGAAACCGA ACGCGAGCAG        480
CTATGCCGGC TCATGGACTG CCAGAAGCTG TCCCTGGAAG CGTGCACCCA CGCCGCGCAG        540
AACGAGAGGC TGCCGCTGCG CGTTGTCGTG CAAGTCCTCT TCTTCGAGCA GCTGCAGCTG        600
AGGACCTCGA TC                                                            612

Type	Position	Orientation
ORF	3 - 110:	forward
ORF	49 - 612:	forward
ORF	104 - 42:	reverse
ORF	251 - 156:	reverse
ORF	450 - 307:	reverse
ORF	483 - 611:	forward
ORF	610 - 494:	reverse
ORF	611 - 420:	reverse
ORF	612 - 484:	reverse

Singlet Info:
AA tgicl singlet
Representative for Uniset

view Blast Searches

Oryza sativa pep on 09-MAR-07
E-val	simil.	overlap	accno	description
06e-62	60	659	TIGR:LOC_Os01g57230.1	LOC_Os01g57230.1\|11971.m11876\|protein transposon protein, putative, Mutator sub-class, expressed
06e-81	77	650	TIGR:LOC_Os12g41910.1	LOC_Os12g41910.1\|11982.m07972\|protein transposon protein, putative, Mutator sub-class, expressed
05e-74	70	641	TIGR:LOC_Os08g03650.1	LOC_Os08g03650.1\|11978.m04509\|protein transposon protein, putative, Mutator sub-class, expressed
01e-87	83	624	TIGR:LOC_Os03g43990.1	LOC_Os03g43990.1\|11973.m09441\|protein transposon protein, putative, Mutator sub-class, expressed
01e-87	83	615	TIGR:LOC_Os03g43990.2	LOC_Os03g43990.2\|11973.m35330\|protein transposon protein, putative, Mutator sub-class, expressed
non redundant GenBank CDS translations \+ PDB \+ SwissProt \+ PIR on 09-MAR-07
E-val	simil.	overlap	accno	description
01e-79	77	718	GenBankAc:ABA99392.1	gb\|ABA99392.1\| transposon protein, putative, mutator sub-class [Oryza sativa (japonica cultivar-group)]
09e-68	69	665	GenBankAc:NP_174332.1	ref\|NP_174332.1\| protein binding / signal transducer [Arabidopsis thaliana]
09e-68	69	662	GenBankAc:AAF19742.1	gb\|AAF19742.1\| Contains a bZIP transcription factor PF\|00170 domain. ESTs gb\|R30400, gb\|AA650964, gb\|AI994521 come from this gene. [Arabidopsis thaliana]
09e-71	70	658	GenBankAc:AAL73542.1	gb\|AAL73542.1\| putative photoreceptor-interacting protein [Sorghum bicolor]
01e-72	70	641	GenBankAc:XP_479933.1	ref\|XP_479933.1\| putative non-phototropic hypocotyl 3 (NPH3)/phototropic response protein [Oryza sativa (japonica cultivar-group)] dbj\|BAD33364.1\| putative non-phototropic hypocotyl 3 (NPH3)/phototropic response protein [Oryza sativa (japonica cultivar-group)] dbj\|BAD09643.1\| putative non-phototropic hypocotyl 3 (NPH3)/phototropic response protein [Oryza sativa (japonica cultivar-group)]
All nt+env_nt+patnt+pdbnt on 31-MAR-10
E-val	simil.	overlap	accno	description
01e-117	84.3	586	GenBankAc:XM_002464132.1	Sorghum bicolor hypothetical protein, mRNA
01e-130	85.3	584	GenBankAc:AK289192.1	Oryza sativa Japonica Group cDNA, clone: J100039P10, full insert sequence
01e-122	85	566	GenBankAc:EU975635.1	Zea mays clone 494946 mRNA sequence
01e-120	84.8	566	GenBankAc:BT063032.1	Zea mays full-length cDNA clone ZM_BFc0018G18 mRNA, complete cds
08e-70	81.3	541	GenBankAc:EU368707.1	Oryza sativa Indica Group SKIP interacting protein 17 (SIP17) mRNA, complete cds
02e-88	84.9	425	GenBankAc:GP624290.1	Sequence 32294 from patent US 7560542
02e-76	83.8	421	GenBankAc:AC147427.2	Oryza sativa chromosome 3 B1394A07 genomic sequence, complete sequence
02e-76	83.8	421	GenBankAc:AL732379.5	Oryza sativa chromosome 3, . BAC OSJNBa0025B02 of library OSJNBa from chromosome 3 of cultivar Nipponbare of ssp. japonica of Oryza sativa (rice), complete sequence
00e1	95.9	411	GenBankAc:EA208852.1	Sequence 73167 from patent US 7214786
07e-27	79.3	381	GenBankAc:EA699478.1	Sequence 78357 from patent US 7365185
07e-27	79.3	381	GenBankAc:AL713940.4	Oryza sativa chromosome 12, . BAC OJ1327_A12 of library Monsanto from chromosome 12 of cultivar Nipponbare of ssp. japonica of Oryza sativa (rice), complete sequence
UniProt 15.12 UniRef100 on 28-DEC-09
E-val	simil.	overlap	accno	description
02e-79	77.3	185	UniProt_UniRef:UniRef100_A7Q1C4	Chromosome chr10 scaffold_43, whole genome shotgun sequence n=1 Tax=Vitis vinifera RepID=A7Q1C4_VITVI
04e-79	77.7	184	UniProt_UniRef:UniRef100_B9GE95	Putative uncharacterized protein n=1 Tax=Oryza sativa Japonica Group RepID=B9GE95_ORYSJ
04e-79	77.7	184	UniProt_UniRef:UniRef100_Q2QM90	Transposon protein, putative, Mutator sub-class, expressed n=1 Tax=Oryza sativa Japonica Group RepID=Q2QM90_ORYSJ
04e-79	77.7	184	UniProt_UniRef:UniRef100_B8BMZ7	Putative uncharacterized protein n=1 Tax=Oryza sativa Indica Group RepID=B8BMZ7_ORYSI
04e-79	77.7	184	UniProt_UniRef:UniRef100_B8Q8A3	SKIP interacting protein 17 n=1 Tax=Oryza sativa Indica Group RepID=B8Q8A3_ORYSI
01e-88	86.1	180	UniProt_UniRef:UniRef100_C5WR83	Putative uncharacterized protein Sb01g013680 n=1 Tax=Sorghum bicolor RepID=C5WR83_SORBI
02e-88	85.6	180	UniProt_UniRef:UniRef100_C0P413	Putative uncharacterized protein n=1 Tax=Zea mays RepID=C0P413_MAIZE
08e-86	83.9	180	UniProt_UniRef:UniRef100_Q6AST7	NPH3 family protein n=1 Tax=Oryza sativa Japonica Group RepID=Q6AST7_ORYSJ
08e-86	83.9	180	UniProt_UniRef:UniRef100_Q10G68	Transposon protein, putative, Mutator sub-class, expressed n=2 Tax=Oryza sativa Japonica Group RepID=Q10G68_ORYSJ
08e-86	83.9	180	UniProt_UniRef:UniRef100_Q10G69	Transposon protein, putative, Mutator sub-class, expressed n=2 Tax=Oryza sativa RepID=Q10G69_ORYSJ
Oryza sativa japonica annotation TIGR 6.1 (cDNA)20091211 on 14-DEC-09
E-val	simil.	overlap	accno	description
01e-133	85.3	584	GabiPD:LOC_Os03g43990.2 TIGR:LOC_Os03g43990.2	LOC_Os03g43990.2\|protein BTBN8 - Bric-a-Brac, Tramtrack, Broad Complex BTB domain with non-phototropic hypocotyl 3 NPH3 and coiled-coil domains, expressed (TIGR 6.1)
01e-133	85.3	584	GabiPD:LOC_Os03g43990.1 TIGR:LOC_Os03g43990.1	LOC_Os03g43990.1\|protein BTBN8 - Bric-a-Brac, Tramtrack, Broad Complex BTB domain with non-phototropic hypocotyl 3 NPH3 and coiled-coil domains, expressed (TIGR 6.1)
UniGeneDec2009.fasta on 14-DEC-09
E-val	simil.	overlap	accno	description
01e-132	85.3	584	GabiPD:Os.61259 unigene:Os.61259	Os.61259
01e-124	85	566	GabiPD:Zm.5126 unigene:Zm.5126	Zm.5126
08e-88	82.3	555	GabiPD:Sof.11542 unigene:Sof.11542	Sof.11542

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