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Expression Template: Les.3217.3.S1_s_at

Template Basic Information

Template name:	Les.3217.3.S1_s_at
Template type:	Probe Set
Platform:	Affymetrix GeneChip Tomato Genome Array
Internal db links:	SGN-U580869 SGN-U580869
External db links:	GenBank: AW040026

Annotations for unigene SGN-U580869 (manual: 3 | blast: 3 | go: 0 )

Manual annotations

Based on clone cLET-1-K2, annotated by Rob Alba	Created 2003-01-20, last modified 2003-01-20
Putative Homology: "rubisco, small subunit 3A/3C" Annotation Keywords: photosynthesis; Calvin cycle; carbon fixation; light-regulated gene

Blast Annotations [Show All]

Database	Program	Best Match	Score	E-value	Identity	Alignment Length	Frame
genbank	blastx	gi\|132112\|sp\|P05349\|RBS3B_SOLLC	355	5e-96	100	504 bp (44.2%)	1
Description:	RecName:
arabidopsis	blastx	At5G38410.1	275	3e-74	76.07	489 bp (42.9%)	1
Description:	ribulose bisphosphate carboxylase small chain 3B / RuBisCO small subunit 3B (RBCS-3B) (ATS3B) &hellip
swissprot	blastx	P07180	355	3e-97	100	504 bp (44.2%)	1
Description:	Ribulose bisphosphate carboxylase small chain 3A/3C, chloroplastic OS=Solanum lycopersicum GN=R&hellip

GO Terms Annotations

No Gene Ontology annotation

Annotations for unigene SGN-U580869 (manual: 3 | blast: 3 | go: 0 )

Manual annotations

Based on clone cLET-1-K2, annotated by Rob Alba	Created 2003-01-20, last modified 2003-01-20
Putative Homology: "rubisco, small subunit 3A/3C" Annotation Keywords: photosynthesis; Calvin cycle; carbon fixation; light-regulated gene

Blast Annotations [Show All]

Database	Program	Best Match	Score	E-value	Identity	Alignment Length	Frame
genbank	blastx	gi\|132112\|sp\|P05349\|RBS3B_SOLLC	355	5e-96	100	504 bp (44.2%)	1
Description:	RecName:
arabidopsis	blastx	At5G38410.1	275	3e-74	76.07	489 bp (42.9%)	1
Description:	ribulose bisphosphate carboxylase small chain 3B / RuBisCO small subunit 3B (RBCS-3B) (ATS3B) &hellip
swissprot	blastx	P07180	355	3e-97	100	504 bp (44.2%)	1
Description:	Ribulose bisphosphate carboxylase small chain 3A/3C, chloroplastic OS=Solanum lycopersicum GN=R&hellip

GO Terms Annotations

No Gene Ontology annotation

Probe Composition (11)

Probe name	Probe type	Template start coord	Template end coord	Spots
Les.3217.3.S1_s_at:ProbePair0	PM	data not available	data not available	data not available
Les.3217.3.S1_s_at:ProbePair1	PM	data not available	data not available	data not available
Les.3217.3.S1_s_at:ProbePair10	PM	data not available	data not available	data not available
Les.3217.3.S1_s_at:ProbePair2	PM	data not available	data not available	data not available
Les.3217.3.S1_s_at:ProbePair3	PM	data not available	data not available	data not available
Les.3217.3.S1_s_at:ProbePair4	PM	data not available	data not available	data not available
Les.3217.3.S1_s_at:ProbePair5	PM	data not available	data not available	data not available
Les.3217.3.S1_s_at:ProbePair6	PM	data not available	data not available	data not available
Les.3217.3.S1_s_at:ProbePair7	PM	data not available	data not available	data not available
Les.3217.3.S1_s_at:ProbePair8	PM	data not available	data not available	data not available
Les.3217.3.S1_s_at:ProbePair9	PM	data not available	data not available	data not available

Graph: Expression Data by Experiment

Table: Expression Data by Experiment (24)

Experimental design name	Experiment name	Tissue	Experiment replicates	Replicates pValue<0.05	Mean	Median	SD	CV
Expression data from various tomato plant tissues	Gene expression data from Micro-Tom cotyledon	cotyledon	2	2	9413.37	9413.37	1999.89	0.21
	Gene expression data from Aft red fruit flesh	endocarp	3	3	9.19	8.96	2.81	0.31
	Gene expression data from Line27859 red fruit flesh	endocarp	3	3	10.70	11.85	2.78	0.26
	Gene expression data from Micro-Tom yellow fruit flesh	endocarp	2	2	28.41	28.41	0.09	0.00
	Gene expression data from Aft mature green fruit peel	exocarp	3	3	2230.83	2339.65	301.38	0.14
	Gene expression data from Aft red fruit peel	exocarp	3	3	9.86	11.06	6.23	0.63
	Gene expression data from Line27859 mature green fruit peel	exocarp	3	3	6576.60	6731.84	817.82	0.12
	Gene expression data from Line27859 red fruit peel	exocarp	3	3	18.17	18.39	2.49	0.14
	Gene expression data from Micro-Tom mature green fruit peel	exocarp	3	3	190.98	184.94	115.36	0.60
	Gene expression data from Micro-Tom orange fruit peel	exocarp	2	2	7.02	7.02	1.55	0.22
	Gene expression data from Micro-Tom red fruit peel	exocarp	3	3	2.55	0.87	3.00	1.18
	Gene expression data from Micro-Tom yellow fruit peel	exocarp	2	2	12.39	12.39	6.53	0.53
	Gene expression data from Momotaro8 red fruit peel	exocarp	4	4	52.08	51.81	26.39	0.51
	Gene expression data from Micro-Tom hypocotyl	hypocotyl	2	2	6894.54	6894.54	572.33	0.08
	Gene expression data from Micro-Tom 3rd leaf	vascular leaf	2	2	9099.54	9099.54	256.26	0.03
	Gene expression data from all leaves of 3-week-old Micro-Tom plant	vascular leaf	3	3	13423.50	14095.10	1535.92	0.11
	Gene expression data from all leaves of 5-week-old Micro-Tom plant	vascular leaf	3	3	11217.50	11432.20	791.99	0.07
	Gene expression data from Aft mature green fruit flesh	mesocarp	3	3	382.27	325.39	130.96	0.34
	Gene expression data from Line27859 mature green fruit flesh	mesocarp	3	3	7269.27	7350.97	500.51	0.07
	Gene expression data from Micro-Tom mature green fruit flesh	mesocarp	3	3	350.63	328.95	151.30	0.43
	Gene expression data from Micro-Tom orange fruit flesh	mesocarp	2	2	14.42	14.42	2.14	0.15
	Gene expression data from Micro-Tom red fruit flesh	mesocarp	3	3	11.64	12.78	5.80	0.50
	Gene expression data from Momotaro8 red fruit flesh	mesocarp	4	4	10.68	12.46	6.70	0.63
	Gene expression data from Micro-Tom root	root	3	3	18.42	19.99	4.63	0.25

Expression Data by Targets (experiment replicates) (67)

Experiment name	Target name	normalized_signal	pVal_call	flag
Gene expression data from Micro-Tom cotyledon	GSM480170 extract 1	7999.23	2e-4	P
	GSM480171 extract 1	10827.5	2e-4	P
Gene expression data from Aft red fruit flesh	GSM480205 extract 1	12.1028	0.432	A
	GSM480203 extract 1	8.96466	0.189	A
	GSM480204 extract 1	6.49416	0.534	A
Gene expression data from Line27859 red fruit flesh	GSM480215 extract 1	11.8489	0.334	A
	GSM480217 extract 1	12.7235	0.334	A
	GSM480216 extract 1	7.53247	0.466	A
Gene expression data from Micro-Tom yellow fruit flesh	GSM480183 extract 1	28.3503	0.150	A
	GSM480184 extract 1	28.4731	0.150	A
Gene expression data from Aft mature green fruit peel	GSM480208 extract 1	2462.69	2e-4	P
	GSM480206 extract 1	1890.16	2e-4	P
	GSM480207 extract 1	2339.65	2e-4	P
Gene expression data from Aft red fruit peel	GSM480209 extract 1	15.4022	0.024	P
	GSM480210 extract 1	11.0566	0.046	P
	GSM480211 extract 1	3.11371	0.432	A
Gene expression data from Line27859 mature green fruit peel	GSM480219 extract 1	5692.29	2e-4	P
	GSM480218 extract 1	6731.84	2e-4	P
	GSM480220 extract 1	7305.67	2e-4	P
Gene expression data from Line27859 red fruit peel	GSM480223 extract 1	18.3911	0.081	A
	GSM480221 extract 1	15.5749	0.150	A
	GSM480222 extract 1	20.5316	0.130	A
Gene expression data from Micro-Tom mature green fruit peel	GSM480192 extract 1	309.246	2e-4	P
	GSM480190 extract 1	184.936	7e-4	P
	GSM480191 extract 1	78.7665	0.002	P
Gene expression data from Micro-Tom orange fruit peel	GSM480195 extract 1	8.11801	0.112	A
	GSM480196 extract 1	5.92355	0.274	A
Gene expression data from Micro-Tom red fruit peel	GSM480197 extract 1	0.767056	0.888	A
	GSM480199 extract 1	6.01399	0.366	A
	GSM480198 extract 1	0.867833	0.870	A
Gene expression data from Micro-Tom yellow fruit peel	GSM480194 extract 1	17.0008	0.056	M
	GSM480193 extract 1	7.76976	0.171	A
Gene expression data from Momotaro8 red fruit peel	GSM480228 extract 1	43.2882	0.024	P
	GSM480229 extract 1	60.3264	0.038	P
	GSM480230 extract 1	83.5391	0.003	P
	GSM480231 extract 1	21.1801	0.036	P
Gene expression data from Micro-Tom hypocotyl	GSM480168 extract 1	6489.84	2e-4	P
	GSM480169 extract 1	7299.24	2e-4	P
Gene expression data from Micro-Tom 3rd leaf	GSM480172 extract 1	9280.74	2e-4	P
	GSM480173 extract 1	8918.33	2e-4	P
Gene expression data from all leaves of 3-week-old Micro-Tom plant	GSM480174 extract 1	14095.1	2e-4	P
	GSM480175 extract 1	14509.3	2e-4	P
	GSM480176 extract 1	11666.2	2e-4	P
Gene expression data from all leaves of 5-week-old Micro-Tom plant	GSM480177 extract 1	10340.3	2e-4	P
	GSM480178 extract 1	11880	2e-4	P
	GSM480179 extract 1	11432.2	2e-4	P
Gene expression data from Aft mature green fruit flesh	GSM480201 extract 1	289.361	7e-4	P
	GSM480200 extract 1	325.39	7e-4	P
	GSM480202 extract 1	532.055	2e-4	P
Gene expression data from Line27859 mature green fruit flesh	GSM480213 extract 1	6732.94	2e-4	P
	GSM480212 extract 1	7350.97	2e-4	P
	GSM480214 extract 1	7723.91	2e-4	P
Gene expression data from Micro-Tom mature green fruit flesh	GSM480181 extract 1	211.346	7e-4	P
	GSM480180 extract 1	328.948	2e-4	P
	GSM480182 extract 1	511.607	2e-4	P
Gene expression data from Micro-Tom orange fruit flesh	GSM480186 extract 1	12.9021	0.274	A
	GSM480185 extract 1	15.9296	0.246	A
Gene expression data from Micro-Tom red fruit flesh	GSM480187 extract 1	16.7865	0.466	A
	GSM480188 extract 1	5.34888	0.534	A
	GSM480189 extract 1	12.7847	0.150	A
Gene expression data from Momotaro8 red fruit flesh	GSM480224 extract 1	1.10606	0.805	A
	GSM480226 extract 1	12.7006	0.274	A
	GSM480225 extract 1	16.7208	0.130	A
	GSM480227 extract 1	12.2097	0.081	A
Gene expression data from Micro-Tom root	GSM480165 extract 1	19.9865	0.046	P
	GSM480166 extract 1	13.2154	0.304	A
	GSM480167 extract 1	22.0617	0.030	P

Correlation analysis (0)

No correlation analysis was found associated to this template

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