Sol Genomics Network

clone(s) in cart (order)

Old browser version detected

This site is optimized for modern web browsers

Please upgrade your browser

Sorry!, some features may not work in outdated browsers

Sol Genomics Network

Search
- Organisms
- Loci & Genes
- Genome features
- Expression
- Accessions and Plots
- QTLs
- Markers
- BACs
- Unigenes
- ESTs and libraries
- Gene Families
- Insitu database
- Images
- People
- FAQ
Maps
- All Maps
- The New Comparative Viewer
- Comparative Viewer
- Submit a map
- Tomato
- Tomato-EXPEN 2000
- Tomato-Kazusa/SolCAP
- Tomato QTLs
- Tomato physical map
- Tomato FPC contig map
- Tomato IL map
- Tomato FISH map
- Tomato AGP map
- Pepper
- Pepper COSII map
- Pepper-AC99
- Pepper-FA03
- Eggplant
- Eggplant COSII map
- Eggplant-LXM 2002
- More Maps
- Potato-TXB 1992
- Tobacco SSR 2007
- Arabidopsis COSII
Genomes
- Sequenced Accessions
- Completed Genomes
- Tomato
- Potato
- Pepper
- Eggplant
- Solanum pennellii
- Solanum lycopersicoides
- Solanum pimpinellifolium
- Solanum lycopersicum var. cerasiforme
- Iochroma cyaneum
- Draft Genomes
- Nicotiana attenuata
- Nicotiana benthamiana
- Nicotiana tabacum
- Petunia axillaris
- Petunia inflata
- Solanum chilense
- Coffea humblotiana
- Resequencing projects
- Solanum lycopersicum inbreds
- 150 Tomato Genome Resequencing Project
- BGI Tomato 360 genomes
- Varitome Project
Projects
- Projects
- Tomato graph pangenome project
- Varitome project
- Nicotiana benthamiana BTI site
- 100 Tomato genomes project
- Tomato Immune Response Resequencing
- Previous Projects
- Solanaceae project (SOL)
- SOL-100 Project
- International Tomato Sequencing Project
- U.S. tomato sequencing project
Tools
- Sequence Analysis
- BLAST
- VIGS Tool
- Alignment Analyzer
- Tree Browser
- Motif Finder
- Mapping
- Genome Browser (Jbrowse)
- Comparative Map Viewer
- CAPS Designer
- solQTL: QTL Mapping
- Molecular Biology
- In Silico PCR
- Tomato Expression Atlas (TEA)
- Tomato Expression Database (TED)
- Systems Biology
- SolCyc Biochemical Pathways
- Coffee Interactomic Data
- SGN Ontology Browser
- Breeder Tools
- Breeders Toolbox
- Bulk Query
- FTP Site
- Download Genome Sequences
- Download Gene Sequences
- Clones, Arrays, Unigenes and BACs
- Unigene Converter
About
- About
- Contact
- Cite SGN
- Links
- Help
- FAQ
- Become SGN Editor
- Forum
- FTP data
- SlideShare
- Twitter
- Facebook

Advanced

This site uses cookies to provide logins and other features. Please accept the use of cookies by clicking Accept.

Expression Template: LesAffx.27409.1.S1_at

Template Basic Information

Template name:	LesAffx.27409.1.S1_at
Template type:	Probe Set
Platform:	Affymetrix GeneChip Tomato Genome Array
Internal db links:	SGN-U584987
External db links:	GenBank: BM413458

Annotations for unigene SGN-U584987 (manual: 1 | blast: 3 | go: 5 )

Manual annotations

Based on clone cLES-5-G24, annotated by Rob Alba	Created 2003-01-20, last modified 2003-01-20
Putative Homology: phytoene dehydrogenase Annotation Keywords: secondary metabolism; carotenoid biosynthesis; xanthopyll biosynthesis; pigment biosynthesis; fruit quality; hormone biosynthesis; gibberellin biosynthesis; abscisic acid biosynthesis

Blast Annotations [Show All]

Database	Program	Best Match	Score	Identity	Alignment Length	Frame
genbank	blastx	gi\|75159637\|sp\|Q8S4R4\|CRTSO_SOLLC	1182	99.67	1797 bp (70.1%)	2
Description:	RecName:
arabidopsis	blastx	At1G06820.1	889	85.15	1584 bp (61.8%)	2
Description:	Symbols: CCR2, CRTISO \| CRTISO (carotenoid isomerase); carotenoid isomerase \| chr1:2093144-209&hellip
swissprot	blastx	Q8S4R4	1182	99.67	1797 bp (70.1%)	2
Description:	Carotenoid isomerase, chloroplastic OS=Solanum lycopersicum GN=CRTISO PE=2 SV=1

GO Terms Annotations

GO:0006118electron transport
GO:0016117carotenoid biosynthesis
GO:0050660FAD binding
GO:0016491oxidoreductase activity
GO:0016705oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen

Probe Composition (11)

Probe name	Probe type	Template start coord	Template end coord	Spots
LesAffx.27409.1.S1_at:ProbePair0	PM	data not available	data not available	data not available
LesAffx.27409.1.S1_at:ProbePair1	PM	data not available	data not available	data not available
LesAffx.27409.1.S1_at:ProbePair10	PM	data not available	data not available	data not available
LesAffx.27409.1.S1_at:ProbePair2	PM	data not available	data not available	data not available
LesAffx.27409.1.S1_at:ProbePair3	PM	data not available	data not available	data not available
LesAffx.27409.1.S1_at:ProbePair4	PM	data not available	data not available	data not available
LesAffx.27409.1.S1_at:ProbePair5	PM	data not available	data not available	data not available
LesAffx.27409.1.S1_at:ProbePair6	PM	data not available	data not available	data not available
LesAffx.27409.1.S1_at:ProbePair7	PM	data not available	data not available	data not available
LesAffx.27409.1.S1_at:ProbePair8	PM	data not available	data not available	data not available
LesAffx.27409.1.S1_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	199.54	199.54	56.27	0.28
	Gene expression data from Aft mature green fruit flesh	endocarp	3	3	294.66	309.24	73.24	0.25
	Gene expression data from Aft red fruit flesh	endocarp	3	3	1307.01	1314.43	84.00	0.06
	Gene expression data from Line27859 mature green fruit flesh	endocarp	3	3	283.29	252.05	85.70	0.30
	Gene expression data from Line27859 red fruit flesh	endocarp	3	3	1112.45	1105.80	63.48	0.06
	Gene expression data from Micro-Tom mature green fruit flesh	endocarp	3	3	324.00	343.28	139.43	0.43
	Gene expression data from Aft mature green fruit peel	exocarp	3	3	215.08	212.34	24.02	0.11
	Gene expression data from Aft red fruit peel	exocarp	3	3	689.00	615.82	135.23	0.20
	Gene expression data from Line27859 mature green fruit peel	exocarp	3	3	278.09	277.85	32.02	0.12
	Gene expression data from Line27859 red fruit peel	exocarp	3	3	501.73	500.09	22.78	0.05
	Gene expression data from Micro-Tom mature green fruit peel	exocarp	3	3	213.30	257.60	96.91	0.45
	Gene expression data from Micro-Tom orange fruit peel	exocarp	2	2	1452.67	1452.67	367.16	0.25
	Gene expression data from Micro-Tom red fruit peel	exocarp	3	3	708.55	708.92	9.61	0.01
	Gene expression data from Micro-Tom yellow fruit peel	exocarp	2	2	1209.57	1209.57	390.34	0.32
	Gene expression data from Momotaro8 red fruit peel	exocarp	4	4	921.75	742.81	456.43	0.50
	Gene expression data from Micro-Tom hypocotyl	hypocotyl	2	2	106.62	106.62	21.67	0.20
	Gene expression data from Micro-Tom 3rd leaf	vascular leaf	2	2	168.10	168.10	19.76	0.12
	Gene expression data from all leaves of 3-week-old Micro-Tom plant	vascular leaf	3	3	165.57	160.37	17.90	0.11
	Gene expression data from all leaves of 5-week-old Micro-Tom plant	vascular leaf	3	3	245.28	243.04	13.44	0.05
	Gene expression data from Micro-Tom orange fruit flesh	mesocarp	2	2	1388.97	1388.97	171.72	0.12
	Gene expression data from Micro-Tom red fruit flesh	mesocarp	3	3	857.96	842.65	57.56	0.07
	Gene expression data from Micro-Tom yellow fruit flesh	mesocarp	2	2	1398.97	1398.97	71.67	0.05
	Gene expression data from Momotaro8 red fruit flesh	mesocarp	4	4	665.97	492.54	434.01	0.65
	Gene expression data from Micro-Tom root	root	3	3	120.06	121.39	21.45	0.18

Expression Data by Targets (experiment replicates) (67)

Experiment name	Target name	normalized_signal	pVal_call	flag
Gene expression data from Micro-Tom cotyledon	GSM480171 extract 1	239.329	7e-4	P
	GSM480170 extract 1	159.745	7e-4	P
Gene expression data from Aft mature green fruit flesh	GSM480201 extract 1	309.241	7e-4	P
	GSM480202 extract 1	215.232	7e-4	P
	GSM480200 extract 1	359.521	7e-4	P
Gene expression data from Aft red fruit flesh	GSM480203 extract 1	1219.54	7e-4	P
	GSM480205 extract 1	1387.05	7e-4	P
	GSM480204 extract 1	1314.43	7e-4	P
Gene expression data from Line27859 mature green fruit flesh	GSM480212 extract 1	217.592	7e-4	P
	GSM480213 extract 1	380.234	7e-4	P
	GSM480214 extract 1	252.046	7e-4	P
Gene expression data from Line27859 red fruit flesh	GSM480217 extract 1	1178.99	7e-4	P
	GSM480215 extract 1	1105.8	7e-4	P
	GSM480216 extract 1	1052.55	7e-4	P
Gene expression data from Micro-Tom mature green fruit flesh	GSM480182 extract 1	175.927	7e-4	P
	GSM480180 extract 1	343.278	7e-4	P
	GSM480181 extract 1	452.785	7e-4	P
Gene expression data from Aft mature green fruit peel	GSM480208 extract 1	240.347	7e-4	P
	GSM480206 extract 1	192.552	7e-4	P
	GSM480207 extract 1	212.335	7e-4	P
Gene expression data from Aft red fruit peel	GSM480209 extract 1	845.043	7e-4	P
	GSM480211 extract 1	606.124	7e-4	P
	GSM480210 extract 1	615.822	7e-4	P
Gene expression data from Line27859 mature green fruit peel	GSM480218 extract 1	246.19	7e-4	P
	GSM480219 extract 1	310.221	7e-4	P
	GSM480220 extract 1	277.85	2e-4	P
Gene expression data from Line27859 red fruit peel	GSM480222 extract 1	500.094	2e-4	P
	GSM480223 extract 1	479.814	7e-4	P
	GSM480221 extract 1	525.29	7e-4	P
Gene expression data from Micro-Tom mature green fruit peel	GSM480192 extract 1	102.167	0.001	P
	GSM480190 extract 1	280.149	7e-4	P
	GSM480191 extract 1	257.595	7e-4	P
Gene expression data from Micro-Tom orange fruit peel	GSM480195 extract 1	1712.29	2e-4	P
	GSM480196 extract 1	1193.05	7e-4	P
Gene expression data from Micro-Tom red fruit peel	GSM480199 extract 1	708.924	7e-4	P
	GSM480197 extract 1	717.97	2e-4	P
	GSM480198 extract 1	698.765	7e-4	P
Gene expression data from Micro-Tom yellow fruit peel	GSM480194 extract 1	933.553	7e-4	P
	GSM480193 extract 1	1485.58	7e-4	P
Gene expression data from Momotaro8 red fruit peel	GSM480228 extract 1	848.227	2e-4	P
	GSM480229 extract 1	637.396	0.001	P
	GSM480230 extract 1	613.498	7e-4	P
	GSM480231 extract 1	1587.87	7e-4	P
Gene expression data from Micro-Tom hypocotyl	GSM480168 extract 1	91.2962	2e-4	P
	GSM480169 extract 1	121.949	7e-4	P
Gene expression data from Micro-Tom 3rd leaf	GSM480172 extract 1	182.066	2e-4	P
	GSM480173 extract 1	154.126	0.001	P
Gene expression data from all leaves of 3-week-old Micro-Tom plant	GSM480174 extract 1	160.368	0.001	P
	GSM480175 extract 1	150.838	7e-4	P
	GSM480176 extract 1	185.491	7e-4	P
Gene expression data from all leaves of 5-week-old Micro-Tom plant	GSM480178 extract 1	233.104	7e-4	P
	GSM480177 extract 1	259.694	7e-4	P
	GSM480179 extract 1	243.036	7e-4	P
Gene expression data from Micro-Tom orange fruit flesh	GSM480186 extract 1	1267.55	2e-4	P
	GSM480185 extract 1	1510.4	7e-4	P
Gene expression data from Micro-Tom red fruit flesh	GSM480188 extract 1	842.649	2e-4	P
	GSM480189 extract 1	921.622	7e-4	P
	GSM480187 extract 1	809.601	7e-4	P
Gene expression data from Micro-Tom yellow fruit flesh	GSM480183 extract 1	1449.65	7e-4	P
	GSM480184 extract 1	1348.29	7e-4	P
Gene expression data from Momotaro8 red fruit flesh	GSM480225 extract 1	369.397	2e-4	P
	GSM480227 extract 1	1309.41	7e-4	P
	GSM480224 extract 1	453.98	2e-4	P
	GSM480226 extract 1	531.106	7e-4	P
Gene expression data from Micro-Tom root	GSM480165 extract 1	97.9721	7e-4	P
	GSM480166 extract 1	121.391	7e-4	P
	GSM480167 extract 1	140.818	0.001	P

Correlation analysis (0)

No correlation analysis was found associated to this template

Your Lists

Public Lists

List Contents

List Validation Report: Failed

Elements not found:

Optional: Add Missing Accessions to A List

Mismatched case

Click the Adjust Case button to align the case in the list with what is in the database.

Multiple mismatched case

Items listed here have mulitple case mismatches and must be fixed manually. If accessions need to be merged, contact the database directly.

List elements matching a synonym

Multiple synonym matches

Multiple synonym matches have to be resolved manually. Contact database administrators if necessary.

Fuzzy Search Results

Synonym Search Results

Create a New List from Unique Names:

Available Seedlots

Accessions	Seedlots
Accessions		Breeding Program	Seedlot Name	Contents	Seedlot Location	Count	Weight(g)

Create a New List from Selected Seedlots:

Manage Seedlots

Your Datasets

Public Datasets

Dataset Contents

Dataset Validation Failed

Elements not found:

Your Calendar

Having trouble viewing events on the calendar?
Are you associated with the breeding program you are interested in viewing?

Calendar Permissions

Add New Event

Project:

Event Type:

Start:

End:

Description:

Web URL:

http://www.

Event Info

Attribute	Value
Project Name:
Start Date:
End Date:
Event Type:
Event Description:
Event Web URL:

Edit Event

Project:

Event Type:

Start:

End:

Description:

Web URL:

Login

Forgot Username

If you've forgotten your username, enter your email address below. An email will be sent with any account username(s) associated with your email address.

Email Address

Reset Password

To reset your password, please enter your email address. A link will be sent to that address with a link that will enable you to reset your password.

Email Address

Create New User

Notice

Before creating a new account, please check if you already have an account using the directory search.
A link will be emailed to you. Please click on it to activate the account.
All fields are required.

First Name:

Last Name:

Organization:

Username:

Username must be at least 7 characters long.

Password:

Password must be at least 7 characters long and different from your username.

Confirm Password:

Password must be at least 7 characters long and different from your username.

Email Address:

An email will be sent to this address requiring you to confirm its receipt to activate your account.