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
- Traits
- 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
Tools
- Sequence Analysis
- BLAST
- VIGS Tool
- Alignment Analyzer
- Tree Browser
- Motif Finder
- Mapping
- Genome Browser (Jbrowse 1)
- SolBrowse Comparative genome viewer
- Jbrowse2 (under development)
- Comparative Map Viewer
- CAPS Designer
- solQTL: QTL Mapping
- Molecular Biology
- In Silico PCR
- Tomato Expression Atlas (TEA)
- Tomato Expression Database (TED)
- Systems Biology
- CRISPget CRISPR designer
- 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.55380.1.S1_at

Template Basic Information

Template name:	LesAffx.55380.1.S1_at
Template type:	Probe Set
Platform:	Affymetrix GeneChip Tomato Genome Array
Internal db links:	SGN-U570954
External db links:	GenBank: BI934729

Annotations for unigene SGN-U570954 (manual: 0 | blast: 3 | go: 8 )

Manual annotations

None manual annotation was found for this unigene

Blast Annotations [Show All]

Database	Program	Best Match	Score	E-value	Identity	Alignment Length	Frame
genbank	blastx	gi\|4584255\|emb\|CAB40577.1\|	417	7e-115	86.55	660 bp (65.0%)	2
Description:	SINA1p [Vitis vinifera]
arabidopsis	blastx	At3G61790.1	394	4e-110	78.02	660 bp (65.0%)	2
Description:	seven in absentia (SINA) family protein \| chr3:22882949-22884518 REVERSE
swissprot	blastx	Q84JL3	394	3e-109	78.02	660 bp (65.0%)	2
Description:	E3 ubiquitin-protein ligase SINAT3 OS=Arabidopsis thaliana GN=SINAT3 PE=2 SV=1

GO Terms Annotations

GO:0008270zinc ion binding
GO:0007275development
GO:0005515protein binding
GO:0004842ubiquitin-protein ligase activity
GO:0005634nucleus
GO:0000151ubiquitin ligase complex
GO:0016567protein ubiquitination
GO:0006511ubiquitin-dependent protein catabolism

Probe Composition (11)

Probe name	Probe type	Template start coord	Template end coord	Spots
LesAffx.55380.1.S1_at:ProbePair0	PM	data not available	data not available	data not available
LesAffx.55380.1.S1_at:ProbePair1	PM	data not available	data not available	data not available
LesAffx.55380.1.S1_at:ProbePair10	PM	data not available	data not available	data not available
LesAffx.55380.1.S1_at:ProbePair2	PM	data not available	data not available	data not available
LesAffx.55380.1.S1_at:ProbePair3	PM	data not available	data not available	data not available
LesAffx.55380.1.S1_at:ProbePair4	PM	data not available	data not available	data not available
LesAffx.55380.1.S1_at:ProbePair5	PM	data not available	data not available	data not available
LesAffx.55380.1.S1_at:ProbePair6	PM	data not available	data not available	data not available
LesAffx.55380.1.S1_at:ProbePair7	PM	data not available	data not available	data not available
LesAffx.55380.1.S1_at:ProbePair8	PM	data not available	data not available	data not available
LesAffx.55380.1.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	95.41	95.41	17.82	0.19
	Gene expression data from Aft mature green fruit flesh	endocarp	3	3	55.95	49.32	11.59	0.21
	Gene expression data from Aft red fruit flesh	endocarp	3	3	38.13	39.54	4.26	0.11
	Gene expression data from Line27859 mature green fruit flesh	endocarp	3	3	47.37	48.34	15.52	0.33
	Gene expression data from Micro-Tom yellow fruit flesh	endocarp	2	2	44.36	44.36	4.46	0.10
	Gene expression data from Momotaro8 red fruit flesh	endocarp	4	4	18.91	17.57	7.01	0.37
	Gene expression data from Aft mature green fruit peel	exocarp	3	3	48.16	44.08	9.85	0.20
	Gene expression data from Aft red fruit peel	exocarp	3	3	35.88	35.38	6.12	0.17
	Gene expression data from Line27859 mature green fruit peel	exocarp	3	3	62.45	55.11	15.68	0.25
	Gene expression data from Line27859 red fruit peel	exocarp	3	3	27.39	27.75	2.07	0.08
	Gene expression data from Micro-Tom mature green fruit peel	exocarp	3	3	37.85	34.34	12.44	0.33
	Gene expression data from Micro-Tom orange fruit peel	exocarp	2	2	48.77	48.77	1.30	0.03
	Gene expression data from Micro-Tom red fruit peel	exocarp	3	3	42.32	43.38	6.34	0.15
	Gene expression data from Micro-Tom yellow fruit peel	exocarp	2	2	38.02	38.02	7.03	0.18
	Gene expression data from Momotaro8 red fruit peel	exocarp	4	4	18.42	16.84	6.66	0.36
	Gene expression data from Micro-Tom hypocotyl	hypocotyl	2	2	122.31	122.31	3.23	0.03
	Gene expression data from Micro-Tom 3rd leaf	vascular leaf	2	2	73.13	73.13	2.48	0.03
	Gene expression data from all leaves of 3-week-old Micro-Tom plant	vascular leaf	3	3	54.64	49.35	16.98	0.31
	Gene expression data from all leaves of 5-week-old Micro-Tom plant	vascular leaf	3	3	55.25	59.61	8.72	0.16
	Gene expression data from Line27859 red fruit flesh	mesocarp	3	3	32.51	33.11	1.32	0.04
	Gene expression data from Micro-Tom mature green fruit flesh	mesocarp	3	3	32.47	32.22	7.45	0.23
	Gene expression data from Micro-Tom orange fruit flesh	mesocarp	2	2	42.66	42.66	7.69	0.18
	Gene expression data from Micro-Tom red fruit flesh	mesocarp	3	3	41.29	36.33	11.47	0.28
	Gene expression data from Micro-Tom root	root	3	3	44.44	45.22	13.67	0.31

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	82.8084	2e-4	P
	GSM480171 extract 1	108.014	2e-4	P
Gene expression data from Aft mature green fruit flesh	GSM480201 extract 1	49.2072	0.001	P
	GSM480202 extract 1	69.3319	2e-4	P
	GSM480200 extract 1	49.3219	7e-4	P
Gene expression data from Aft red fruit flesh	GSM480203 extract 1	33.3399	0.001	P
	GSM480205 extract 1	39.5447	2e-4	P
	GSM480204 extract 1	41.4986	0.001	P
Gene expression data from Line27859 mature green fruit flesh	GSM480212 extract 1	31.3865	0.003	P
	GSM480213 extract 1	48.3422	0.001	P
	GSM480214 extract 1	62.3843	2e-4	P
Gene expression data from Micro-Tom yellow fruit flesh	GSM480183 extract 1	47.5082	7e-4	P
	GSM480184 extract 1	41.2055	0.001	P
Gene expression data from Momotaro8 red fruit flesh	GSM480224 extract 1	14.6682	0.056	M
	GSM480225 extract 1	12.3992	0.068	A
	GSM480226 extract 1	20.4678	0.006	P
	GSM480227 extract 1	28.1038	7e-4	P
Gene expression data from Aft mature green fruit peel	GSM480206 extract 1	44.0759	2e-4	P
	GSM480207 extract 1	41.0047	7e-4	P
	GSM480208 extract 1	59.3936	0.001	P
Gene expression data from Aft red fruit peel	GSM480210 extract 1	42.2369	7e-4	P
	GSM480211 extract 1	35.3761	7e-4	P
	GSM480209 extract 1	30.0329	0.002	P
Gene expression data from Line27859 mature green fruit peel	GSM480220 extract 1	55.1068	7e-4	P
	GSM480218 extract 1	51.7928	7e-4	P
	GSM480219 extract 1	80.4486	0.001	P
Gene expression data from Line27859 red fruit peel	GSM480223 extract 1	29.258	7e-4	P
	GSM480221 extract 1	27.7454	0.008	P
	GSM480222 extract 1	25.1727	0.002	P
Gene expression data from Micro-Tom mature green fruit peel	GSM480192 extract 1	27.554	0.002	P
	GSM480191 extract 1	34.3376	0.002	P
	GSM480190 extract 1	51.668	2e-4	P
Gene expression data from Micro-Tom orange fruit peel	GSM480196 extract 1	47.8464	2e-4	P
	GSM480195 extract 1	49.6892	7e-4	P
Gene expression data from Micro-Tom red fruit peel	GSM480198 extract 1	43.3766	0.003	P
	GSM480199 extract 1	35.5193	2e-4	P
	GSM480197 extract 1	48.068	0.002	P
Gene expression data from Micro-Tom yellow fruit peel	GSM480194 extract 1	42.9918	0.001	P
	GSM480193 extract 1	33.0556	0.001	P
Gene expression data from Momotaro8 red fruit peel	GSM480228 extract 1	12.1503	0.002	P
	GSM480230 extract 1	16.9097	0.004	P
	GSM480231 extract 1	27.836	0.002	P
	GSM480229 extract 1	16.7644	7e-4	P
Gene expression data from Micro-Tom hypocotyl	GSM480169 extract 1	120.027	7e-4	P
	GSM480168 extract 1	124.593	7e-4	P
Gene expression data from Micro-Tom 3rd leaf	GSM480172 extract 1	74.8895	7e-4	P
	GSM480173 extract 1	71.38	2e-4	P
Gene expression data from all leaves of 3-week-old Micro-Tom plant	GSM480175 extract 1	40.9305	0.004	P
	GSM480174 extract 1	49.3541	0.001	P
	GSM480176 extract 1	73.6252	7e-4	P
Gene expression data from all leaves of 5-week-old Micro-Tom plant	GSM480179 extract 1	59.6096	0.002	P
	GSM480178 extract 1	45.2158	0.001	P
	GSM480177 extract 1	60.9307	0.001	P
Gene expression data from Line27859 red fruit flesh	GSM480217 extract 1	33.1091	7e-4	P
	GSM480215 extract 1	31.0049	7e-4	P
	GSM480216 extract 1	33.4239	0.014	P
Gene expression data from Micro-Tom mature green fruit flesh	GSM480182 extract 1	25.1515	0.001	P
	GSM480181 extract 1	32.2159	7e-4	P
	GSM480180 extract 1	40.0504	0.003	P
Gene expression data from Micro-Tom orange fruit flesh	GSM480186 extract 1	48.0958	0.001	P
	GSM480185 extract 1	37.2203	0.002	P
Gene expression data from Micro-Tom red fruit flesh	GSM480189 extract 1	36.3284	2e-4	P
	GSM480187 extract 1	33.1291	0.001	P
	GSM480188 extract 1	54.4072	0.001	P
Gene expression data from Micro-Tom root	GSM480166 extract 1	45.218	2e-4	P
	GSM480165 extract 1	30.4034	0.011	P
	GSM480167 extract 1	57.7103	0.002	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

Show Password

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.