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Gene Structure Additions/Modifications - Guidelines
Marker and Polymorphism Data
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If you are submitting more than 150 entries, please e-mail curator@arabidopsis.org for additional instructions otherwise please submit your data by using the following preformatted spreadsheet:
Download: marker_polymorphism_data_form.xls (CHANG
Send completed marker files or any related questions to: curator@arabidopsis.org
Instructions on how to use the preformatted spreadsheet:
If available, always indicate the digest pattern/PCR length/base pair of Col-0 as a reference (not necessary for deletions/insertions).
Examples:
| Marker Name | Marker Type | Polymorphism Type | Polymorphism | Restriction Site | Ecotype |
|---|---|---|---|---|---|
| MARKER1 | CAPS | digest_pattern | 400;230 | 1 | Col-0 |
| MARKER1 | CAPS | digest_pattern | 630 | 0 | Hi-0 |
| MARKER2 | SNPlex | SNP | G | Col-0 | |
| MARKER2 | SNPlex | SNP | A | Hi-0 |
In the case where a marker or polymorphism is shared by several ecotypes, please list all ecotypes in the same row, as shown in this example:
| Marker Name | Marker Type | Polymorphism Type | Polymorphism | Ecotype |
|---|---|---|---|---|
| MARKER3 | SSLP | PCR_product_length | 165 | Col-0;Gr-6;Gu-0 |
| MARKER3 | SSLP | PCR_product_length | 150 | RLD;Wil-1;Wt-5 |
Fields indicated in blue are required. Fields marked with an asterisk (*) can contain multiple entries but these must be separated by a semicolon with no intervening spaces (e.g. Col-0;Ler-0). Note that examples have been included in the column headers; please retain headers as the first line in your files. You can find your Community ID and the Citation/Reference ID by using the links to our TAIR search pages provided in the template below.
If you have any questions or suggestions, please contact us at: curator@arabidopsis.org
| Field | Description | Values/Constraints | Example |
|---|---|---|---|
| Contact Person Name* | Last name,First name | No space between first and last names or between semicolon | Buschmann,Henrik |
| Contact Person Community ID* | unique identifier for a community member in TAIR. You must be registered to have a community ID | TAIR accession from TAIR Community Search | community:1035 |
| Contact Person E-mail Address | current email address | buschmann@gsf.de | |
| Marker/Polymorphism Name | PT1 or Salk_0228 | ||
| Alternative Names* | AtPT1 | ||
| Chromosome | The chromosome in which the marker/polymorphism is found | 1,2,3,4,5 or unknown | 5 |
| Genetic Marker Type | CAPS, SSLP, AFLP, RFLP, RAPD, SNPlex or Taqman | CAPS | |
| Polymorphism Type | Dependent on Marker Type | Digest_pattern (CAPS or RFLP), PCR_product_length (SSLP, AFLP, or RAPD), substitution, insertion, deletion | Digest_pattern |
| Polymorphism Lengths * | Length of digest or PCR product | numeric, in kb or bp | 0.12, 120 |
| Polymorphism Length Units | bp or kb | kb | |
| Flank Sequence Type | Required for all but RFLP submissions | PCR_primer or Flank | flank |
| Flank Sequence 1 | Required for all but RFLP submissions. The first PCR primer sequence | ATGGTGCCGTGACGT | |
| Flank Sequence 2 | Required for all but RFLP submissions. The second PCR primer sequence | AATTGGGTGTGCTAG | |
| Special Conditions | Indicate any special conditions required for marker detection | annealing temp 62C | |
| Restriction Enzyme Name* | Name of the restriction enzyme used to detect the polymorphism (required for CAPS, AFLP, or RFLP markers). | consult REBASE for standard enzyme name. | HindIII;EcoRV |
| Restriction Enzyme Number of sites* | Number of recognition sites for each restriction enzyme. The order of number of sites should match the order of restriction enzyme names in previous column. | numeric | 3 |
| Ecotype/Accession Name* | The ecotype which shows the specific polymorphism. If more than one ecotype shares a polymorphism, list all ecotypes. | Col-0 should always be shown as reference | Col-O;RLD;Ler |
| Accession Stock ID | For accessions that correspond to an ABRC stock, this is the stock ID number for that accession. | CS3455;CS3444 | |
| Polymorphic Sequence | Sequence of the polymorphic region for the given ecotype/accession | ATGTGGCCTCTT | |
| Map Position1 | Position of the SNP, insertion site, start position of 5' PCR primer/flanking sequence | 20215474 | |
| Map Position2 | End position of 3' PCR primer/flanking sequence | 26877049 | |
| TAIR Version | version of the TAIR genome assembly that your experiment is based on | TAIR9 | |
| Inheritance | The mode of inheritance of the polymorphism | recessive, dominant, co-dominant, semi-dominant, unknown | dominant |
| Marker/Polymorphism Citation/Reference_id | For a reference that describe the marker/polymorphism, this is the unique identifier in TAIR. For articles referring to the markers that are not yet in TAIR, please contact a curator to update this information into the database when the paper is published. | TAIR accession from TAIR Publication Search | publication:12344 |
Phenotypes
We accept phenotype data for all mapped and/or sequenced Arabidopsis mutants, including existing ABRC stocks, stocks from other stock centers, and lines that have not been deposited in a public repository. If you are submitting phenotype data for stocks not in ABRC we encourage you to consider also submitting the seed stock.
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Description of column headers
| Field | Description |
|---|---|
| Contact Person | Please provide name and email of the contact person/corresponding author |
| Reference (Pubmed ID, DOI, or other format) | PMID: 18485063 - we prefer Pubmed ID, but the following format without Pubmed ID is OK too:Plant J (2008), 55: 798 |
| Allele Symbol / Polymorphism Name | For example: rpp3, rpp4(SALK_12345), atswc6(SAIL_1142_C03) |
| Accession | Example, Ws, Col-0 |
| Locus | If this polymorphism is an allele of a locus, enter the unique locus code here. Otherwise, leave empty. Example: AT4G32520 |
| Mutagen | EMS, X-rays, T-DNA insertion, transposon, fast neutron etc. |
| Mutation Site | Please describe the mutation site (3rd intron, 2nd exon, promoter, 3'UTR, 5'UTR etc). Please also give details of the mutation if known (for instance, contains a G to A subsitution at nucleotide position 123) |
| Genotype | Select from homozygous, heterozygous, hemizygous, and unknown. |
| Inheritance | Select from dominant, recessive, incompletely dominant, co-dominant, and unknown. |
| Allele Mode | Select from hypermorphic, hypomorphic, haplo-insufficient, antimorphic, gain-of-function, loss-of-function, and unknown. |
| Phenotype | Please provide a brief description of the mutant phenotype. Note: please specify if the phenotype is for double/triple mutants (for example, mop3/mop4). |
Protocols
TAIR encourages the research community to share their protocols. To submit a protocol to TAIR, send the protocol in one of the following formats.
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