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Please READ: Community Standards for Arabidopsis Genetics [download PDF]. Standards of gene nomenclature have been adopted by the Arabidopsis community and should be followed in publications and presentations.
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Designation of unique locus identifiers is performed as part of the genome sequence annotation at TAIR. The following section describes the syntax of chromosome based locus nomenclature and how locus identifiers are assigned. In some cases locus identifiers have been made obsolete. If you have information about a sequenced locus that has not been given a locus identifier, please contact curator@arabidopsis.org.
Guidelines for use of unique gene
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ids (modified from MIPS)
- Format of chromosomal based nomenclature
- AT (Arabidopsis thaliana)
- 1,2,3,4,5 (chromosome number) or M for mitochondrial or C for chloroplast.
- G (gene), other letters possible for repeats etc.)
- 12300 (five-digit code, numbered from top/north to bottom/south of chromosome)
- Chromosome based locus identifiers are assigned to
- protein-coding genes
- RNA coding genes (sn, r, tRNAs)
- pseudogenes
- Chromosome based locus identifiers are not assigned to
- transposons
- Usage
- The first AGI locus identifier release made use of locus identifiers ending in zero, eg 10010, 10020, 10030 and so on so that intervening numbers could be used for newly discovered genes.
- Where there are gaps in the sequence, the first release skipped at least 200 codes for each 100 kb of gap.
- In the first release, some genes were present as fragments as they lie across the boundary of two BACS. Each fragment got its own locus identifier if there was no way to represent the whole gene. There gene fragments were merged into a single locus in later releases, and one of the AGI locus identifiers became obsolete.
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The following table lists prefixes used by functional genomics projects for naming T-DNA insertions. This information can be used to search for all of the . For example, to find all of the deletions identified by the Stanford Genome Sequencing Center you can search by Polymorphism name starts with SGC and type is deletion.
| Prefix | Source | Comment |
|---|---|---|
| SGC | Stanford Genome Center | Includes insertions, deletions and single nucleotide polymorphisms |
| CER | Cereon Genomics | Includes insertions, deletions and single nucleotide polymorphisms. Available only to registered users from non-profit and academic institutions. |
Names used for large sets of T-DNA or transposon insertions
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The following table lists prefixes used by functional genomics projects for naming T-DNA insertions. This information can be used to search for all of the insertion lines generated by a project. For example, to find all of the T-DNA insertion lines generated by Joe Ecker's group at the SALK institute you can search by Polymorphism name starts with SALK.
| Prefix | Source | Comment |
|---|---|---|
| SALK | Joe Ecker et.al. | Sequence indexed library of insertion mutations generated using the pROK2 T-DNA vector. |
| SGT | V.Sundareson et.al. | Gene trap lines from the Institute for Molecular Agrobiology (IMA) |
| SET | V.Sundareson et.al. | Enhancer trap lines from Institute for Molecular Agrobiology (IMA) |
Clone and Vector Names
Arabidopsis clones are usually named with the acronym of the vector followed by the plate and row numbers of the isolated clone. For example, CIC (YAC), T (TAMU BAC), F (IGF BAC) are some common vector acronyms.The following table gives information about nomenclature for clones and vectors in TAIR. You can use the prefix in a wild card search for all clones from a particular source or vector. For example, you can use the DNA search to find all TAMU clones by choosing clone name [starts with] T.
| Vector type | Clone Prefix | Vector Name | Source | Description |
|---|---|---|---|---|
| BAC | T | pBeLoBAC11 | TAMU (Texas A&M University) | from bacterial artificial chromosome library used for genomic sequencing |
| BAC | F | pBELoBACkan | IGF (Institut fur Genbiologische) | from bacterial artificial chromosome library used for genomic sequencing |
| P1 | M | pAd10sacBII | Mitsui et.al. | from Bacteriophage P1 library used for genomic sequencing |
| TAC | K | pTAC-YL7 | Kazuza | transformation-competent bacterial artificial chromosome vector |
| YAC | CIC | pYAC4 | CEPH/INRA/CNRS | From yeast artificial chromosome libary |
| YAC | EG | pYAC41 | Grill and Somerville | from EG1 yeast artificial chromosome library |
| YAC | EW | pYAC3 | E. Ward et.al. | from yeast artificial chromosome library |
| YAC | yUP | pYAC4 | Joe Ecker et.al. | yeast artificial chromosome library |
| Cosmid | G | Howard Goodman et.al. | From cosmid library prepared by H.Goodman et.al. |
GenBank Accessions
Certain objects such as genes, clones, clone ends and some insertions in TAIRs database can be accessed by searching with the associated Genbank accession number. Each accession number in GenBank is unique. See http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html#AccessionB for information about GenBank accession numbers.