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This tool is used primarily to find location of genes on the B73 assembly.
For other information about your gene, you may wish to use the Data Center 'Gene/Gene models'.
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Enter a
locus name
and this tool will return the best available chromosomal coordinates.
Do you want to look up two linked loci at the same time?
(?) How this tool works
The Locus Lookup tool works by:
- checking if the locus is associated to any gene models and the coordinates for the gene model is returned.
- checks physical map coordinates to find out whether the locus is already placed. If so, your physically mapped locus is highlighted in red in the region returned.
- checks the locus record at MaizeGDB to find out if any placed BACs are known to detect the locus and that BAC is returned within its genomic context.
- genetically mapped probes that are nearest the input locus are identified, the tool checks whether those probes have known genomic coordinates (working outward until appropriate probes are identified) and finally the region of the genome contained by the identified probes is reported with bounding probes shown in red.
Note well: even though your locus physically maps to a known location within a BAC, because most BAC sequences currently are comprised of concatenated sequence fragments of unknown order and orientation, the locus' position on each individual BAC sequence may be anywhere on the BAC associated with a physically mapped probe [i.e., for (4) above, the sequence for the probe and/or locus of interest could be anywhere on BAC(s) associated with the probe(s) identified, even outside of the region bounded by the physically mapped probe locations]. For this reason, a conservative window showing the entire BAC(s) to which the probe(s) have been physically mapped, is shown.
This tool works by finding the nearest genetically mapped loci that flank the input locus, and have an association with the B73 genome sequence. Sometimes, the input locus will fall outside the predicted region. This is due to the intrinsic nature of the genetic consensus maps, and the current status of the B73 genome sequence.
