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Detailed view of individual locus

A locus is a collection of one or more models. This page provides information relating to the locus as a whole and to indivudual models within the locus.

The locus name and LLNL unique locus id are indicated at the top of the page. Links to additional views of the locus are available:

: displays the Map Browser view of the chromosome containing the locus.

: displays the locus externally within the UCSC Genome Browser with LLNL models and motifs added as extra tracks.

Genomic Motifs

A listing of all motifs identified within the locus (excluding motifs on the opposite strand) is displayed 5' to 3'. Motifs listed were identified computationally by analysis of genomic sequence (using profile HMMs) and are not guranteed to be biologically active nor to be expressed in all (or even any!) of the models.

An indication of the possible functionality of a motif can be (partially) inferred by the # of stop codons it contains and the HMMER e-value. In the case of finger motifs, the finger is indicated as being canonical if the corresponding peptide sequence follows the basic pattern of C-X2-C-X12-H-X3-H where X represents any residue and C and H represent, respectively, the cysteine and histidine resides responsible for the caging of a zinc ion in the folded finger structure.

More detailed information (including sequence) for each motif can be obtained by clicking on the motif name.

Model Summary

A listing of all models (including possible alternative transcripts) assigned to the given locus. A schematic summary of the motifs identified in the genomic sequence and predicted to be translated (in frame) within a given model is provided. For detailed information listing the location and expression profile of all identified motifs within a given model, click on the model id.

Summary of Model Variations

List some information about how the locus' models vary from each other. For a graphical view of model structures please use the UCSC link at the top of the page.

  • Total # Models assigned to locus: Number of models assigned to locus
  • Total # distinct coding sequences represented by models: Number of different proteins predicted to be encoded by all models assigned to the locus. This number would be less than the total number of models if some of the models only differ in their non-coding regions.
  • Models show variation in their 5' UTRs: 'true' if two or more models have differences in their 5' UTRs
  • Alternate Transcription Starts: 'true' if two or more models have different transcriptional starts
  • Alternate Translation Starts: 'true' if two or more models have different translation starts
  • Models show variation in their 3' UTRs: 'true' if two or more models have differences in their 3' UTRs
  • Alternate Transcription Ends: 'true' if two or more models have different transcriptional ends
  • Alternate Translation Ends: 'true' if two or more models have different translation ends