PubMed Nucleotide Protein Genome Structure Taxonomy

Strongylocentrotus purpuratus genome data and search tips Revised October 18 2006

The Map Viewer help document describes how to use the Map Viewer software. This page describes the data available for Strongylocentrotus purpuratus, and the search tips specific to that organism. Upon familiarization, you may return to the Strongylocentrotus purpuratus genome overview page or stop by the Map Viewer home page, where you can search the genome data of any organism represented in MapViewer.


Scope of Data back to top

The Map Viewer provides a view of S. purpuratus data from a variety of sources described below.

S. purpuratus Genomic Sequence Data:
whole genome shotgun (WGS) and BAC data		 back to top

The current S. purpuratus reference assembly is based on the Spur_v2.1 assembly produced by the Human Genome Sequencing Center at Baylor College of Medicine. The sequencing strategy produced an ~8-fold mixed assembly of whole-genome shotgun (WGS) and BAC sequences.

The current build also includes an alternate assembly, NCBI_super-scaffold_of_Spur_v2.1, produced by NCBI. This alternate assembly includes super-scaffolds assembled by NCBI using sequence overlaps together with mRNA, EST, protein and paired read alignments to order and orient WGS scaffolds from the Baylor College of Medicine Human Genome Sequencing Center's Spur_v2.1 assembly.

The mitochondrial genome presented in the current build, NC_001453, is derived from a distinct specimen than that used for the nuclear genome.

Map Viewer also displays the first sea urchin assembly as a Previous Build, with a static display of the previous maps associated with that assembly for search and comparison with the current build.

BLAST of S. purpuratus Genomic Sequence back to top

The complete set of S. purpuratus sequence databases available for BLAST searching are shown on the Sea Urchin BLAST page, which includes a link to the database descriptions.

Additional Sea Urchin Genome Resources back to top

In addition to the S. purpuratus data available in the Map Viewer and through BLAST, links to NCBI resources and external sites are available from the Sea Urchin Genome Resource Guide.

Available Maps back to top

NOTE: The WGS sequences in Strongylocentrotus purpuratus build 2.1 are not localized to chromosomes, so the sequence maps cannot be queried by chromosome number or by the chromosome number links.

The available maps for Strongylocentrotus purpuratus include:

Sequence Maps back to top

Ab initio

The Assembly map allows users to visualize all of the sequence data available for a given region of the genome, and separates the data by assembly. Data are currently available for two assemblies, Spur_v2.1 and NCBI_super-scaffold_of_Spur_v2.1.

Assembly

Models generated by Gnomon. mRNA alignments were used to segment the genomic sequence by putative gene boundaries, and Gnomon was executed on these segments to predict genes. Gnomon uses protein alignments in addition to transcript alignments and, in order to capture as much coding information in the genome as possible in this assembly, Gnomon models may represent partial as well as complete coding sequences. Models built using alignments are blue, the models with frameshifts or premature stops are green, and the pure ab initio predictions are brown.

Component

The component map provides the tiling path of GenBank "AAGJ01xxxxxx" accessions used to build the "NW_xxxxxx" WGS contigs.
Contig

Shows the chromosomal placement of NW_xxxxxx contigs on the assembly of whole genome shotgun (WGS) data.
Ech_RNA Alignment of individual transcripts from sea urchins other than S. purpuratus to the assembled genomic sequence.

Spu_RNA Alignment of individual S. purpuratus transcripts to the assembled genomic sequence.

GenBank_DNA

Shows the placement of S. purpuratus genomic DNA sequences from GenBank on the assembly of whole genome shotgun (WGS) data. Placement is based on the alignment of the sequences to the components (AAGJxxxxxxxx) of the contigs. It includes S. purpuratus genomic sequences longer than 500 bp that have at least 97% identity to the components for at least 98 base pairs. If a sequence extends beyond a contig, that portion of sequence is not shown. The 'hits' link leads to a tabular display that shows the matching regions (base spans) of the assembly component and the GenBank genomic DNA record that has been aligned to it.

The length of a line represents the upper and lower-most points on the genome assembly to which sequence fragments from a single GenBank record were aligned.

When the GenBank_DNA map is displayed as the master map, in the default verbose mode, the descriptive text includes several columns: Total Bases which shows the total number of bases in the GenBank record; Aligned Bases which shows the total number of bases from that record that were aligned to the genome; % identity for the alignment; % coverage which shows how much of the Genbank record aligned to the genome as a percentage; Alignment-length ratio, which is the ratio of the alignment length in the genome to the alignment length of the Genbank record; and Breed from which the Genbank record was derived, when available.

Genes_Sequence

Genes that have been annotated on the genomic contigs. This includes known and putative genes placed as a result of alignments of mRNAs to the contigs.

If multiple models exist for a single gene, corresponding to splicing variants, the Gene_Sequence map presents a flattened view of all the exons that can be spliced together in various ways. For example, if one splice variant uses exons 1, 3, 4, and another splice variant uses exons 2, 3, 4, the Gene_Sequence map shows exons 1, 2, 3, 4. (In comparison, the Transcript (RNA) map shows what combinations of exons are valid based on mRNA sequences from RefSeq and GenBank.)

Genes shown on the left of the grey line are transcribed in the - orientation (from bottom up), and those on the right in the + orientation (from top down).

When Gene_Sequence is selected as the Master map, the verbose display (detailed labeling, shown by default) includes arrows to the right of each gene name indicate its direction of transcription as well as links to:

  • sv - sequence viewer (more...)
  • pr - protein (more...)
  • dl - view/download sequence data from a chromosome region (more...)

Additional information about these links is also provided in the Entrez Map Viewer Help Document, under Links to Related Resources.

Gene models are shown in five colors, depending on the type of evidence that was used to construct the models. The one or two letter code shown in the evidence column (that is displayed when Gene_Sequence is the master map) also indicates the type of evidence.

 
Gene Color Evidence Code Type of evidence used to construct gene model
Blue C Confirmed gene model - model based on alignment of mRNA, or mRNAs plus ESTs, to the genomic sequence (see additional notes, below)
Light Green E EST only - model based on EST evidence only
Dark Brown PE Predicted+EST - model predicted by Gnomon and EST evidence (more about Gnomon)
Light Brown P Predicted only - model predicted by Gnomon (more about Gnomon)
Orange ? Conflict - there is some discrepancy between the mRNA sequence and the gene model (see additional notes, below)
  I Interim LocusID - model based alignment of mRNAs, or mRNAs plus ESTs, to the genome, in which the aligning transcripts could not be unambiguously assigned to a preexisting LocusID (see additional notes, below)

  Additional Notes:

In general, a gene model is shown in blue if there is a clean alignment between a RefSeq or GenBank mRNA sequence and the genomic sequence, and if there is an exact match between the protein product that was annotated in the mRNA sequence record and the conceptual translation of the genomic sequence gene model.

A gene model is shown in orange if there is some discrepancy between the mRNA sequence and the gene model, either in the alignment of the two and/or in their protein products. Examples of the former can include gaps, or the alignment of an mRNA to two or more genomic regions. Examples of the latter can include differences between the amino acid sequence given in an mRNA sequence record and the conceptual translation of the corresponding gene model, or premature termination of a coding region in the genomic sequence. Both of those can be caused by base pair mismatches between the mRNA and genomic sequence.

Models with Interim LocusIDs (evidence code I) may be paralogs, genes not yet curated, duplications because of assembly errors, or pseudogenes. The genome assembly and annotation pipeline assigns interim IDs when there is no unambiguous solution to what they should be. Interim LocusIDs are always associated with a RefSeq XM_* accessions (model mRNAs), although supporting alignments may (or may not) include RefSeq NM_* accessions (known mRNAs). More about RefSeq and RefSeq accessions can be found at the RefSeq homepage.

RefSeq RNA

Diagrams of the RNAs that are predicted on the genomic contigs. The RNA map and Gene_Sequence map are built in the same way, using the same types of evidence, described above. The Gene_Sequence map, however, shows a view of all the exons in a gene, while the RNA map shows the combinations of exons (i.e., splice variants) that are valid, based on mRNA sequences.

ugSpu Alignment of S. purpuratus EST clusters to the assembled genomic sequence. ESTs are clustered based on shared introns and alignment to a common position on the genome. Those ESTs can come from one or more UniGene clusters, whose IDs are noted by the EST cluster. (UniGene clusters are made with a different build procedure, so there is not necessarily a one-to-one correspondence between EST clusters on the Spu_UniG map and clusters in the UniGene resource.)
Constructing queries back to top

Searchable Terms back to top

The Map Viewer supports searching on any term that describes an element on any map, including:

  • symbols
    A search for symbol TBP will retrieve the locus named TATA binding protein. Sometimes two or more symbols refer to the same locus and are considered synonyms or aliases. In this case, either term will retrieve the same information for viewing.
  • GenBank accessions
    e.g., a search for accession U86586 will retrieve the map representing the chromosome to which this sequence aligns.
  • text terms
    e.g., a search for actin will retrieve all map objects containing that word in their description. If multiple terms are entered, they will automatically be combined with the 'AND' Boolean operator.

Map Positions back to top

As noted in the Search By Position section of the Entrez Map Viewer Help Document, there are three main ways to search by map position from the Map View of a chromosome:
  1. enter a range of interest in the Region text boxes on the left sidebar
  2. click on the region of interest in the chromosome thumbnail graphic in the sidebar
  3. click on a region of interest in the enlarged Map View of the chromosome

Allowable Values back to top

For Strongylocentrotus purpuratus, the following types of map positions can be entered in the left sidebar text boxes noted in option 1:

  • symbols - You can enter gene symbols, marker names, or alternate symbols or marker names to display a region of the chromosome between those mapped elements. Note that both mapped elements must be present on the maps that share the same coordinate system in order for the range search to work properly.
  • numerical positions - It is not necessary to specify units. The Map Viewer will interpret the range in the units of the master map (i.e. bases for sequence maps).

It is not necessary to enter a value in both Region text boxes. If you enter a value only in the upper box, the Map Viewer will display the region of the chromosome starting from that point and ending at the lower end of the chromosome. If you enter a value only in the lower box, the Map Viewer will display the region of the chromosome starting at the upper end of the chromosome and ending at the value entered.

General Tips back to top

As mentioned in the Searchable Terms section of the Entrez Map Viewer Help Document, any term entered in the query box will be treated as an independent entity to be joined by the 'AND' Boolean operator. It is also possible to construct more complex queries by using explicit Boolean operators (AND, OR, NOT), field restriction, or limiting retrieval to records that have certain properties.

The Advanced Search page allows you to use a number of query options by simply checking boxes or radio buttons that represent various search fields, properties, and object types. It also allows you to limit your query to one or more chromosomes. The Advanced Search page is accessible from the header region of the genome view page.

Constructing URLs that link to Map Viewer back to top

If you would like to create WWW links to the Map Viewer, the instructions for constructing URLs are given in the general Map Viewer Help document. You can construct URLs that either perform a search or display a specific mapped object or chromosomal region. For example:


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