Gene Search

Strongylocentrotus purpuratus gene search

Parastichopus parvamensis gene search

The Gene Search page serves as an entry into the databases of information on annotated genes predicted from the genome sequence of the purple sea urchin, Strongylocentrotus purpuratus, the variegated sea urchin, Lytechinus variegatus or the bat star, Patiria miniata. Each search returns a list of matches that are linked to the individual gene information pages as indicated. The query can take the form of a text fragment and wild card symbols. The asterisk " * " denotes any alphanumeric text. (bra* = Sp-Bra or brachyury or Sp-Cobra). The question mark " ? " denotes one alphanumeric character.( br? = Sp-Bra or Sp-Fibropellin)

The search categories are as follows

1. Gene ID (Example: SPU_000001).
This query uses the SpBase form of the official gene identifier unique in the database. The form of the identifier is 3 letters "SPU" followed by an underscore and 6 numbers. The SpBase identifier is derived from and continues on the Official Gene Set identifiers generated at Baylor, the GLEAN numbers. The relationship between SPU numbers and GLEAN number sis as follows:

GLEAN3_##### = SPU_0#####

SPU numbers higher that the original 28,944 GLEAN3 numbers denote annotated genes for which no GLEAN prediction existed. These genes came from individually sequenced cDNAs or other evidence.

2. Scaffold (Example: Scaffold100, Scaffold3148)

The scaffold identifier refers to the assembly scaffold from the Version 0.5 of the genome assembly (URL?). This query uses the number of the scaffold after the identifier"Scaffold" with no space between. It will return a list of the annotated genes predicted from the v0.5 scaffold sequence. To see all the genes predicted from that scaffold, view the scaffold in Gbrowse with the GLEAN:Prediction track displayed.

3. Gene Name (Example: Sp-SFK1, Sp-Exotose, Sp-Chordin)

The official gene names of the annotated sea urchin genes take the following form:

Sp-gene_symbol

The first three characters are always the "Sp-". Symbols are usually 3-5 characters but additional characters may be added as necessary up to 10 in order to distinguish similar symbols. Symbols should begin with an uppercase letter followed by all lowercase letters unless e4xtensive previous usage dictates otherwise. Punctuation is only used to separate two adjacent numbers (e.g., Lamb1-2) or for designating related (e.g., Es10-rs1). sequences and pseudogenes (e.g., Adh5-ps1).

The query can be a text fragment and doesn't need to include the general prefix (Sp-). A list of the genes whose names match the text fragment will be returned.

4. Synonym (Example: Src,EXT,chrd)

In order to account for variable usage of gene names, we have tried to collect any synonyms known for annotated genes. For example Sp-Bra has been called brachyury in many publications. A mouse name that has been for brachyury is "T" or small-T locus. Our synonym category can be searched with text fragments as above. A list of genes whose synonyms match the query will be returned.

5. PubMed ID (Example: 10068473)

PubMed is the bibliographic component of the NCBI's Entrez retrieval system. It accesses a database designed to provide access to citations from biomedical journals. It resides at the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM), one of the institutes of the National Institutes of Health (NIH). PubMed links also lead to full-text journal articles at Web sites of participating publishers, as well as to other related Web resources. The PubMed ID (PMID) takes the form of a 8-digit number (Example: 9628328). Wild cards are not useful here.

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Gene Search