Difference between revisions of "FlyBase:Sequence Feature Report"
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==Collection Information== | ==Collection Information== | ||
| − | + | Selected information about any datasets or reagent collections to which the sequence feature belongs. | |
{| class="wikitable" style="width: 100%;" | {| class="wikitable" style="width: 100%;" | ||
|- | |- | ||
| − | |Symbol || style="width: 80%;" | | + | |Symbol || style="width: 80%;" | The FlyBase symbol used for the dataset/collection. |
|} | |} | ||
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{| class="wikitable" style="width: 100%;" | {| class="wikitable" style="width: 100%;" | ||
|- | |- | ||
| − | |Species of derivation || style="width: 80%;" | | + | |Species of derivation || style="width: 80%;" | The species origin of the biological material used for the dataset/collection. |
|} | |} | ||
| Line 103: | Line 103: | ||
{| class="wikitable" style="width: 100%;" | {| class="wikitable" style="width: 100%;" | ||
|- | |- | ||
| − | |Vector or progenitor construct || style="width: 80%;" | | + | |Vector or progenitor construct || style="width: 80%;" | The strain origin of the biological material used for the dataset/collection. |
| + | |} | ||
| + | |||
| + | {| class="wikitable" style="width: 100%;" | ||
| + | |- | ||
| + | !'''Stage''' !! '''Tissue/Position''' !! '''Reference''' | ||
| + | |- | ||
| + | | style="width: 33%;" | The developmental stage used as the source of biological material. || style="width: 33%;" | The tissue used as the source of biological material. || style="width: 33%;" | The reference from which the sample information was obtained. || | ||
| + | |} | ||
| + | |||
| + | {| class="wikitable" style="width: 100%;" | ||
| + | |- | ||
| + | |'''Cell Line''' || The cell line used as the source of biological material. | ||
|} | |} | ||
===Description=== | ===Description=== | ||
| − | + | A description of the dataset/collection to which the sequence feature belongs. | |
===Additional data=== | ===Additional data=== | ||
| − | + | Description of how the dataset/collection was prepared. | |
===Cell lines=== | ===Cell lines=== | ||
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{| class="wikitable" style="width: 100%;" | {| class="wikitable" style="width: 100%;" | ||
|- | |- | ||
| − | |Observed in || style="width: 80%;" | | + | |Observed in || style="width: 80%;" | Cell lines in which the sequence feature was observed. Implemented only for features of type origin_of_replication. |
|- | |- | ||
| − | |Not observed in || | + | |Not observed in || Cell lines in which the sequence feature was not observed. Implemented only for features of type origin_of_replication. |
|} | |} | ||
Revision as of 20:45, 24 June 2015
Last Updated: 24 June 2015
The Sequence Feature Report contains the information for an individual sequence feature. This includes many different types of features, for example: region, regulatory region, enhancer, silencer, insulator, TF_binding_site, protein_binding_site, TSS, exon_junction, origin_of_replication, modified_RNA_base_feature (A-to-I editing site).
This is a field-by-field guide to the information provided in the Sequence Feature Report.
FlyBase attributes data to the publication that reported it, so that users can easily refer back to the original publication if they wish. Thus, where possible in the fields below, the publication(s) that are the source of the information are listed, typically in parentheses to the right of the data.
General Information
| Symbol | The valid symbol that is used in FlyBase. |
| Species | The organism that the sequence feature originates from, with the initial letter of the genus and the full species name listed. |
| Feature Type | The type of sequence feature described in the report. |
| FlyBase ID | The Primary FlyBase identifier number of the sequence feature, used to uniquely identify the sequence feature in the database.
A sequence feature may also have any number of Secondary FlyBase identifier numbers, which are listed in the Secondary FlyBase IDs section of the Sequence feature Report. |
| Collection | The large scale dataset or reagent collection of which this sequence feature is a member. |
| Associated gene(s) | Genes associated with this sequence feature. |
Genomic Location
| Chromosome Arm | The chromosome arm that the sequence is located on. |
| Sequence location | The genomic location of the sequence feature: arm:start..stop [strand]. |
| Map | A GBrowse thumbnail showing the sequence feature (highlighted in yellow) in relation to other genes and sequence features. A link to the region shown in GBrowse is provided at the left. |
Recent Updates
This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms).
Sequence Data
| Length | The size (nucleotides) of the sequence feature. |
| Comments | Comments on the sequence feature's size. |
| Sequence | Nucleotide sequence of the feature (FASTA). |
Associated Information
| Gene(s) (targeted or local) | Genes associated with the sequence feature. |
| Allele(s) | Alleles associated with the sequence feature. |
| Transcripts(s) | Transcripts associated with the sequence feature. |
| Polypeptide(s) | Polypeptides associated with the sequence feature. |
| Construct | Constructs associated with the sequence feature. |
Experimental Data
Progenitors
This section applies to reagents generated in vitro: for example, "RNAi_reagent".
| PCR template | Source of PCR template (genomic or cDNA). |
| Primer 1 | Left primer used in PCR. |
| Primer 2 | Right primer used in PCR. |
| Comments | Additional information about the PCR amplification of the reagent. |
Collection Information
Selected information about any datasets or reagent collections to which the sequence feature belongs.
| Symbol | The FlyBase symbol used for the dataset/collection. |
Source and Progenitors
| Species of derivation | The species origin of the biological material used for the dataset/collection. |
Strain of derivation
| Vector or progenitor construct | The strain origin of the biological material used for the dataset/collection. |
| Stage | Tissue/Position | Reference | |
|---|---|---|---|
| The developmental stage used as the source of biological material. | The tissue used as the source of biological material. | The reference from which the sample information was obtained. |
| Cell Line | The cell line used as the source of biological material. |
Description
A description of the dataset/collection to which the sequence feature belongs.
Additional data
Description of how the dataset/collection was prepared.
Cell lines
| Observed in | Cell lines in which the sequence feature was observed. Implemented only for features of type origin_of_replication. |
| Not observed in | Cell lines in which the sequence feature was not observed. Implemented only for features of type origin_of_replication. |
Comments
Miscellaneous free text comments about the sequence feature.
Stocks Listed in FlyBase
A list of the stocks from the public Stock Centers that contain this sequence feature; for each Stock Center, stock number and genotype are displayed. Clicking on the genotype will take you to the appropriate Stock Report.
External Crossreferences and Linkouts
Synonyms and Secondary IDs
Reported As
| Symbol Synonym | A list of symbols that have been used in the literature, or by FlyBase, to describe the sequence feature. |
Secondary FlyBase IDs
A list of Secondary FlyBase identifier numbers of the sequence feature.
References
A list of publications that discuss the sequence feature, subdivided into fields by type of publication. Only fields containing data are displayed in an individual Sequence Feature Report.