Difference between revisions of "FlyBase:Sequence Feature Report"
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Both endogenous features and reagent features are included in the '''Sequence Feature''' data class. Endogenous DNA features include: TF_binding_site, protein_binding_site, transcription_start_site, origin_of_replication, regulatory_region, enhancer, silencer, insulator. Features of RNAs that overlap a particular genomic site are also captured in this report format, for example, exon_junction (based on RNASeq), and modified_RNA_base_feature (A-to-I editing site). Reagent features include RNAi_reagent and transgenic enhancer candidates (classified as “region”). | Both endogenous features and reagent features are included in the '''Sequence Feature''' data class. Endogenous DNA features include: TF_binding_site, protein_binding_site, transcription_start_site, origin_of_replication, regulatory_region, enhancer, silencer, insulator. Features of RNAs that overlap a particular genomic site are also captured in this report format, for example, exon_junction (based on RNASeq), and modified_RNA_base_feature (A-to-I editing site). Reagent features include RNAi_reagent and transgenic enhancer candidates (classified as “region”). | ||
| − | PLEASE NOTE: The Sequence Feature Report will | + | PLEASE NOTE: The appearance of the Sequence Feature Report will vary for different kinds of features. In part this is because fields that contain no data for that specific sequence feature may not be displayed in the Sequence Feature Report. In part this is due to JBrowse views that are customized to the feature type. |
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. | 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. | ||
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|Sequence location || The genomic location of the sequence feature: arm:start..stop [strand]. | |Sequence location || The genomic location of the sequence feature: arm:start..stop [strand]. | ||
|- | |- | ||
| − | |Map || A | + | |Map || A JBrowse thumbnail showing the sequence feature (highlighted in yellow) in relation to other genes and sequence features; the other types of data shown for context will depend on the sequence feature type. Links at the far left provide views of the feature in JBrowse. |
|} | |} | ||
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|Length || style="width: 80%;" | The size (nucleotides) of the sequence feature. | |Length || style="width: 80%;" | The size (nucleotides) of the sequence feature. | ||
|- | |- | ||
| − | |Comments || Comments on the sequence feature's size or location. | + | |Comments || Comments on the sequence feature's size or location. For features of type "modified_RNA_base_feature" (A-to-I RNA editing sites), the effects of editing on any overlapping coding sequence is also reported. |
|- | |- | ||
|Sequence || Nucleotide sequence of the feature (FASTA). | |Sequence || Nucleotide sequence of the feature (FASTA). | ||
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|Bound moiety || style="width: 80%;" | The gene symbol(s) of the protein factor(s) bound to the sequence feature. | |Bound moiety || style="width: 80%;" | The gene symbol(s) of the protein factor(s) bound to the sequence feature. | ||
|- | |- | ||
| − | |Comments on moiety || Additional information on the factor bound to the moiety (for example, isoform | + | |Comments on moiety || Additional information on the factor bound to the moiety (for example, the specific isoform or modified form of the factor that is bound to the sequence feature). |
|- | |- | ||
|Mapped to restriction fragment || Information on restriction fragments that contain this sequence feature. | |Mapped to restriction fragment || Information on restriction fragments that contain this sequence feature. | ||
|- | |- | ||
|Evidence or Assay || Assay used to characterize factor binding to the sequence feature. For example: experimental, predicted. | |Evidence or Assay || Assay used to characterize factor binding to the sequence feature. For example: experimental, predicted. | ||
| + | |} | ||
| + | |||
| + | ===RNA-Seq Read Counts=== | ||
| + | |||
| + | This section applies to sequence feature of type "exon_junction". Each dataset with information on the sequence feature is listed in a separate sub-section (the dataset name is listed at the left, hyperlinked to the associated dataset report). | ||
| + | |||
| + | {| class="wikitable" style="width: 100%;" | ||
| + | |- | ||
| + | !'''Expression stage(s)''' !! '''Read Count''' | ||
| + | |- | ||
| + | | style="width: 50%;" | The developmental stage of biological material from which the data is derived. || style="width: 50%;" | The number of reads in which the edited site was observed. | ||
|} | |} | ||
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{| class="wikitable" style="width: 100%;" | {| class="wikitable" style="width: 100%;" | ||
|- | |- | ||
| − | |Species of derivation || style="width: 80%;" | The species | + | |'''Species of derivation''' || style="width: 80%;" | The species origin of the biological material used for the dataset/collection. |
| − | |||
| − | |||
| − | |||
| − | |||
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|} | |} | ||
Latest revision as of 17:44, 20 December 2022
Last Updated: 11 Dec. 2017
The Sequence Feature Report contains the information for an individual sequence feature mapped to the genome. This is a field-by-field guide to the information provided in the Sequence Feature Report.
Both endogenous features and reagent features are included in the Sequence Feature data class. Endogenous DNA features include: TF_binding_site, protein_binding_site, transcription_start_site, origin_of_replication, regulatory_region, enhancer, silencer, insulator. Features of RNAs that overlap a particular genomic site are also captured in this report format, for example, exon_junction (based on RNASeq), and modified_RNA_base_feature (A-to-I editing site). Reagent features include RNAi_reagent and transgenic enhancer candidates (classified as “region”).
PLEASE NOTE: The appearance of the Sequence Feature Report will vary for different kinds of features. In part this is because fields that contain no data for that specific sequence feature may not be displayed in the Sequence Feature Report. In part this is due to JBrowse views that are customized to the feature type.
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 JBrowse thumbnail showing the sequence feature (highlighted in yellow) in relation to other genes and sequence features; the other types of data shown for context will depend on the sequence feature type. Links at the far left provide views of the feature in JBrowse. |
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 or location. For features of type "modified_RNA_base_feature" (A-to-I RNA editing sites), the effects of editing on any overlapping coding sequence is also reported. |
| 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. |
Binding data
This section applies to genomic or transcript features defined as a binding site for some factor: TF_binding_site, protein_binding_site, origin_of_replication.
| Bound moiety | The gene symbol(s) of the protein factor(s) bound to the sequence feature. |
| Comments on moiety | Additional information on the factor bound to the moiety (for example, the specific isoform or modified form of the factor that is bound to the sequence feature). |
| Mapped to restriction fragment | Information on restriction fragments that contain this sequence feature. |
| Evidence or Assay | Assay used to characterize factor binding to the sequence feature. For example: experimental, predicted. |
RNA-Seq Read Counts
This section applies to sequence feature of type "exon_junction". Each dataset with information on the sequence feature is listed in a separate sub-section (the dataset name is listed at the left, hyperlinked to the associated dataset report).
| Expression stage(s) | Read Count |
|---|---|
| The developmental stage of biological material from which the data is derived. | The number of reads in which the edited site was observed. |
RNA Editing Sites
This section applies to sequence feature of type "modified_RNA_base_feature". Each dataset with information on the sequence feature is listed in a separate sub-section (the dataset name is listed at the left, hyperlinked to the associated dataset report).
| Expression stage(s) | Read Count | Editing Frequency |
|---|---|---|
| The developmental stage of biological material from which the data is derived. | The number of reads in which the edited site was observed. | The proportion of reads spanning the editing site that have been edited. |
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; provides link to the complete dataset/collection report. |
| Title | The dataset/collection's title. |
Source and Progenitors
| Species of derivation | The species 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
Links to information for this sequence feature available from external web sites.
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.