Add Features

gene/mRNA/CDS

gene

Gene opens a dialog that adds a gene feature and associated qualifiers to the current sequence.

What is a gene? A region of biological interest identified as a gene and for which a name has been assigned.

For details, see gene feature description

When working on a set of sequences, before adding any feature to a sequence, be sure that the specific sequence – NOT Nucleotides - is chosen in the ‘Sequences’ menu in the upper right on the flatfile record view window:

GWB Record View Window Sequences Choice Menu Nucleotides

GWB Record View Window Sequences Choice Menu Specific Seq

The gene dialog has five sections: Gene, Location, Synonyms, Comment, and General

The Gene section appears by default when the dialog is opened and allows the addition of free text for four qualifiers:

GWB Features Gene Mrna Cds Gene Dialog

  • Locus (the name/symbol of the gene; NOT the name of the associated protein or other product derived from the gene; appears as a /gene qualifier on the gene feature)
  • Allele (name of the allele for the gene)
  • Description (free text information about the gene; appears as a /note qualifier on the gene feature)
  • Locus Tag (a submitter-supplied, systematic, stable identifier for a gene and its associated features; used for tracking purposes)

OK verifies and adds a gene feature as described by the associated information provided. Cancel closes the dialog without taking any action.

The Location section allows the addition of the nucleotide intervals and related information of the gene on the current sequence:

GWB Features Gene Mrna Cds Gene Dialog Location

  • Partialness (describes whether the 5’ end and the 3’ end are either complete or partial; default is set to complete for both, meaning that the entire gene can be identified by the nucleotide intervals entered)
  • From/To (enter the first and last nucleotide of the gene; if the gene has multiple intervals, enter each set of first and last nucleotides of the intervals sequentially)
  • Strand (the location defaults to the Plus (positive) strand; change to Minus (minus) strand if applicable for each interval; intervals on the Minus strand are described as ‘complement’ in the record)
  • SeqID (identifies the SequenceID of the sequence to which this gene feature will apply; defaults to the current sequence)
  • Insert Controls (allow a blank row for nucleotide intervals to be inserted above or below the row on which it is chosen)
  • Arrow Controls (allow an existing row to be moved up or down in a list of multiple intervals)
  • Delete (removes a row of intervals)
  • Save As (defaults to Join, which indicates that multiple intervals are biologically related and act as a single gene feature; choose Order if each interval describes a separate instance of the gene feature on the current sequence)
  • OK and Cancel function the same in the Gene section

The Synonyms section allows the addition of synonymous, replaced, obsolete, or former gene names (symbols) in the free text box. A primary gene name or locus-tag must be present on the gene feature before a gene synonym can be added. OK and Cancel function the same as in the Gene section.

GWB Features Gene Mrna Cds Gene Dialog Synonims

The Comment section allows the addition of free text description of the gene feature. The text will appear as a /note qualifier on the gene feature in the record. OK and Cancel function the same as in the Gene section.

GWB Features Gene Mrna Cds Gene Dialog Comment

The General section allows the addition of special notations:

GWB Features Gene Mrna Cds Gene Dialog General

  • Pseudogene (choose appropriate explanation from the pull-down menu: processed, unprocessed, unitary, allelic, or unknown; see qualifier list for definitions)
  • Exception (choose appropriate reason from the pull-down list why non-standard biology applies; see qualifier list for definitions)
  • Dbxrefs (Database Cross References; enter database name and identifier)
  • Feature Identifiers (assigned in GenBank processing)
  • Experiments (choose appropriate Category from pull-down menu and provide brief free text description of work; PubMedID or doi of journal paper describing work is optional; see qualifier list for definitions)
  • Inferences (choose appropriate Category and Type from the pull-down menus of the structured description of non-experimental evidence that supports the feature identification or assignment)
  • Citations (choose a reported Reference that indicates the citation providing the claim of and/or evidence for a feature
  • OK and Cancel function the same as in the Gene section.

mRNA

mRNA opens a dialog that adds a messenger RNA (mRNA) feature and associated qualifiers to the current sequence.

What is a mRNA? A region of transcribed sequence that includes 5'untranslated region (5'UTR), coding sequences (CDS, exon), and 3'untranslated region (3'UTR) and that transfers the information needed to make proteins from DNA to the cell’s ribosomes.

For details, see mRNA feature description.

When working on a set of sequences, before adding any feature to a sequence, be sure that the specific sequence – NOT Nucleotides - is chosen in the ‘Sequences’ menu in the upper right on the flatfile record view window:

GWB Record View Window Sequences Choice Menu Nucleotides

GWB Record View Window Sequences Choice Menu Specific Seq

The mRNA dialog has five sections: RNA, Location, Gene, Comment, GenBank Qualifiers, and General.

The RNA section appears by default when the dialog is opened and allows the choice of RNA type and addition of free text for the Name of the mRNA’s protein, which will appear as a /product qualifier on the mRNA feature in the sequence record. The protein/product name should be identical the protein/product name applied the corresponding CDS feature.

GWB Features Gene Mrna Cds Mrna Dialog Mrna Name

  • mRNA’ is chosen as the type by default; if mRNA is not the intended RNA, choose the correct RNA type from the pull-down list
  • Enter the name of the mRNA’s protein in the Name field (for example, ‘actin’ or ‘cytochrome oxidase subunit I’)
  • The name will appear as a /product qualifier on the mRNA feature in the sequence record
  • OK (verifies and adds the rRNA feature as described by the associated description provided)
  • Cancel (closes the dialog without taking any action)

The Location section allows the addition of the nucleotide intervals and related information of the mRNA on the current sequence:

GWB Features Gene Mrna Cds Mrna Dialog Location

  • Partialness (describes whether the 5’ end and the 3’ end are either complete or partial; default is set to complete for both, meaning that the entire mRNA is identified by the nucleotide intervals entered)
  • From/To (displays the first and last nucleotide of the rRNA; if the rRNA has multiple intervals, enter each set of first and last nucleotides of the intervals sequentially)
  • Strand (the location defaults to the Plus (positive) strand; change to Minus (minus) strand if applicable for each interval; intervals on the Minus strand are described as ‘complement’ in the record)
  • SeqID (identifies the SequenceID of the sequence to which this rRNA feature will apply; defaults to the current sequence)
  • Insert Controls (allow a blank row for nucleotide intervals to be inserted above or below the row on which it is chosen)
  • Arrow Controls (allow an existing row to be moved up or down in a list of multiple intervals)
  • Delete (removes a row of intervals)
  • Save As (defaults to Join, which indicates that multiple intervals are biologically related and act as a single rRNA feature; choose Order if each interval describes a separate, unrelated instance of the rRNA feature on the current sequence)
  • OK and Cancel are the same as the RNA section

The Gene section allows an existing or new Gene feature to be associated with the mRNA feature. For an existing mRNA-Gene association, the dialog allows the Gene to be suppressed and/or the mapping type between the mRNA and Gene to changed.

GWB Features Gene Mrna Cds Mrna Dialog Gene

  • Gene (displays a scrolling list of existing genes on the record to associate with the mRNA; includes the choice ‘New’ that allows an new Gene feature to be added to the record and associated with the mRNA.
  • Map by (choose between default Overlap or Cross-reference when necessary)
  • Suppress Gene (removes association between mRNA and chosen Gene)
  • Edit Gene (opens a new Gene feature dialog in which changes can be made to the existing Gene’s information)
  • Locus/Allele/Description/Locus Tag (when ‘New’ is chosen as the Gene to associate with the CDS, allows one or more of these four labels to be input for the new Gene)
  • OK and Cancel are the same as the RNA section

The Comment section allows the addition of free text description of the mRNA feature. The text will appear as a /note qualifier on the mRNA feature in the record. OK and Cancel are the same as the RNA section

GWB Features Gene Mrna Cds Mrna Dialog Comment

The GenBank Qualifiers sections allows the addition of specific qualifiers and their free text values to the mRNA: allele, artificial-location, evidence, function, old-locus-tag, and transcript-id. OK and Cancel are the same as the RNA section

GWB Features Gene Mrna Cds Mrna Dialog Gen Bank Qualifiers

The General section allows the addition of special notations:

GWB Features Gene Mrna Cds Mrna Dialog General

  • Pseudogene (choose appropriate explanation from the pull-down menu: processed, unprocessed, unitary, allelic, or unknown; see definitions)
  • Exception (choose appropriate reason from the pull-down list why non-standard biology applies; see definitions)
  • Dbxrefs (Database Cross References; enter database name and identifier)
  • Feature Identifiers (will be assigned in processing)
  • Experiments (choose appropriate Category from pull-down menu and provide brief free text description of work; PubMedID or doi of journal paper describing work is optional; see definitions)
  • Inferences (choose appropriate Category and Type from the pull-down menus of the structured description of non-experimental evidence that supports the feature identification or assignment)
  • Citations (choose a reported Reference that indicates the citation providing the claim of and/or evidence for a feature)
  • OK and Cancel are the same as the RNA section

CDS

CDS opens a dialog that adds a coding region feature and associated qualifiers to the current sequence.

What is a CDS? A sequence of nucleotides that corresponds with the sequence of amino acids in a protein. A complete CDS location includes a valid start and a valid stop codon.

For details, see CDS feature description.

When working on a set of sequences, before adding any feature to a sequence, be sure that the specific sequence – NOT Nucleotides - is chosen in the ‘Sequences’ menu in the upper right on the record view window:

GWB Record View Window Sequences Choice Menu Nucleotides

GWB Record View Window Sequences Choice Menu Specific Seq

The CDS dialog has nine sections: Coding Region, Protein Name and Description, Location, Protein Properties, Translation Exceptions, Misc, Gene, Comment, and General.

The Coding Region section appears by default when the dialog is opened and allows the addition of and display of information related to the protein translation:

GWB Features Gene Mrna Cds Dialog

  • Genetic Code (this is set automatically when a valid organism name is provided and an organelle (mitochondrion, chloroplast, etc), if applicable, is chosen; (see a complete description of the Genetic Codes valid for use in GenBank records
  • Reading Frame (indicates the offset at which the first complete codon of a CDS can be found, relative to the first base of the feature; input value is 1 or 2 or 3)
  • Protein Length (displays the length of the CDS’s translation in amino acids)
  • Protein Product (displays the internal identifier for the CDS’s translation)
  • Protein translation box (displays translation)
  • Predict Interval (provides likely nucleotide intervals in the Location section on the current sequence when a protein is imported)
  • Retranslate (allows a new translation of the provided information when the information has been changed and before the CDS dialog is closed)
  • Adjust for Stop Codon (recognizes valid stop codon)
  • Import Protein Sequence (allows a protein sequence to be imported for a CDS feature instead of being translated from other information provided)
  • Retranslate on OK (automatically retranslates CDS based on information provided when ‘OK’ button is clicked; used when you do not need to view retranslation after changes before closing CDS dialog; is checked by default)
  • Update mRNA span (automatically changes corresponding mRNA feature’s intervals to match interval changes in the CDS when ‘OK’ is clicked)
  • Update Gene span (automatically changes corresponding Gene feature’s intervals to match interval changes the CDS when ‘OK’ is clicked; is checked by default)
  • OK (verifies and adds a CDS feature as described by the information provided)
  • Cancel (closes the feature dialog without taking any action)

The Protein Name and Description section allows the addition of the translated protein’s name, name synonyms, and free text description of the protein.

GWB Features Gene Mrna Cds Dialog Prot Name Description

  • Protein name (input an accepted or new name of the CDS’s translated protein; appears as /product on CDS feature in record view; after name information is input in the default free text box, another box will appear in which a protein name synonym may be input; ‘Delete’ removes the text in the box)
  • Description (input additional free text information that describes the CDS’s protein; not for protein function, which is input in the Protein Properties section as ‘Activity’)
  • Make overlapping mRNA product match protein name (makes corresponding mRNA feature’s product name the same as the CDS Protein name accepted when ‘OK’ is clicked)
  • OK and Cancel are the same as the Coding Region section page

The Location section allows the addition of the nucleotide intervals and related information of the CDS on the current sequence:

GWB Features Gene Mrna Cds Dialog Location

  • Partialness (describes whether the 5’ end and the 3’ end are either complete or partial; default is set to complete for both, meaning that the CDS has both a valid start codon and a valid stop codon)
  • From/To (enter the first and last nucleotide of the CDS; if the CDS has multiple intervals, enter each set of first and last nucleotides of the intervals sequentially)
  • Strand (the location defaults to the Plus (positive) strand; change to Minus (minus) strand if applicable for each interval; intervals on the Minus strand are described as ‘complement’ in the record)
  • SeqID (identifies the SequenceID of the sequence to which this gene feature will apply; defaults to the current sequence)
  • Insert Controls (allow a blank row for nucleotide intervals to be inserted above or below the row on which it is chosen)
  • Arrow Controls (allow an existing row to be moved up or down in a list of multiple intervals)
  • Delete (removes a row of intervals)
  • Save As (defaults to Join, which indicates that multiple intervals are biologically related and act as a single CDS feature; choose Order if each interval describes a separate instance of the CDS feature on the current sequence)
  • OK and Cancel function the same as on the Coding Region section page

The Protein Properties section allows the addition of Enzyme Commission (E.C.) Numbers and description of the function of the translated protein.

GWB Features Gene Mrna Cds Dialog Protein Properties

  • Enzyme Commission Numbers (valid values for EC numbers are defined in the list prepared by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) (published in Enzyme Nomenclature 1992, Academic Press, San Diego, or a more recent revision thereof); displayed as /EC_number qualifier on the CDS feature; protein names and their EC numbers can be searched
  • Activity (describes the function of the CDS’s translated protein; displayed as /function qualifier on the CDS feature in the record)
  • OK and Cancel are the same as the Coding Region section page

The Translation Exceptions section allows the input of one or more codons whose translation does not conform to the genetic code defined for the corresponding organism and cited for the CDS in the Coding Region section.

GWB Features Gene Mrna Cds Dialog Translation Exceptions

  • AA (enter the amino acid position for the which non-conforming codon translation occurs)
  • Amino Acid (choose the amino acid from the pull-down menu that is translated from the non-conforming codon; option include a Termination codon)
  • OK and Cancel are the same as the Coding Region section page

The Misc section allows the CDS to be marked as non-functional and be converted to a misc_feature (miscellaneous feature) on the record. Protein name and other descriptive information are not retained.

GWB Features Gene Mrna Cds Dialog Misc

The Gene section allows an existing or new Gene feature to be associated with the CDS feature. For an existing CDS-Gene association, allows the Gene to be suppressed and/or the mapping type between the CDS and Gene to changed.

GWB Features Gene Mrna Cds Dialog Gene

  • Gene (displays a scrolling list of existing genes on the record to associate with the CDS; includes the choice ‘New’ that will allow an additional Gene feature to be added to the record and associated with the CDS.
  • Map by (choose between default Overlap or Cross-reference when necessary)
  • Suppress Gene (removes association between CDS and chosen Gene)
  • Edit Gene (opens a new Gene feature dialog in which changes can be made to the existing Gene’s information)
  • Locus/Allele/Description/Locus Tag (when ‘New’ is chosen as the Gene to associate with the CDS, allows one or more of these four labels to be input for the new Gene)
  • OK and Cancel are the same as the Coding Region section page

The Comment section allows free text to be added to the description of the CDS that cannot be added with any other provided qualifier. Displays as a /note qualifier on the CDS in the record.

GWB Features Gene Mrna Cds Dialog Comment

  • Clear deletes text in the box.
  • OK and Cancel are the same as the Coding Region section page

The General section allow the addition of the following information:

GWB Features Gene Mrna Cds Dialog General

GWB Features Gene Mrna Cds Dialog General Pseudogene

GWB Features Gene Mrna Cds Dialog General Exception

  • Pseudogene (in the default display of this section; allows the identification of a CDS derived from a pseudogene; choose the correct pseudogene type from the pull-down menu)
  • Exception (in the default display of this section; allows the choice of non-conforming biology to be chosen to describe the CDS such as alternative start codon and RNA editing)
  • Dbxrefs (allows the addition of a database cross-reference, a pointer to related information in another database; see the controlled list of allowed databases ; a Database name and Object ID (identifier) in the cited database must be input)
  • Feature Identifiers (provided in GenBank processing)
  • Experiments (allows a brief description of experimental evidence that supports the CDS’s identification or assignment; choose Category from pull-down menu and input brief Experiment description and/or PubMed ID or doi of related publication)
  • Inferences (allows a structured description of non-experimental evidence that supports the CDS’s identification or assignment; choose both Category and Type from the pull-down menus)
  • Citations (allows the choice of one or more References on the record to be specifically associated with the CDS
  • OK and Cancel are the same as the Coding Region section page

operon

WORK IN PROGRESS

intron

WORK IN PROGRESS

exon

WORK IN PROGRESS

5'UTR

WORK IN PROGRESS

3'UTR

WORK IN PROGRESS

Structural RNAs

WORK IN PROGRESS

rRNA

rRNA opens a dialog that adds a ribosomal RNA (rRNA) feature and associated qualifiers to the current sequence.

GWB Features Structural Rnas Rrna Dialog

What is a ribosomal RNA? The RNA component of the ribonucleoprotein particle (ribosome) that assembles amino acids into proteins.

For details, see rRNA feature description.

When working on a set of sequences, before adding any feature to a sequence, be sure that the specific sequence – NOT Nucleotides - is chosen in the ‘Sequences’ menu in the upper right on the record view window:

GWB Record View Window Sequences Choice Menu Nucleotides

GWB Record View Window Sequences Choice Menu Specific Seq

The rRNA dialog has six sections: RNA, Location, Gene, Comment, GenBank Qualifiers, and General

The RNA section appears by default when the dialog is opened and allows the choice of RNA type and addition of free text for the Name of the rRNA.

GWB Features Structural Rnas Rrna Dialog Rrna Name

  • ‘rRNA’ is chosen as the type by default; if rRNA is not the intended RNA, choose the correct RNA type from the pull-down list
  • Enter the name of the rRNA in the Name field (for example, 12S ribosomal RNA or small ribosomal RNA); autocomplete will help find the correct name
  • The name will appear as a /product qualifier on the rRNA feature in the record
  • OK (verifies and adds the rRNA feature as described by the associated description provided)
  • Cancel (closes the dialog without taking any action)

The Location section allows the addition of the nucleotide intervals and related information of the rRNA on the current sequence:

GWB Features Structural Rnas Rrna Dialog Location

  • Partialness (describes whether the 5’ end and the 3’ end are either complete or partial; default is set to complete for both, meaning that the entire rRNA is identified by the nucleotide intervals entered)
  • From/To (displays the first and last nucleotide of the rRNA; if the rRNA has multiple intervals, enter each set of first and last nucleotides of the intervals sequentially)
  • Strand (the location defaults to the Plus (positive) strand; change to Minus (minus) strand if applicable for each interval; intervals on the Minus strand are described as ‘complement’ in the record)
  • SeqID (identifies the SequenceID of the sequence to which this rRNA feature will apply; defaults to the current sequence)
  • Insert Controls (allow a blank row for nucleotide intervals to be inserted above or below the row on which it is chosen)
  • Arrow Controls (allow an existing row to be moved up or down in a list of multiple intervals)
  • Delete (removes a row of intervals)
  • Save As (defaults to Join, which indicates that multiple intervals are biologically related and act as a single rRNA feature; choose Order if each interval describes a separate, unrelated instance of the rRNA feature on the current sequence)
  • OK and Cancel are the same as the RNA section

The Gene section allows an existing or new Gene feature to be associated with the rRNA feature. For an existing rRNA-Gene association, the dialog allows the Gene to be suppressed and/or the mapping type between the rRNA and Gene to changed.

GWB Features Structural Rnas Rrna Dialog Gene

  • Gene (displays a scrolling list of existing genes on the record to associate with the rRNA; includes the choice ‘New’ that allows an additional Gene feature to be added to the record and associated with the rRNA.
  • Map by (choose between default Overlap or Cross-reference when necessary)
  • Suppress Gene (removes association between rRNA and chosen Gene)
  • Edit Gene (opens a new Gene feature dialog in which changes can be made to the existing Gene’s information)
  • Locus/Allele/Description/Locus Tag (when ‘New’ is chosen as the Gene to associate with the CDS, allows one or more of these four labels to be input for the new Gene)
  • OK and Cancel are the same as the RNA section

The Comment section allows the addition of free text description of the rRNA feature. The text will appear as a /note qualifier on the rRNA feature in the record. OK and Cancel are the same as the RNA section

GWB Features Structural Rnas Rrna Dialog Comment

The GenBank Qualifiers sections allows the addition of specific qualifiers and their free text values to the rRNA: allele, evidence, function, and old-locus-tag. OK and Cancel are the same as the RNA section

GWB Features Structural Rnas Rrna Dialog GenBank Qualifiers

The General section allows the addition of special notations:

GWB Features Structural Rnas Rrna Dialog General

  • Pseudogene (choose appropriate explanation from the pull-down menu: processed, unprocessed, unitary, allelic, or unknown; see definitions)
  • Exception (choose appropriate reason from the pull-down list why non-standard biology applies; see qualifier list
  • Dbxrefs (Database Cross References; enter database name and identifier)
  • Feature Identifiers (will be assigned in processing)
  • Experiments (choose appropriate Category from pull-down menu and provide brief free text description of work; PubMedID or doi of journal paper describing work is optional; see qualifier list
  • Inferences (choose appropriate Category and Type from the pull-down menus of the structured description of non-experimental evidence that supports the feature identification or assignment)
  • Citations (choose a reported Reference that indicates the citation providing the claim of and/or evidence for a feature
  • OK and Cancel are the same as the RNA section

tRNA

tRNA opens a dialog that adds a transfer RNA (tRNA) feature and associated qualifiers to the current sequence.

What is a transfer RNA? A small RNA molecule (75-85 bases long) that mediates the translation of a nucleic acid sequence into an amino acid sequence.

For details, see tRNA feature description.

When working on a set of sequences, before adding any feature to a sequence, be sure that the specific sequence – NOT Nucleotides - is chosen in the ‘Sequences’ menu in the upper right on the record view window:

GWB Record View Window Sequences Choice Menu Nucleotides

GWB Record View Window Sequences Choice Menu Specific Seq

The tRNA dialog has six sections: RNA, Location, Gene, Comment, GenBank Qualifiers, and General.

The RNA section appears by default when the dialog is opened and allows the choice of RNA type and addition of biological qualifiers for the tRNA.

GWB Features Structural Rnas Trna Dialog

  • tRNA’ is chosen as the type by default; if tRNA is not the intended RNA, choose the correct RNA type from the pull-down list
  • Product: Choose the correct Amino Acid from the pull-down menu (for example, A - Alanine or Y - Tyrosine); if the tRNA is for M – Methionine, ‘fMet’ or ‘iMet’ can also be chosen if needed; the correct tRNA name will appear as a /product qualifier on the tRNA feature in the record (for example, tRNA-Ala or tRNA-Tyr)
  • Codons Recognized: Provide the correct codon(s) recognized by tRNA identified
  • Anticodon: Provide the location of the anticodon of the named tRNA; Save As (defaults to Join, which indicates that multiple intervals are biologically related and act as a single feature; choose Order if each interval describes a separate, unrelated instance of the feature on the current sequence)
  • OK (verifies and adds the rRNA feature as described by the associated description provided)
  • Cancel (closes the dialog without taking any action)

The Location section allows the addition of the nucleotide intervals and related information of the tRNA on the current sequence:

GWB Features Structural Rnas Trna Dialog Location

  • Partialness (describes whether the 5’ end and the 3’ end are either complete or partial; default is set to complete for both, meaning that the entire rRNA is identified by the nucleotide intervals entered)
  • From/To (displays the first and last nucleotide of the rRNA; if the rRNA has multiple intervals, enter each set of first and last nucleotides of the intervals sequentially)
  • Strand (the location defaults to the Plus (positive) strand; change to Minus (minus) strand if applicable for each interval; intervals on the Minus strand are described as ‘complement’ in the record)
  • SeqID (identifies the SequenceID of the sequence to which this rRNA feature will apply; defaults to the current sequence)
  • Insert Controls (allow a blank row for nucleotide intervals to be inserted above or below the row on which it is chosen)
  • Arrow Controls (allow an existing row to be moved up or down in a list of multiple intervals)
  • Delete (removes a row of intervals)
  • Save As (defaults to Join, which indicates that multiple intervals are biologically related and act as a single rRNA feature; choose Order if each interval describes a separate, unrelated instance of the rRNA feature on the current sequence)
  • OK and Cancel are the same as the RNA section

The Gene section allows an existing or new Gene feature to be associated with the rRNA feature. For an existing rRNA-Gene association, the dialog allows the Gene to be suppressed and/or the mapping type between the rRNA and Gene to changed.

GWB Features Structural Rnas Trna Dialog Gene

  • Gene (displays a scrolling list of existing genes on the record to associate with the rRNA; includes the choice ‘New’ that allows an additional Gene feature to be added to the record and associated with the rRNA.
  • Map by (choose between default Overlap or Cross-reference when necessary)
  • Suppress Gene (removes association between rRNA and chosen Gene)
  • Edit Gene (opens a new Gene feature dialog in which changes can be made to the existing Gene’s information)
  • Locus/Allele/Description/Locus Tag (when ‘New’ is chosen as the Gene to associate with the CDS, allows one or more of these four labels to be input for the new Gene)
  • OK and Cancel are the same as the RNA section

The Comment section allows the addition of free text description of the rRNA feature. The text will appear as a /note qualifier on the rRNA feature in the record. OK and Cancel are the same as the RNA section.

GWB Features Structural Rnas Trna Dialog Comment

The GenBank Qualifiers sections allows the addition of specific qualifiers and their free text values to the rRNA: allele, anticodon, function, and old-locus-tag. OK and Cancel are the same as the RNA section.

GWB Features Structural Rnas Trna Dialog GenBank Qualifiers

The General section allows the addition of special notations:

GWB Features Structural Rnas Trna Dialog General

  • Pseudogene (choose appropriate explanation from the pull-down menu: processed, unprocessed, unitary, allelic, or unknown; see definitions)
  • Exception (choose appropriate reason from the pull-down list why non-standard biology applies; see definitions)
  • Dbxrefs (Database Cross References; enter database name and identifier)
  • Feature Identifiers (assigned in processing)
  • Experiments (choose appropriate Category from pull-down menu and provide brief free text description of work; PubMedID or doi of journal paper describing work is optional; see definitions)
  • Inferences (choose appropriate Category and Type from the pull-down menus of the structured description of non-experimental evidence that supports the feature identification or assignment)
  • Citations (choose a reported Reference that indicates the citation providing the claim of and/or evidence for a feature
  • OK and Cancel are the same as the RNA section

ncRNA

ncRNA opens a dialog that adds a non-coding RNA (ncRNA) feature and associated qualifiers to the current sequence.

What is a non-coding RNA? A non-protein-coding gene (other than ribosomal RNA and transfer RNA) whose functional molecule is the RNA transcript.

For details, see ncRNA feature description.

When working on a set of sequences, before adding any feature to a sequence, be sure that the specific sequence – NOT Nucleotides - is chosen in the ‘Sequences’ menu in the upper right on the flatfile record view window:

GWB Record View Window Sequences Choice Menu Nucleotides

GWB Record View Window Sequences Choice Menu Specific Seq

The ncRNA dialog has six sections: RNA, Location, Gene, Comment, GenBank Qualifiers, and General

The RNA section appears by default when the dialog is opened and allows the choice of RNA type and addition of biological qualifiers for the ncRNA.

GWB Features Structural Rnas Ncrna Dialog Rna

  • ncRNA’ is chosen as the type by default; if ncRNA is not the intended RNA, choose the correct RNA type from the pull-down list
  • Class: choose the correct Class name from the pull-down menu; if ‘other’ is chosen, provide a name or short description in the free text box.
  • Product: Provide a product name, if applicable
  • OK (verifies and adds the ncRNA feature as described by the associated information provided)
  • Cancel (closes the dialog without taking any action)

The Location section allows the addition of the nucleotide intervals and related information of the tRNA on the current sequence:

GWB Features Structural Rnas Ncrna Dialog Location

  • Partialness (describes whether the 5’ end and the 3’ end are either complete or partial; default is set to complete for both, meaning that the entire ncRNA is identified by the nucleotide intervals entered)
  • From/To (displays the first and last nucleotide of the ncRNA; if the ncRNA has multiple intervals, enter each set of first and last nucleotides of the intervals sequentially)
  • Strand (the location defaults to the Plus (positive) strand; change to Minus (minus) strand if applicable for each interval; intervals on the Minus strand are described as ‘complement’ in the record)
  • SeqID (identifies the SequenceID of the sequence to which this ncRNA feature will apply; defaults to the current sequence)
  • Insert Controls (allow a blank row for nucleotide intervals to be inserted above or below the row on which it is chosen)
  • Arrow Controls (allow an existing row to be moved up or down in a list of multiple intervals)
  • Delete (removes a row of intervals)
  • Save As (defaults to Join, which indicates that multiple intervals are biologically related and act as a single ncRNA feature; choose Order if each interval describes a separate, unrelated instance of the ncRNA feature on the current sequence)
  • OK and Cancel are the same as the RNA section

The Gene section allows an existing or new Gene feature to be associated with the ncRNA feature. For an existing ncRNA-Gene association, the dialog allows the Gene to be suppressed and/or the mapping type between the ncRNA and Gene to changed.

GWB Features Structural Rnas Ncrna Dialog Gene

  • Gene (displays a scrolling list of existing genes on the record to associate with the ncRNA; includes the choice ‘New’ that allows an additional Gene feature to be added to the record and associated with the ncRNA.
  • Map by (choose between default Overlap or Cross-reference when necessary)
  • Suppress Gene (removes association between ncRNA and chosen Gene)
  • Edit Gene (opens a new Gene feature dialog in which changes can be made to the existing Gene’s information)
  • Locus/Allele/Description/Locus Tag (when ‘New’ is chosen as the Gene to associate with the CDS, allows one or more of these four labels to be input for the new Gene)
  • OK and Cancel are the same as the RNA section

The Comment section allows the addition of free text description of the ncRNA feature. The text will appear as a /note qualifier on the ncRNA feature in the record. Clear deletes any text provided in the box. OK and Cancel are the same as the RNA section.

GWB Features Structural Rnas Ncrna Dialog Comment

The GenBank Qualifiers sections allows the addition of specific qualifiers and their free text values to the ncRNA: ncRNA-class, allele, evidence, function, and old-locus-tag. OK and Cancel are the same as the RNA section

GWB Features Structural Rnas Ncrna Dialog GenBank Qualifiers

The General section allows the addition of special notations (click the ‘+’ to expand the list):

GWB Features Structural Rnas Ncrna Dialog General

  • Pseudogene (choose appropriate explanation from the pull-down menu: processed, unprocessed, unitary, allelic, or unknown; see definitions)
  • Exception (choose appropriate reason from the pull-down list why non-standard biology applies; see definitions)
  • Dbxrefs (Database Cross References; enter database name and identifier)
  • Feature Identifiers (will be assigned in sequence processing)
  • Experiments (choose appropriate Category from pull-down menu and provide brief free text description of work; PubMedID or doi of journal paper describing work is optional; see definitions)
  • Inferences (choose appropriate Category and Type from the pull-down menus of the structured description of non-experimental evidence that supports the feature identification or assignment)
  • Citations (choose a reported Reference that indicates the citation providing the claim of and/or evidence for a feature
  • OK and Cancel are the same as the RNA section

preRNA

WORK IN PROGRESS

tmRNA

WORK IN PROGRESS

miscRNA

WORK IN PROGRESS

Regulatory

WORK IN PROGRESS

promoter

WORK IN PROGRESS

enhancer

WORK IN PROGRESS

ribosome_binding_site

WORK IN PROGRESS

riboswitch

WORK IN PROGRESS

terminator

WORK IN PROGRESS

regulatory

WORK IN PROGRESS

Protein Features

WORK IN PROGRESS

mat_peptide

WORK IN PROGRESS

sig_peptide

WORK IN PROGRESS

proprotein

WORK IN PROGRESS

trans_peptide

WORK IN PROGRESS

Other Features

WORK IN PROGRESS

centromere

WORK IN PROGRESS

D-loop

WORK IN PROGRESS

misc_binding

WORK IN PROGRESS

misc_difference

WORK IN PROGRESS

misc_feature

misc_feature opens a dialog that adds a miscellaneous feature and associated qualifiers to the current sequence.

What is a miscellaneous feature? A region of biological interest that cannot be described by any other feature; a new or rare feature.

For details, see misc_feature description.

When working on a set of sequences, before adding any feature to a sequence, be sure that the specific sequence – NOT Nucleotides - is chosen in the ‘Sequences’ menu in the upper right on the flatfile record view window:

GWB Record View Window Sequences Choice Menu Nucleotides

GWB Record View Window Sequences Choice Menu Specific Seq

The misc_feature dialog has five sections: Import Feature, Location, Gene, Comment, and General

The Import Feature section appears by default when the dialog is opened and allows the choice of Other Features and the addition of biological qualifiers for the misc_feature.

GWB Features Other Features Misc Feature Dialog Import Feature

  • misc_feature’ is chosen by default; if misc_feature is not the intended other feature, choose the correct other feature from the pull-down list
  • Allele: provide the name of the allele for the gene associated with the misc_feature
  • Evidence: provide free text description of any evidence that supports the name or description of the misc_feature
  • Function: provide free text description of the function (activity) of the feature
  • Number: provide an applicable number (1, 2, 3, etc) for the feature
  • Old-locus-tag: provide the feature tag assigned for tracking purposes to the misc_feature; can be used where the misc_feature’s associated Gene has a valid gene name and where a locus-tag is already present
  • Phenotype: provide the name of the phenotype (a physical, biochemical, or behavioral characteristic or set of characteristics) conferred by the misc_feature
  • OK (verifies and adds the misc_feature as described by the information provided)
  • Cancel (closes the dialog without taking any action)

The Location section allows the addition of the nucleotide intervals and related information of the misc_feature on the current sequence:

GWB Features Other Features Misc Feature Dialog Location

  • Partialness (describes whether the 5’ end and the 3’ end are either complete or partial; default is set to complete for both, meaning that the entire misc_feature is identified by the nucleotide intervals entered)
  • From/To (displays the first and last nucleotide of the misc_feature; if the misc_feature has multiple intervals, enter each set of first and last nucleotides of the intervals sequentially)
  • Strand (the location defaults to the Plus (positive) strand; change to Minus (minus) strand if applicable for each interval; intervals on the Minus strand are described as ‘complement’ in the record)
  • SeqID (identifies the SequenceID of the sequence to which this misc_feature will apply; defaults to the current sequence)
  • Insert Controls (allow a blank row for nucleotide intervals to be inserted above or below the row on which it is chosen)
  • Arrow Controls (allow an existing row to be moved up or down in a list of multiple intervals)
  • Delete (removes a row of intervals)
  • Save As (defaults to Join, which indicates that multiple intervals are biologically related and act as a single misc_feature; choose Order if each interval describes a separate, unrelated instance of the misc_feature on the current sequence)
  • OK and Cancel are the same as the Import Feature section

The Gene section allows an existing or new Gene feature to be associated with the misc_feature. For an existing misc_feature-Gene association, the dialog allows the Gene to be suppressed and/or the mapping type between the misc_feature and Gene to changed.

GWB Features Other Features Misc Feature Dialog Gene

  • Gene (displays a scrolling list of existing genes on the record to associate with the misc_feature; includes the choice ‘New’ that allows an additional Gene feature to be added to the record and associated with the misc_feature.
  • Map by (choose between default Overlap or Cross-reference when necessary)
  • Suppress Gene (removes association between misc_feature and chosen Gene)
  • Edit Gene (opens a new Gene feature dialog in which changes can be made to the existing Gene’s information)
  • Locus/Allele/Description/Locus Tag (when ‘New’ is chosen as the Gene to associate with the misc_feature, allows one or more of these four labels to be input for the new Gene)
  • OK and Cancel are the same as the Import Feature section

The Comment section allows the addition of free text description of the misc_feature. The text will appear as a /note qualifier on the misc_feature in the record. Clear deletes any text provided in the box. OK and Cancel are the same as the Import Feature section

GWB Features Other Features Misc Feature Dialog Comment

The General section allows the addition of special notations (click the ‘+’ to expand the list):

GWB Features Other Features Misc Feature Dialog General

  • Pseudogene (choose appropriate explanation from the pull-down menu: processed, unprocessed, unitary, allelic, or unknown; see definitions)
  • Exception (choose appropriate reason from the pull-down list why non-standard biology applies; see definitions)
  • Dbxrefs (Database Cross References; enter database name and identifier)
  • Feature Identifiers (added in sequence processing)
  • Experiments (choose appropriate Category from pull-down menu and provide brief free text description of work; PubMedID or doi of journal paper describing work is optional; see definitions)
  • Inferences (choose appropriate Category and Type from the pull-down menus of the structured description of non-experimental evidence that supports the feature identification or assignment)
  • Citations (choose a reported Reference that indicates the citation providing the claim of and/or evidence for a feature
  • OK and Cancel are the same as the Import Feature section

misc_recomb

WORK IN PROGRESS

mobile_element

WORK IN PROGRESS

oriT

WORK IN PROGRESS

protein_bind

WORK IN PROGRESS

rep_origin

WORK IN PROGRESS

repeat_region

WORK IN PROGRESS

Site

WORK IN PROGRESS

telomere

WORK IN PROGRESS

variation

WORK IN PROGRESS

For more information please see the full documentation for NCBI Genome Workbench Editing Package.

Support Center

Last updated: 2019-07-09T21:24:26Z