Eukaryotic Genome Annotation Guide
Annotation
Sequin and tbl2asn use a simple, five-column, tab-delimited table of feature locations and qualifiers to generate annotation.
The format of this feature table allows different kinds of features (e.g. gene, CDS (coding region), tRNA, repeat_region) and qualifiers (e.g. /product, /note) to be indicated. The validator will check for errors such as internal stops in coding regions.
Guidelines for prokaryotic genome submissions .
If you do not understand any of the instructions presented here or you have questions, please contact us by email at [email protected] prior to creating your submission. This will save us both a lot of time.
Table of Contents
- Prepare annotation table
- Gene features
locus_tagprotein_idtranscript_id- CDS (coding region) features
- Partial coding regions in incomplete genomes
- Gene fragments
- Transpliced Genes
- Split genes on two contigs
- Ribosomal RNA, tRNA and other RNA features
- mRNA features
- Alternatively spliced genes
- Evidence Qualifiers
- Data base cross references
- Gene Ontology
Prepare annotation table
The features must be in a simple five-column tab-delimited table, called the feature table. The feature table specifies the location and type of each feature for tbl2asn or Sequin to include in the GenBank submission that is created. The first line of the table contains the following basic information:
>Features SeqID table_name
The SeqID must be the same as the sequence's SeqID in the FASTA file. The table_name is optional. Subsequent lines of the table list the features. Columns are separated by tabs.
- Column 1: Start location of feature
- Column 2: Stop location of feature
- Column 3: Feature key
- Column 4: Qualifier key
- Column 5: Qualifier value
Figure 2 shows a sample feature table and illustrates a number of points about the feature table format. The GenBank flatfile corresponding to this table is shown in Figure 3 . The allowed features and their qualifiers are listed in the Feature Table documentation .
Features that are on the complementary strand, such as the genes Ngs_3038 and Ngs_11232 and their corresponding features shown in Figure 2 , are indicated by reversing the interval locations.
Please avoid unnecessary capitalization in all text entered in your table.
Additional requirements, as well as suggestions for various types of annotation, are included in the following sections.
Gene features
Gene features are always a single interval, and their location should cover the intervals of all the relevant features such as promoters and polyA binding sites.
Gene names should follow the standard nomenclature rules of the particular organism. For example, mouse gene names begin with an uppercase letter, and the remaining letters are lowercase.
Coding regions (CDS) and RNAs, such as tRNAs and rRNAs, must have a corresponding gene feature. However, other features such as repeat_regions and misc_features do not have a corresponding gene or locus_tag.
locus_tag
All genes should be assigned a systematic gene identifier which should receive the locus_tag qualifier on the gene feature in the table. Genes may also have functional names as assigned in the scientific literature. In this example, KCS_0001 is the systematic gene identifier, while Abc5 is the functional gene name.
Table view of gene with both biological name and locus_tag
1 1575 gene
gene Abc5
`locus_tag` KCS_0001
Flatfile view
gene 1..1575
/gene="Abc5"
/`locus_tag`="KCS_0001"
Table view of gene with only locus_tag
1 1575 gene
`locus_tag` KCS_0001
Flatfile view
gene 1..1575
/`locus_tag`="KCS_0001"
For consistency the same locus_tag prefix must be used throughout the entire genome. Therefore, all the chromosomes of a genome should have the same locus_tag prefix.
To improve the use of locus_tags we are now requiring that all locus_tag prefixes be registered and that they be unique. We recommend having the BioProject registration process auto-assign a locus_tag prefix, as they are not meant to convey meaning. The locus_tag prefix should be 3-12 alphanumeric characters and the first character may not be a digit. The locus_tag prefix is followed by an underscore and then an alphanumeric identification number that is unique within the given genome. Other than the single underscore used to separate the prefix from the identification number, no special characters can be used in the locus_tag.
The chromosome number can be embedded in the locus_tag, if desired, in the format Prefix\_#g#####, where the first # is the chromosome number and ##### is the unique number of the gene. For example, Ajs_4g00123 for a gene on chromosome 4.
Read more about locus_tags and their intended usage.
Please register your genome project and proposed locus_tag prefix on the BioProject registration page prior to preparing your submission to GenBank. Each project that is registered here is assigned a project_id, and in the future we intend that the project_id will appear on all entries associated with a particular genome project.
The use of locus_tag is supported in Sequin version 4.35 or later. If you have an older version of Sequin please download the current version . The latest version of tbl2asn is available from the tbl2asn page.
protein_id
All proteins in a WGS or complete genome must be assigned an identification number by the submitter. We use this number to track proteins when sequences are updated. This number is indicated in the table by the CDS qualifier protein_id, and should have the format gnl|dbname|string, where dbname is a version of your lab name that you think will be unique (eg SmithUCSD), and string is the unique protein SeqID assigned by the submitter. This identifier is saved with the record (in ASN.1 format), but it is not visible in the flatfile. We recommend using the locus_tag as the protein SeqID. In this example, the protein_id for ABC5 is gnl|SmithUCSD|KCS_0001.
Example:
<1 >1575 gene
gene Abc5
locus_tag KCS_0001
1 1575 CDS
product ABC5
protein_id gnl|SmithUCSD|KCS_0001
Since the protein_id is used for internal tracking in our database, it is important that the complete protein_id (dbname + SeqID) not be duplicated by a genome center. Thus, if your genome center is submitting more than one complete genome, please be sure to use unique protein_id's for all of the genomes.
The protein_id is also included as a qualifier on the corresponding mRNA feature, to allow the CDS and mRNA to be paired during processing.
Note that when WGS submissions are processed, the dbname in the protein_id is automatically changed to 'WGS:XXXX', where XXXX is the project's accession number prefix.
After your genome is released into GenBank, the proteins are assigned accession numbers. We will provide a table of the protein SeqIDs and accession numbers for you to use in future updates .
transcript_id
The transcript_id is included as a qualifier for both the CDS and its corresponding mRNA. It has the same format as the protein_id, gnl|dbname|identifier. Because each transcript_id and protein_id must be unique, we suggest adding 'mrna' or 't' to the protein_id identifier as a simple way to create the corresponding (unique) transcript_id. However, you can use whatever naming convention you choose, as long as all of the identifiers are unique.
63574 87173 gene
`locus_tag` Ngs_17131
63574 63907 mRNA
75690 75730
84396 85536
85598 85773
85836 86109
86173 86467
86555 86670
86731 87173
product hypothetical protein
protein_id gnl|ncbi|Ngs_17131
transcript_id gnl|ncbi|mrna.Ngs_17131
84402 85536 CDS
85598 85773
85836 86109
86173 86467
86555 86670
86731 86882
product hypothetical protein
protein_id gnl|ncbi|Ngs_17131
transcript_id gnl|ncbi|mrna.Ngs_17131
CDS (coding region) features
All CDS features must have a product qualifier (protein name). NCBI protein naming conventions are adopted in part from the UniProt-Swiss-Prot Protein Knowledgebase
Consistent nomenclature is indispensable for communication, literature searching and data retrieval. Many species-specific communities have established gene nomenclature committees that try to assign consistent and, if possible, meaningful gene symbols. Other scientific communities have established protein nomenclatures for a set of proteins based on sequence similarity and/or function. But there is no established organization involved in the standardization of protein names, nor are there any efforts to establish naming rules that are valid across the largest spectrum of species possible.
Ambiguities regarding gene/protein names are a major problem in the literature and it is even worse in the sequence databases which tend to propagate the confusion. For this reason, we ask that you follow some basic guidelines in naming your proteins. The protein naming guidelines are based on the premise that a good and stable recommended name for a protein is a name that is as neutral as possible.
Guidelines for naming proteins:
- If it exists, use the approved nomenclature.
- Use a concise name, not a description or phrase.
- Ideally the name should be unique and attributed to all orthologs.
- The protein name should not contain specific characteristics of the protein, and it should not reflect the function of the protein, its subcellular location, its domain structure, its molecular weight or its species of origin. This information can be included in the note.
- In cases where the protein name is not known use "unknown" or "hypothetical protein" as the product name. We recommend the use of "hypothetical protein" as this will allow the
locus_tagidentifier to be appended to the product name in BLAST and Entrez summary lines. - Protein names may be denoted by the same symbol as the corresponding gene, but in the correct format for the organism. For example, mouse proteins have the same symbol as the gene name, but the protein name has all capital letters.
- Avoid the use of molecular weights in protein names; "unicornase subunit A" is preferred to "unicornase 52 kDa subunit"
- Do not use the term "homolog" in a protein as this infers an evolutionary relationship that has generally not been determined.
- Where possible, avoid the use of commas in protein names
- Use lowercase letters, except when uppercase are required (for example, in acronyms such as DNA or ATP).
- Wherever appropriate, the name should use American spelling conventions.
- Avoid the use of Roman numerals where possible. Use instead Arabic numbers.
- Do not build molecular weights into abbreviations
- For proteins that belong to a multigene family, it is recommended that you choose a coherent nomenclature with numbers to specify the different members of the family.
- When naming proteins which can be grouped into a family based on homology or according to a notion of shared function, the different members should be enumerated with a dash "-" followed by an Arabic number. e.g. "desmoglein-1", "desmoglein-2", etc.
- Greek letters must be written in full e.g. "alpha", and written entirely in lower case with the exception of "Delta" in the context of steroid/fatty acid metabolism nomenclature. Additionally the Greek letters that are followed by a number should be preceded or followed by a dash "-" e.g. "unicornase alpha-1".
- Do not use diacritics, such as accents, umlauts. Many computer sytems (ours included) can only understand ASCII characters.
- Do not use plurals in a protein name. e.g. "ankyrin repeats-containing protein 8" is wrong.
- Proteins of unknown function which contain a defined domain or motif, can be named according to the domain present. The name should be of the following type: "
Here are some examples of good protein names:
- **cytochrome b**
- **CytB**
- **aconitate hydrase B**
- **hypothetical protein**
- **cytochrome b-like protein**
- **4Fe-4S cluster binding protein**
- **adenylyltransferase/ADP-heptose synthase**
- **2-hydroxyhepta-2,4-diene-1,7-dioate isomerase**
- **short-chain specific acyl-CoA dehydrogenase**
- **formylmethanofuran--tetrahydromethanopterin formyltransferase**
- **serine/threonine-protein kinase**
- **translation initiation factor 1**
- **triphosphoribosyl-dephospho-CoA synthetase**
- **thiamine biosynthesis protein ThiC**
- **PAS domain-containing protein 5**
- **ABC transporter ATP-binding protein AlbC**
- **stage 0 sporulation protein J**
- _These names all concisely describe the function of the protein, where known, and avoid references to structure, homology and species._
Here are some examples of bad protein names:
- **required for the efficient incorporation of molybdate into molybdoproteins**
- _This describes the protein's role in a biosynthetic process but is not a protein name._
- **chaperone Hsp70; DNA biosynthesis; autoregulated heat shock proteins**
- _The name "chaperone Hsp70" is fine however the remaining comments would be best fielded as a note or in the function qualifier._
- **putative carbonic anhdrase (EC 4.2.1.1)**
- _The EC number should not be part of the protein name but instead fielded in the EC_number qualifier_
- **similar to aconitrate hydrase B**
- _This statement is fine as a note, however as a protein name aconitrate hydrase B-like protein is preferred_
- **related to protein of unknown function**
- _uninformative name_
- **cytochrome b-like**
- _cytochrome b-like protein is preferred_
- **ABC transporter related**
- _vague name, there are many ABC transporters and subunits, be more specific_
- **pirin, N-terminal:pirin, C-terminal**
- _uniformative name noting similarity in N and C terminus_
- **helix-turn-helix motif**
- _Describes a motif or structural domain but is not an appropriate protein name._
- **PP-loop**
- _Describes a motif or structural domain but is not an appropriate protein name._
- **alpha/beta hydrolast fold**
- _Describes a motif or structural domain but is not an appropriate protein name._
- **pentapeptide repeat**
- _Describes a motif or structural domain but is not an appropriate protein name._
- **phosphopantetheine-binding domain**
- _Describes a motif or structural domain but is not an appropriate protein name._
- **protein of unknown function:conserved**
- _uninformative name_
- **hypothetical 32.5 kDa protein homologous to phytoene and squalene synthethases**
- _Hypothetical protein alone is appropriate. The remaining comments should be fielded as a note._
- **ribosomal protein L3 (E. coli)**
- _Protein names should not contain references to organism names. Ribosomal protein L3 is an appropriate name by itself._
- **saccharopine dehydrogenase or related protein**
- _"saccharopine dehydrogenase" or "saccharopine dehydrogenase-like protein" would be more appropriate_
- **tyrosine-protein kinase (capsular polysaccharide biosynthesis)**
- _tyrosine-protein kinase is fine as a protein name but capsular polysaccharide biosynthesis would be more appropriate as a function._
- **RimM protein, required for 16S rRNA processing**
- _RimM is fine as a protein name but descriptive comments should be placed in the note._
- **involved in flagellar biosynthesis**
- _This is a functional comment and not a protein name._
Notes
Please avoid including notes indicating a specific percentage of similarity to other entries in the database, since the corresponding record that you have pointed to may change and make your current note inaccurate, incorrect and obsolete. Descriptions, notes describing similarity to other proteins, and functional comments must be placed in the appropriate CDS qualifiers such as note, or prot_desc, as they are descriptors of the product. E.C. numbers must be fielded in an EC_number qualifier.
start stop CDS
product DNA gyrase subunit B
EC_number 5.99.1.3
Qualifiers that can be used on the CDS feature are:
start stop CDS
product
prot_desc
function
EC_number
note
experiment
inference
go_component
go_process
go_function
db_xref
pseudo
exception
transl_except
Multiple note qualifiers are supported. tbl2asn or Sequin concatenate multiple note qualifiers into a single note with semicolons as separators.
Bifunctional proteins:
If a protein contains two separate and distinct functions or if it has more than one name, these can be annotated in several ways, as outlined below. Table view:
start stop CDS
product adenylyltransferase/ADP-heptose synthase
note bifunctional
or
start stop CDS
product bifunctional adenylyltransferase/ADP-heptose synthase cyclohydrolase
or
start stop CDS
product FolD
function adenylyltransferase
function ADP-heptose synthase cyclohydrolase
note bifunctional
Partial coding regions in incomplete genomes
To annotate an partial coding region, you should use the "<" or ">" in your feature table to designate the feature as either 5' or 3' partial. The coding region should begin at the first nucleotide present, however the translation will start at the first complete codon.
Example
In the first example below, the "<" designates this coding region as 5' partial and "codon_start 3" tells the software to start translation with the third nucleotide of the CDS. Note that if the codon_start is not specified, then the software assumes a codon_start of 1. The second coding region below is partial at the 3' end so ">" is used to indicate a 3' partial feature.
<1 497 CDS
product ABC5
note similar to Bacillus subtilis aldolase
codon_start 3
protein_id gnl|dbname|KCS_0001
transcript_id gnl|dbname|KCS_mrna0001
600 >1575 CDS
product actin-like protein
protein_id gnl|dbname|KCS_0002
transcript_id gnl|dbname|KCS_mrna0002
Here are more examples of formatting partial CDS features .
Partial genes within a sequence should begin or end at consensus splice sites.
The use of partial coding regions is reserved for incomplete genomes only. All coding regions annotated on finished genomes should be complete at both the 5' and 3' ends.
Gene fragments
Sometimes a genome will have adjacent or nearby genes that seem to be only part of a protein. In many cases these indicate a possible problem with the sequence and/or annotation. A related issue is the presence of internal stop codons in the conceptual translation of a CDS that looks like it should be a real CDS. These problems may be due to a variety of reasons, including mutations or sequencing artifacts. They can be annotated in a number of ways:
- Annotate the gene as a pseudogene. If multiple gene fragments were present initially, then add a single gene feature which covers all of the potential coding regions and add the pseudo qualifier indicating that this is a pseudogene. If known, a note qualifier may be added indicating why this gene is disrupted.
1 200 gene
gene Abc5
`locus_tag` KCS_0001
gene_desc alkaline phosphatase
pseudo
note frameshift
- Alternatively, if you are not sure if the disrupted gene is a "pseudogene" you can just use a gene feature without the /pseudo. Please use the complete nucleotide spans of the frameshifted gene. If known, the reason for the incomplete translation can be included in a note.
1 200 gene
gene Abc5
`locus_tag` KCS_0001
gene_desc alkaline phosphatase
note nonfunctional due to frameshift
- If the feature is just noting a similarity to genes in the database and is probably not translated, then it should be annotated as a misc_feature without a corresponding gene feature.
1 200 misc_feature
note similar to Abc5
Transpliced Genes
Transpliced genes are the exception to the rule for annotating gene feature spans. Transpliced genes are similar to intron-containing genes, except that the two pieces of the gene occur on different regions of the chromosome. These genes are transcribed as two or more separate RNA products that are transpliced into a single mRNA or tRNA. To annotate this using a table, enter the nucleotide spans so that the complementary (minus strand) spans are arranged from high to low, and vice-versa for the plus strand.
36700 36618 gene
86988 87064
`locus_tag` NEQ_t38
exception trans-splicing
36631 36618 misc_feature
note sequence cleaved during processing of trans-spliced tRNAs
36673 36635
87030 87064 tRNA
product tRNA-Glu
exception trans-splicing
note this trans-spliced tRNA consists of two halves on mixed strands; it shares a 3' half with another tRNA
gene join(complement(36618..36700),86988..87064)
/`locus_tag`="NEQ_t38"
/trans_splicing
misc_feature complement(36618..36631)
/`locus_tag`="NEQ_t38"
/note="sequence cleaved during processing of trans-spliced tRNAs"
tRNA join(complement(36635..36673),87030..87064)
/`locus_tag`="NEQ_t38"
/product="tRNA-Glu"
/trans_splicing
/note="this trans-spliced tRNA consists of two halves on
mixed strands; it shares a 3' half with another tRNA"
Split genes on two contigs
Sometimes, in incomplete genomes, the ends of a gene may be on different contigs. When you are certain that the two pieces are part of the same gene, annotate these as separate genes with unique locus_tag features, plus separate CDS/mRNA features with different protein_id and transcript_id qualifiers. In addition, link the features together with note qualifiers that refer to the other part of the gene. However, do not create extremely short features; for example, if one end is only the start methionine, or only a few amino acids before the stop codon.
Example
>Feature Cont01.00111
5000 >7500 gene
`locus_tag` KCS_2223A
5000 5500 mRNA
6000 >7200
product enolase
protein_id gnl|dbname|KCS_2223A
transcript_id gnl|dbname|KCS_mrna2223A
5488 5500 CDS
6000 >7200
product enolase
protein_id gnl|dbname|KCS_2223A
transcript_id gnl|dbname|KCS_mrna2223A
note 5' end; 3' end is gene KCS_2223B on contig Cont01.00224
>Feature Cont01.00224
<1 1000 gene
`locus_tag` KCS_2223B
<100 1000 mRNA
product enolase
protein_id gnl|dbname|KCS_2223B
transcript_id gnl|dbname|KCS_mrna2223B
<100 876 CDS
product enolase
protein_id gnl|dbname|KCS_2223B
transcript_id gnl|dbname|KCS_mrna2223B
note 3' end; 5' end is gene KCS_2223A on contig Cont01.00111
Ribosomal RNA, tRNA and other RNA features
RNA features (rRNA, tRNA, ncRNA) need a corresponding gene feature with a locus_tag qualifier. If the amino acid of a tRNA is unknown, use tRNA-Xxx as the product, as in the example. Many submitters like to label the tRNAs such as tRNA-Gly1, etc. If you wish to do this please include "tRNA-Gly1" as a note and not in /gene. The use of /gene is reserved for the actual biological gene symbol such as "trnG". If a tRNA is a pseudogene, please use the /pseudo qualifier.
Annotate ncRNAs that belong to one of the INSDC nRNA_class as an ncRNA feature, with the appropriate value in the required /ncRNA_class qualifier. Regions of an RNA should be annotated as a misc_feature (eg, leader sequences), or a misc_binding feature if they bind a known molecule (eg, riboswitches). If the RFAM identifier is known, it can be included as a db_xref.
Some rRNA, tRNA and ncRNA examples:
<1 400 gene
`locus_tag` KCS_00011
<1 400 rRNA
product 16S ribosomal RNA
488 560 gene
`locus_tag` KCS_00012
488 560 tRNA
product tRNA-Lys
570 601 gene
`locus_tag` KCS_00020
pseudo
570 601 tRNA
product tRNA-Phe
pseudo
700 780 gene
`locus_tag` KCS_00013
700 780 tRNA
product tRNA-Xxx
900 923 gene
`locus_tag` KCS_00014
900 923 ncRNA
ncRNA_class miRNA
product mir-9c
950 1000 gene
`locus_tag` KCS_00015
950 1000 tmRNA
product tmRNA
misc_feature and misc_binding features do not have an associated gene feature. To tag these features with a locus_tag-like identifier, include that value in the note, separated from other information by a semicolon and space.
Riboswitches should be annotated using the misc_binding feature if the bound moiety is known; for example:
1 100 misc_binding
note cobalamin riboswitch
bound_moiety adenosylcobalamin
If the bound moiety is unknown or if the sequence is a leader sequence, annotate as a `misc_feature, for example:
1 100 misc_feature
note yybP-ykoY element
mRNA features
Include an mRNA feature for each translated CDS. Several things to note are:
- Use the same product name for the mRNA and its corresponding CDS.
- If there is no UTR information, then the mRNA's location will agree with its CDS's location, but the mRNA will be partial at its 5' and 3' ends.
- Extend the gene feature to include the entire mRNA.
- If the mRNA is partial, then make the gene partial.
Example
The first example is a complete CDS whose 5' and 3' UTRs are known.
>Feature Cont54
10400 12512 gene
locus_tag CCC_03116
10400 10462 mRNA
10533 10577
10651 11098
11182 11642
11716 12512
product hypothetical protein
protein_id gnl|dbname|CCC_03116
transcript_id gnl|dbname|CCC_mrna03116
10450 10462 CDS
10533 10577
10651 11098
11182 11642
11716 12233
product hypothetical protein
protein_id gnl|dbname|CCC_03116
transcript_id gnl|dbname|CCC_mrna03116
The second example is a CDS that is partial at the 5' end and lacks any 3' UTR information.
>Feature Cont3
<1 >497 gene
locus_tag CCC_111011
<1 497 CDS
note similar to Bacillus subtilis aldolase
product aldolase-like protein
codon_start 3
protein_id gnl|dbname|CCC_111011
transcript_id gnl|dbname|CCC_mrna111011
<1 >497 mRNA
product aldolase-like protein
protein_id gnl|dbname|CCC_111011
transcript_id gnl|dbname|CCC_mrna111011
Alternatively spliced genes
In many cases a gene can be alternatively spliced, yielding alternative transcripts. These transcripts may differ in the coding region and produce different products, or they may differ in the non-translated 5' or 3' UTR and produce the same protein. To annotate alternatively spliced genes, include one mRNA and CDS for each transcript, and include only one gene over all of the features. Give the corresponding mRNA and CDS the same name, and include a note with the value alternatively spliced on each. If there are multiple CDS with the same name, then add a note to each mRNA and CDS to refer to each other; e.g., transcript variant A and encoded by transcript variant A for one mRNA/CDS pair. If the CDS have different translations, then they should have different product names. Make sure that all the proteins have unique protein_id values.
Examples
Example 1 (different products):
>Feature Cont01.00055
10 5000 gene
locus_tag CCC_04562
10 500 mRNA
722 1555
2548 3901
4400 5000
product CCC_04562 isoform A
note alternatively spliced
protein_id gnl|dbname|CCC_04562A
transcript_id gnl|dbname|CCC_mrna04562A
102 500 CDS
722 1555
2548 3901
4400 4566
product CCC_04562 isoform A
note alternatively spliced
protein_id gnl|dbname|CCC_04562A
transcript_id gnl|dbname|CCC_mrna04562A
10 500 mRNA
2548 3901
4400 5000
product CCC_04562 isoform B
note alternatively spliced
protein_id gnl|dbname|CCC_04562B
transcript_id gnl|dbname|CCC_mrna04562B
102 500 CDS
2548 3901
4400 4566
product CCC_04562 isoform B
note alternatively spliced
protein_id gnl|dbname|CCC_04562B
transcript_id gnl|dbname|CCC_mrna04562B
Example 2 (same product):
>Feature Cont01.00056
100 1000 gene
locus_tag CCC_03222
100 333 mRNA
444 678
800 1000
product hypothetical protein
note transcript variant A; alternatively spliced
protein_id gnl|dbname|CCC_03222A
transcript_id gnl|dbname|CCC_mrna03222A
456 678 CDS
800 865
product hypothetical protein
note encoded by transcript variant A; alternatively spliced
protein_id gnl|dbname|CCC_03222A
transcript_id gnl|dbname|CCC_mrna03222A
100 360 mRNA
444 678
800 1000
product hypothetical protein
note transcript variant B; alternatively spliced
protein_id gnl|dbname|CCC_03222B
transcript_id gnl|dbname|CCC_mrna03222B
456 678 CDS
800 865
product hypothetical protein
note encoded by transcript variant B; alternatively spliced
protein_id gnl|dbname|CCC_03222B
transcript_id gnl|dbname|CCC_mrna03222B
Evidence Qualifiers
The International Nucleotide Sequence Database Collaboration, DDBJ, EMBL and GenBank has adopted a set of new qualifiers to describe the evidence for feature annotation in GenBank records. These are:
/experimental="text" /inference="TYPE:text", where 'TYPE' is from a select list and 'text' is structured text.
The use of the new evidence qualifiers is supported in Sequin version 6.0 or later, and tbl2asn version 5.1 or later. If you have an older version, please download the current version of Sequin or tbl2asn .
These new qualifiers replace /evidence=experimental and /evidence=non-experimental, respectively, which will no longer be supported.
See more information about the Evidence Qualifiers .
Database cross references
A variety of database cross references can be added to a feature. These appear as /db_xref on the features. This qualifier serves as a vehicle for linking of sequence records to other external databases. See the full list of db_xref databases.
1 100 CDS
product RecA
protein_id gnl|center_name|Test_0001
db_xref InterPro:IPR000111
180 210 misc_feature
note yybP-ykoY element
db_xref RFAM:RF00080
Gene Ontology
GO (Gene Ontology) terms can be included in genomes in order to describe protein functionality. Gene Ontology (GO) terms can be indicated with the following qualifiers
1 100 CDS
product helicase
go_process chromatin assembly or disassembly|0006333||IEA
go_process antimicrobial humoral response|0019730|16163390|IMP
go_component nucleus|0005634|14668392|IDA
go_component chromatin|0000785||IEA
go_function ATP-dependent helicase activity|0008026||ISS
go_function nucleic acid binding|0003676||IEA
go_function ATP binding|0005524||IEA
The value field is separated by vertical bars '|' into a descriptive string, the GO identifier (leading zeroes are retained), and optionally a PubMed ID and one or more evidence codes. The evidence code is the fourth token, so include blank fields, as necessary (eg the last qualifier has no PubMed ID so the third field is blank).