Entry Upload Templates - Guidelines on Accepted Sequence Flatfile Formats
Introduction
The EMBL flat file format is the only way to submit all types of functional sequence annotation to ENA. See the example flat file page for general information on this format.
The Entry Upload Templates provided on this page are skeletons of actual flatfiles, to adapt for submission. All submissions should include the topology of the ID line, the description from the DE line, and the feature table (FT lines). Other parts of the final flatfile will be collected during submission, including release date and references, rather than being present in the submitted file. This includes any fields filled with ‘XXX’: these can be left as they are and our pipeline will infer them later.
To use one of the templates, copy the boxed example and save into a plain text file. It is essential that you use a plain text format, as hidden characters and formatting associated with other file types will result in automatic rejection of your submission.
Please carefully read the accompanying notes for the template you choose, and make sure that all tokens (shown in curly brackets {} ) are replaced with actual values, and any unused parts of the FT block are removed. Please use only the ASCII character set; extended ASCII (including special characters and characters not native to English) is not accepted and may cause validation errors. Please use the nearest ASCII equivalent.
The templates provide the basic and minimal information required for constructing your flatfile. Advanced users may wish to add further annotation within the scope of the feature table. In this case, please refer to the INSDC WebFeat documentation.
Most templates here assume that the sequences are nuclear in origin. For organellar sequences, the qualifier /organelle=”{organelle}” should be included, with the value of {organelle} taken from the INSDC controlled vocabulary.
Sequences extracted from mixed samples of anonymous organisms (metagenomic samples) where independent identification, such as culturing, has not been done are environmental samples by INSDC definition. The organism feature for these sequences should reference a taxon whose name starts with ‘uncultured’. In addition, these should include the flag ‘/environmental sample’ within the source feature.
Sequences should always be submitted on the forward strand. When submitting a multi-feature region with loci on both strands, you will need to apply the complement operator to the coordinates for reverse strand features. Refer to the Feature Table Document or similarly-annotated records in the database.
The nucleotide sequence itself should comprise only characters from the IUPAC nucleotide nomenclature. An unsequenced region of unsure length should be represented with a string of 100 Ns; gaps of known length may use the exact number, but if this is very large (e.g. >200bp) then it is advisable to condense the gap to one of unknown length (100 Ns).
Unsequenced regions should be annotated with a gap feature, shown below. Gaps formed as artefacts of alignment are not allowed. If the gap covers an entire intron, then the corresponding intron block should be removed from the annotation.
FT gap {X..Y}
FT /estimated_length={unknown or known}
When you have prepared your flatfile, you will need to submit it using Webin-CLI.
Available templates:
HLA Gene With Sequenced Introns
HLA genes have strictly controlled formats in ENA flat files. Please adhere to the below conventions to avoid having your submission rejected.
{organism} is a species-rank organism present in the database. Search available taxa at ENA Search.
{gene} has a value such as HLA-A, HLA-B, HLA-DRB
{allele} takes the form {gene*allele designation}, e.g. HLA-A*01:01, HLA-B*40:32
{product} takes the form MHC class I antigen or MHC class II antigen
{reading frame} should be 1 where the start codon is present, otherwise 1, 2 or 3 depending on the reading frame of the 5’ partial coding sequence
{partial} - delete if coding region is complete, otherwise just remove the curly brackets
{a to n} are the exon/intron/CDS coordinates
{A and N} are the coding region 5’ and 3’ coordinates, which may differ from exon coordinates due to UTR. If the start or stop codon is absent, please include partiality symbols, e.g. <1..250 or 2917..>2960
Incompleteness of any features should be described using partiality symbols, e.g. <1..250 or 2917..>2960
{sequence} should be the sequence in IUPAC nucleotide characters, as described above
Add or remove exon and intron blocks as required
HLA gene with sequenced introns:
ID XXX; XXX; linear; XXX; XXX; XXX; XXX.
XX
AC XXX;
XX
DE {organism} {partial} {gene} gene for {product}, allele {allele}
XX
FH Key Location/Qualifiers
FH
FT source 1..{sequence length}
FT /organism="{organism}"
FT /mol_type="genomic DNA"
FT CDS join(A..b,c..d,e..f,g..h,i..j,k..l,m..N)
FT /codon_start={reading frame}
FT /gene="{gene}"
FT /allele="{allele}"
FT /product="{product}"
FT /function="antigen presenting molecule"
FT exon {a..b}
FT /number=1
FT /gene="{gene}"
FT /allele="{allele}"
FT intron {b+1..c-1}
FT /number=1
FT /gene="{gene}"
FT /allele="{allele}"
FT exon {c..d}
FT /number=2
FT /gene="{gene}"
FT /allele="{allele}"
FT intron {d+1..e-1}
FT /number=2
FT /gene="{gene}"
FT /allele="{allele}"
FT exon {e..f}
FT /number=3
FT /gene="{gene}"
FT /allele="{allele}"
FT intron {f+1..g-1}
FT /number=3
FT /gene="{gene}"
FT /allele="{allele}"
FT exon {g..h}
FT /number=4
FT /gene="{gene}"
FT /allele="{allele}"
FT intron {h+1..i-1}
FT /number=4
FT /gene="{gene}"
FT /allele="{allele}"
FT exon {i..j}
FT /number=5
FT /gene="{gene}"
FT /allele="{allele}"
FT intron {j+1..k-1}
FT /number=5
FT /gene="{gene}"
FT /allele="{allele}"
FT exon {k..l}
FT /number=6
FT /gene="{gene}"
FT /allele="{allele}"
FT intron {l+1..m-1}
FT /number=6
FT /gene="{gene}"
FT /allele="{allele}"
FT exon {m..n}
FT /number=7
FT /gene="{gene}"
FT /allele="{allele}"
XX
SQ
{sequence}
//
HLA Gene With Unsequenced Introns
HLA genes have strictly controlled formats in ENA flat files. Please adhere to the below conventions to avoid having your submission rejected. When introns are unsequenced, exons should be concatenated in order with 100 Ns representing gaps of unknown length.
{organism} is a species-rank organism present in the database. Search available taxa at ENA Search.
{gene} has a value such as HLA-A, HLA-B, HLA-DRB
{allele} takes the form {gene*allele designation}, e.g. HLA-A*01:01, HLA-B*40:32
{product} takes the form MHC class I antigen or MHC class II antigen
{reading frame} should be 1 where the start codon is present, otherwise 1, 2 or 3 depending on the reading frame of the 5’ partial coding sequence
{partial} - delete if coding region is complete, otherwise just remove the curly brackets
{a to h} are the exon/intron/CDS coordinates
{A and H} are the coding region 5’ and 3’ coordinates, which may differ from exon coordinates due to UTR. If the start or stop codon is absent, please include partiality symbols, e.g. <1..250 or 2917..>2960
Incompleteness of any features should be described using partiality symbols, e.g. <1..250 or 2917..>2960
Add or remove exon and intron blocks as required
{sequence} should be the sequence in IUPAC nucleotide characters, as described above
ID XXX; XXX; linear; XXX; XXX; XXX; XXX.
XX
AC XXX;
XX
DE {organism} {partial} {gene} gene for {product}, allele {allele}
XX
FH Key Location/Qualifiers
FH
FT source 1..{sequence length}
FT /organism="{organism}"
FT /mol_type="genomic DNA"
FT CDS join(A..b,b+101..c,c+101..d,d+101..e,e+101..f,f+101..g,g+101..H)
FT /codon_start={reading frame}
FT /gene="{gene}"
FT /allele="{allele}"
FT /product="{product}"
FT /function="antigen presenting molecule"
FT exon {a..b}
FT /number=1
FT /gene="{gene}"
FT /allele="{allele}"
FT gap b+1..b+100
FT /estimated_length=unknown
FT exon {b+101..c}
FT /number=2
FT /gene="{gene}"
FT /allele="{allele}"
FT gap c+1..c+100
FT /estimated_length=unknown
FT exon {c+101..d}
FT /number=3
FT /gene="{gene}"
FT /allele="{allele}"
FT gap d+1..d+100
FT /estimated_length=unknown
FT exon {d+101..e}
FT /number=4
FT /gene="{gene}"
FT /allele="{allele}"
FT gap e+1..e+100
FT /estimated_length=unknown
FT exon {e+101..f}
FT /number=5
FT /gene="{gene}"
FT /allele="{allele}"
FT gap f+1..f+100
FT /estimated_length=unknown
FT exon {f+101..g}
FT /number=6
FT /gene="{gene}"
FT /allele="{allele}"
FT gap g+1..g+100
FT /estimated_length=unknown
FT exon {g+101..h}
FT /number=7
FT /gene="{gene}"
FT /allele="{allele}"
XX
SQ
{sequence}
//
Bacterial Operon
Bacterial operons contain multiple ORFs which are transcribed together. In ENA records, the annotation contains an operon feature and multiple CDS features.
{organism} is a species-rank organism present in the database. Search available taxa at ENA Search.
{strain} is the strain identifier. You may change this to /isolate if you prefer
{operon} is the name of the operon and has a value like gal or lac
{geneX} is the gene symbol and has a value like galA or lacZ
{productX} is the product/protein name and has a value like galactose- permease, beta-galactosidase
{reading frame} should be 1 where the start codon is present, otherwise 1, 2 or 3 depending on the reading frame of the 5’ partial coding sequence
{a to l} are the coordinates of the operon and CDS 5’ and 3’ ends
Incompleteness of any features should be described using partiality symbols, e.g. <1..250 or 2917..>2960
{sequence} should be the sequence in IUPAC nucleotide characters, as described above
Add or remove CDS blocks as required
Advanced users: consider including other features, such as promoter, -35_signal and -10_signal. See the WebFeat page for more information
Optional features
FT promoter a..l
FT /operon="{operon}"
FT -35_signal X..Y
FT /operon="{operon}"
FT -10_signal X..Y
FT /operon="{operon}
Bacterial operon:
ID XXX; XXX; linear; XXX; XXX; XXX; XXX.
XX
AC XXX;
XX
DE {organism} {operon} operon, strain {strain}
XX
FH Key Location/Qualifiers
FH
FT source 1..{sequence length}
FT /organism="{organism}"
FT /strain="{strain}"
FT /mol_type="genomic DNA"
FT operon a..l
FT /operon="{operon}"
FT CDS a..b
FT /codon_start={reading frame}
FT /transl_table=11
FT /operon="{operon}"
FT /gene="{gene1}"
FT /product="{product1}"
FT CDS c..d
FT /transl_table=11
FT /operon="{operon}"
FT /gene="{gene2}"
FT /product="{product2}"
FT CDS e..f
FT /transl_table=11
FT /operon="{operon}"
FT /gene="{gene3}"
FT /product="{product3}"
FT CDS g..h
FT /transl_table=11
FT /operon="{operon}"
FT /gene="{gene4}"
FT /product="{product4}"
FT CDS i..j
FT /transl_table=11
FT /operon="{operon}"
FT /gene="{gene5}"
FT /product="{product5}"
FT CDS k..l
FT /transl_table=11
FT /operon="{operon}"
FT /gene="{gene6}"
FT /product="{product6}"
XX
SQ
{sequence}
//
Multi-Exon Gene
This template should be used as a starting point for submitting multi-exon genes. Where optional qualifiers are not used, please remove the entire line from the template.
{organism} is a species-rank organism present in the database. Search available taxa at ENA Search.
{identifier} is a form of sample or organism identification. You must use at least one from the below list and fill in the {ID} field with it. Other qualifiers are available in WebFeat.
Isolate: any sample or isolate name
Strain: the strain of the sequenced organism
Clone: the clone name of the sequence
Note: the breed of a domesticate
Cultivar: a cultivated variety of a plant or fungus
Variety: a natural variety of a plant or fungus
{gene} is the gene symbol, putative or official. This is optional, but highly recommended
{product} is the product/protein name and is mandatory. If uncertain, use “hypothetical protein”
{allele} is the allele name. This is optional.
{reading frame} should be 1 where the start codon is present, otherwise 1, 2 or 3 depending on the reading frame of the 5’ partial coding sequence
{partial} - delete if coding region is complete, otherwise just remove the curly brackets
{a to n} are the exon/intron/CDS coordinates
{A to N} are the coding region 5’ and 3’ coordinates, which may differ from exon coordinates due to UTR. If the start or stop codon is absent, please include partiality symbols, e.g. <1..250 or 2917..>2960
Incompleteness of any features should be described using partiality symbols, e.g. <1..250 or 2917..>2960
{sequence} should be the sequence in IUPAC nucleotide characters, as described above
Add or remove exon, intron and gap blocks as required
Multi-exon genes
ID XXX; XXX; linear; XXX; XXX; XXX; XXX.
XX
AC XXX;
XX
DE {organism} {partial} {gene} gene for {product}, {identifier} {ID}
XX
FH Key Location/Qualifiers
FH
FT source 1..{sequence length}
FT /organism="{organism}"
FT /mol_type="genomic DNA"
FT /{identifier}="{ID}"
FT CDS join(A..b,c..d,e..f,g..h,i..j,k..l,m..N)
FT /codon_start={reading frame}
FT /gene="{gene}"
FT /product="{product}"
FT /allele="{allele}"
FT /function="{function}"
FT exon {a..b}
FT /number=1
FT /gene="{gene}"
FT /allele="{allele}"
FT intron {b+1..c-1}
FT /number=1
FT /gene="{gene}"
FT /allele="{allele}"
FT exon {c..d}
FT /number=2
FT /gene="{gene}"
FT /allele="{allele}"
FT intron {d+1..e-1}
FT /number=2
FT /gene="{gene}"
FT /allele="{allele}"
FT exon {e..f}
FT /number=3
FT /gene="{gene}"
FT /allele="{allele}"
FT intron {f+1..g-1}
FT /number=3
FT /gene="{gene}"
FT /allele="{allele}"
FT exon {g..h}
FT /number=4
FT /gene="{gene}"
FT /allele="{allele}"
FT intron {h+1..i-1}
FT /number=4
FT /gene="{gene}"
FT /allele="{allele}"
FT exon {i..j}
FT /number=5
FT /gene="{gene}"
FT /allele="{allele}"
FT intron {j+1..k-1}
FT /number=5
FT /gene="{gene}"
FT /allele="{allele}"
FT exon {k..l}
FT /number=6
FT /gene="{gene}"
FT /allele="{allele}"
FT intron {l+1..m-1}
FT /number=6
FT /gene="{gene}"
FT /allele="{allele}"
FT exon {m..n}
FT /number=7
FT /gene="{gene}"
FT /allele="{allele}"
XX
SQ
{sequence}
//
Multi-Feature Region
{organism} is a species-rank organism present in the database. Search available taxa at ENA Search.
{organelle} with the value taken from the INSDC controlled vocabulary. The organelle should also be added to the DE line. Remove this entirely if the sequence is of nuclear origin.
{identifier} is a form of sample or organism identification. You must use at least one from the below list and fill in the {ID} field with it. Other qualifiers are available in WebFeat.
Isolate: any sample or isolate name
Strain: the strain of the sequenced organism
Clone: the clone name of the sequence
Note: the breed of a domesticate
Cultivar: a cultivated variety of a plant or fungus
Variety: a natural variety of a plant or fungus
{gene} is the gene symbol, putative or official. It is optional, but highly recommended. For tRNAs, the INSDC standard is tRNA-Aaa where Aaa is the 3-letter amino acid code (e.g. tRNA-Gly). For rRNAs, the standard is XXS ribosomal RNA, where XX is the sedimentation coefficient (e.g. 16S ribosomal RNA)
{product} is the product/protein name and is mandatory. If uncertain, use “hypothetical protein”
{reading frame} should be 1 where the start codon is present, otherwise 1, 2 or 3 depending on the reading frame of the 5’ partial coding sequence
{a to h} are the feature coordinates. For CDS features, this is the first and last base of the coding sequence, whether or not the start or stop codons are present.
{short note} should describe any misc_feature in simple terms, e.g. intergenic spacer region. It is useful here to refer to similar entries in the database. For tRNAs, the INSDC standard is tRNA-Aaa where Aaa is the 3-letter amino acid code (e.g. tRNA-Gly). For rRNAs, the standard is XXS ribosomal RNA, where XX is the sedimentation coefficient (e.g. 16S ribosomal RNA)
Incompleteness of any features should be described using partiality symbols, e.g. <1..250 or 2917..>2960
{sequence} should be the sequence in IUPAC nucleotide characters, as described above
Any of the feature blocks can be replicated/removed as required
The DE line should be written using the templated format but will need to be expanded according to the number and type of features in the sequence
Multi-feature region:
ID XXX; XXX; linear; XXX; XXX; XXX; XXX.
XX
AC XXX;
XX
DE {organism} {organelle} {partial} {gene1} gene, {gene2} gene, {gene3} gene and {short note}, {identifier} {ID}
XX
FH Key Location/Qualifiers
FH
FT source 1..{sequence length}
FT /organism="{organism}"
FT /mol_type="genomic DNA"
FT /{identifier}="{ID}"
FT CDS a..b
FT /codon_start={reading frame}
FT /gene="{gene1}"
FT /product="{product1}"
FT tRNA c..d
FT /gene="{gene2}"
FT /product="{product2}"
FT rRNA e..f
FT /gene="{gene3}"
FT /product="{product3}"
FT misc_feature g..h
FT /note="{short note}"
SQ
{sequence}
//
rDNA Region (ITS And rRNA Features)
The ITS/rDNA region can be submitted using an annotation checklist but this provides all details within a single misc_RNA feature. If you wish to add individual feature annotation for each rRNA and ITS, you will need to generate the file yourself. This section provides a skeleton for that.
{organism} is a species-rank organism present in the database. Search available taxa at ENA Search.
{identifier} is a form of sample or organism identification. You must use at least one from the below list and fill in the {ID} field with it. Other qualifiers are available in WebFeat.
Isolate: any sample or isolate name
Strain: the strain of the sequenced organism
Clone: the clone name of the sequence
Note: the breed of a domesticate
Cultivar: a cultivated variety of a plant or fungus
Variety: a natural variety of a plant or fungus
{a to f} are the feature coordinates. Incompleteness of any features (rRNA, misc_RNA) should be described using partiality symbols, e.g. <1..250 or 2917..>2960
{sequence} should be the sequence in IUPAC nucleotide characters, as described above
Any of the feature blocks can be replicated/removed as required
Please update the DE line to reflect the addition/removal of features
rDNA region:
ID XXX; XXX; linear; XXX; XXX; XXX; XXX.
XX
AC XXX;
XX
DE {organism} 18S rRNA gene, ITS1, 5.8S rRNA gene, ITS2 and 28S rRNA gene, {identifier} {ID}
XX
FH Key Location/Qualifiers
FH
FT source 1..{sequence length}
FT /organism="{organism}"
FT /mol_type="genomic DNA"
FT /{identifier}="{ID}"
FT rRNA a..b
FT /gene="18S rRNA"
FT /product="18S ribosomal RNA"
FT misc_RNA b+1..c
FT /note="internal transcribed spacer 1, ITS1"
FT rRNA c+1..d
FT /gene="5.8S rRNA"
FT /product="5.8S ribosomal RNA"
FT misc_RNA d+1..e
FT /note="internal transcribed spacer 2, ITS2"
FT rRNA e+1..f
FT /gene="28S rRNA"
FT /product="28S ribosomal RNA"
SQ
{sequence}
//
Precursor mRNA
Precursor mRNA can be submitted using an annotation checklist called “Single-CDS mRNA” but this does not annotation of features that arise from processing of the transcript, such as sig_peptide or mat_peptide features. To add these, you will need to prepare the file yourself with the template below.
{organism} is a species-rank organism present in the database. Search available taxa at ENA Search.
{organelle} with the value taken from the INSDC controlled vocabulary. The organelle should also be added to the DE line. Remove this entirely if the sequence is of nuclear origin.
{identifier} is a form of sample or organism identification. You must use at least one from the below list and fill in the {ID} field with it. Other qualifiers are available in WebFeat.
Isolate: any sample or isolate name
Strain: the strain of the sequenced organism
Clone: the clone name of the sequence
Note: the breed of a domesticate
Cultivar: a cultivated variety of a plant or fungus
Variety: a natural variety of a plant or fungus
Dev_stage: the developmental stage of the organism
Tissue_type: the tissue type sampled
Cell_type: the type sampled
Sex: the sex of the animal
Mating_type: the mating type of the prokaryote/lower eukaryote
{a to l} are the feature coordinates. Incompleteness of any features (CDS, sig_peptide, mat_peptide) should be described using partiality symbols, e.g. <1..250 or 2917..>2960
{gene} is the gene symbol, putative or official. It is optional, but highly recommended. If you remove this line, also remove it from the DE line.
{precursor} is the protein precursor name, and is mandatory
{reading frame} should be 1 where the start codon is present, otherwise 1, 2 or 3 depending on the reading frame of the 5’ partial coding sequence
{mat_peptide N} is the name of the Nth mature peptide
{partial} - delete if coding region is complete, otherwise just remove the curly brackets
{sequence} should be the sequence in IUPAC nucleotide characters, as described above
Precursor mRNA:
ID XXX; XXX; linear; XXX; XXX; XXX; XXX.
XX
AC XXX;
XX
DE {organism} {partial} mRNA for {precursor} ({gene} gene), {identifier} {ID}
XX
FH Key Location/Qualifiers
FH
FT source 1..{sequence length}
FT /organism="{organism}"
FT /organelle="{organelle}"
FT /mol_type="genomic DNA"
FT /{identifier}="{ID}"
FT CDS a..b
FT /codon_start={reading frame}
FT /gene="{gene}"
FT /product="{precursor}"
FT sig_peptide e..f
FT /gene="{gene}"
FT mat_peptide g..h
FT /gene="{gene}"
FT /product="{mat_peptide 1}"
FT mat_peptide i..j
FT /gene="{gene}"
FT /product="{mat_peptide 2}"
FT mat_peptide k..l
FT /gene="{gene}"
FT /product="{mat_peptide 3}"
SQ
{sequence}
//
Synthetic Construct
{other DNA or RNA} refers to the molecule type, and also appears in the ID line. Use other DNA or other RNA as the value as appropriate
Note that the /focus source has organism name synthetic construct. This is the standard taxon for this type of sequence. If you have named a vector sequence specifically, e.g. Cloning vector ABC, you may use this in place and a taxon will be added to the database according to NCBI Taxonomy’s operating procedures
{organism} is a species-rank organism present in the database referring to the originating organism. Search available taxa at ENA Search.
{a to h} are the feature coordinates. Incompleteness of any features (except source) should be described using partiality symbols, e.g. <1..250 or 2917..>2960
{gene} is the gene symbol, putative or official. It is optional, but highly recommended. If you remove this line, also remove it from the DE line.
{product} is the protein/product name. This is mandatory for CDS.
{table} is the translation table under which the coding region is translated. Learn more at the Translation Tables page
{short note 1} should provide additional information on the promoter, e.g. Eu and SRalpha promoter
{short note 2} should provide additional information for the CDS, e.g. preferential codon usage changed for expression in {organism 2}
{short note 3} should support the miscellaneous feature, e.g. additional stop codon
{sequence} should be the sequence in IUPAC nucleotide characters, as described above
Synthetic construct:
ID XXX; XXX; linear; XXX; XXX; XXX; XXX.
XX
AC XXX;
XX
DE Synthetic construct for {organism} {gene} gene for {product}
XX
FH Key Location/Qualifiers
FH
FT source 1..{sequence length}
FT /organism="synthetic construct"
FT /mol_type="{other DNA or RNA}"
FT /focus
FT source a..b
FT /organism="{organism}"
FT /mol_type="other DNA"
FT promoter c..d
FT /note="{short note 1}"
FT CDS e..f
FT /transl_table={table}
FT /gene="{gene}"
FT /product="{product}"
FT /note="{short note 2}"
FT misc_feature g..h
FT /note="{short note 3}"
XX
SQ
{sequence}
//