.. _embl_code: .. note:: This article is copy-pasted from `ENA user manual ` The ENA flat-file format ======================== 3.3 Structure of an Entry The entries in the database are structured so as to be usable by human readers as well as by computer programs. The explanations, descriptions, classifications and other comments are in ordinary English, and the symbols and formatting employed for the base sequences themselves have been chosen for readability. Wherever possible, symbols familiar to molecular biologists have been used. At the same time, the structure is systematic enough to allow computer programs easily to read, identify, and manipulate the various types of data included. Each entry in the database is composed of lines. Different types of lines, each with its own format, are used to record the various types of data which make up the entry. In general, fixed format items have been kept to a minimum, and a more syntax-oriented structure adopted for the lines. The two exceptions to this are the sequence data lines and the feature table lines, for which a fixed format was felt to offer significant advantages to the user. Users who write programs to process the database entries should not make any assumptions about the column placement of items on lines other than these two: all other line types are free-format. Note that each line begins with a two-character line code, which indicates the type of information contained in the line. Example of an entry:: ID X56734; SV 1; linear; mRNA; STD; PLN; 1859 BP. XX AC X56734; S46826; XX DT 12-SEP-1991 (Rel. 29, Created) DT 25-NOV-2005 (Rel. 85, Last updated, Version 11) XX DE Trifolium repens mRNA for non-cyanogenic beta-glucosidase XX KW beta-glucosidase. XX OS Trifolium repens (white clover) OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; OC Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; OC fabids; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium. XX RN [5] RP 1-1859 RX DOI; 10.1007/BF00039495. RX PUBMED; 1907511. RA Oxtoby E., Dunn M.A., Pancoro A., Hughes M.A.; RT "Nucleotide and derived amino acid sequence of the cyanogenic RT beta-glucosidase (linamarase) from white clover (Trifolium repens L.)"; RL Plant Mol. Biol. 17(2):209-219(1991). XX RN [6] RP 1-1859 RA Hughes M.A.; RT ; RL Submitted (19-NOV-1990) to the INSDC. RL Hughes M.A., University of Newcastle Upon Tyne, Medical School, Newcastle RL Upon Tyne, NE2 4HH, UK XX DR EuropePMC; PMC99098; 11752244. XX FH Key Location/Qualifiers FH FT source 1..1859 FT /organism="Trifolium repens" FT /mol_type="mRNA" FT /clone_lib="lambda gt10" FT /clone="TRE361" FT /tissue_type="leaves" FT /db_xref="taxon:3899" FT mRNA 1..1859 FT /experiment="experimental evidence, no additional details FT recorded" FT CDS 14..1495 FT /product="beta-glucosidase" FT /EC_number="3.2.1.21" FT /note="non-cyanogenic" FT /db_xref="GOA:P26204" FT /db_xref="InterPro:IPR001360" FT /db_xref="InterPro:IPR013781" FT /db_xref="InterPro:IPR017853" FT /db_xref="InterPro:IPR018120" FT /db_xref="UniProtKB/Swiss-Prot:P26204" FT /protein_id="CAA40058.1" FT /translation="MDFIVAIFALFVISSFTITSTNAVEASTLLDIGNLSRSSFPRGFI FT FGAGSSAYQFEGAVNEGGRGPSIWDTFTHKYPEKIRDGSNADITVDQYHRYKEDVGIMK FT DQNMDSYRFSISWPRILPKGKLSGGINHEGIKYYNNLINELLANGIQPFVTLFHWDLPQ FT VLEDEYGGFLNSGVINDFRDYTDLCFKEFGDRVRYWSTLNEPWVFSNSGYALGTNAPGR FT CSASNVAKPGDSGTGPYIVTHNQILAHAEAVHVYKTKYQAYQKGKIGITLVSNWLMPLD FT DNSIPDIKAAERSLDFQFGLFMEQLTTGDYSKSMRRIVKNRLPKFSKFESSLVNGSFDF FT IGINYYSSSYISNAPSHGNAKPSYSTNPMTNISFEKHGIPLGPRAASIWIYVYPYMFIQ FT EDFEIFCYILKINITILQFSITENGMNEFNDATLPVEEALLNTYRIDYYYRHLYYIRSA FT IRAGSNVKGFYAWSFLDCNEWFAGFTVRFGLNFVD" XX SQ Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other; aaacaaacca aatatggatt ttattgtagc catatttgct ctgtttgtta ttagctcatt 60 cacaattact tccacaaatg cagttgaagc ttctactctt cttgacatag gtaacctgag 120 tcggagcagt tttcctcgtg gcttcatctt tggtgctgga tcttcagcat accaatttga 180 aggtgcagta aacgaaggcg gtagaggacc aagtatttgg gataccttca cccataaata 240 tccagaaaaa ataagggatg gaagcaatgc agacatcacg gttgaccaat atcaccgcta 300 caaggaagat gttgggatta tgaaggatca aaatatggat tcgtatagat tctcaatctc 360 ttggccaaga atactcccaa agggaaagtt gagcggaggc ataaatcacg aaggaatcaa 420 atattacaac aaccttatca acgaactatt ggctaacggt atacaaccat ttgtaactct 480 ttttcattgg gatcttcccc aagtcttaga agatgagtat ggtggtttct taaactccgg 540 tgtaataaat gattttcgag actatacgga tctttgcttc aaggaatttg gagatagagt 600 gaggtattgg agtactctaa atgagccatg ggtgtttagc aattctggat atgcactagg 660 aacaaatgca ccaggtcgat gttcggcctc caacgtggcc aagcctggtg attctggaac 720 aggaccttat atagttacac acaatcaaat tcttgctcat gcagaagctg tacatgtgta 780 taagactaaa taccaggcat atcaaaaggg aaagataggc ataacgttgg tatctaactg 840 gttaatgcca cttgatgata atagcatacc agatataaag gctgccgaga gatcacttga 900 cttccaattt ggattgttta tggaacaatt aacaacagga gattattcta agagcatgcg 960 gcgtatagtt aaaaaccgat tacctaagtt ctcaaaattc gaatcaagcc tagtgaatgg 1020 ttcatttgat tttattggta taaactatta ctcttctagt tatattagca atgccccttc 1080 acatggcaat gccaaaccca gttactcaac aaatcctatg accaatattt catttgaaaa 1140 acatgggata cccttaggtc caagggctgc ttcaatttgg atatatgttt atccatatat 1200 gtttatccaa gaggacttcg agatcttttg ttacatatta aaaataaata taacaatcct 1260 gcaattttca atcactgaaa atggtatgaa tgaattcaac gatgcaacac ttccagtaga 1320 agaagctctt ttgaatactt acagaattga ttactattac cgtcacttat actacattcg 1380 ttctgcaatc agggctggct caaatgtgaa gggtttttac gcatggtcat ttttggactg 1440 taatgaatgg tttgcaggct ttactgttcg ttttggatta aactttgtag attagaaaga 1500 tggattaaaa aggtacccta agctttctgc ccaatggtac aagaactttc tcaaaagaaa 1560 ctagctagta ttattaaaag aactttgtag tagattacag tacatcgttt gaagttgagt 1620 tggtgcacct aattaaataa aagaggttac tcttaacata tttttaggcc attcgttgtg 1680 aagttgttag gctgttattt ctattatact atgttgtagt aataagtgca ttgttgtacc 1740 agaagctatg atcataacta taggttgatc cttcatgtat cagtttgatg ttgagaatac 1800 tttgaattaa aagtcttttt ttattttttt aaaaaaaaaa aaaaaaaaaa aaaaaaaaa 1859 // The currently used line types, along with their respective line codes, are listed below: ==================================== ================================= ID - identification (begins each entry; 1 per entry) AC - accession number (>=1 per entry) PR - project identifier (0 or 1 per entry) DT - date (2 per entry) DE - description (>=1 per entry) KW - keyword (>=1 per entry) OS - organism species (>=1 per entry) OC - organism classification (>=1 per entry) OG - organelle (0 or 1 per entry) RN - reference number (>=1 per entry) RC - reference comment (>=0 per entry) RP - reference positions (>=1 per entry) RX - reference cross-reference (>=0 per entry) RG - reference group (>=0 per entry) RA - reference author(s) (>=0 per entry) RT - reference title (>=1 per entry) RL - reference location (>=1 per entry) DR - database cross-reference (>=0 per entry) CC - comments or notes (>=0 per entry) AH - assembly header (0 or 1 per entry) AS - assembly information (0 or >=1 per entry) FH - feature table header (2 per entry) FT - feature table data (>=2 per entry) XX - spacer line (many per entry) SQ - sequence header (1 per entry) CO - contig/construct line (0 or >=1 per entry) bb - (blanks) sequence data (>=1 per entry) // - termination line (ends each entry; 1 per entry) ==================================== ================================= Note that some entries will not contain all of the line types, and some line types occur many times in a single entry. As indicated, each entry begins with an identification line (ID) and ends with a terminator line (//). The various line types appear in entries in the order in which they are listed above (except for XX lines which may appear anywhere between the ID and SQ lines).