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<h2 id="eukaryotic-genome-submission-exa">Eukaryotic Genome Submission Examples</h2>
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<h4 id="fig1">Figure 1: Sample FASTA-formatted sequence</h4>
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<pre><code>>HTE831 [organism=Drosophila yakuba] [strain=HTE831]
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tagagcaaaaaatagacattttaatggcgctaatcatacaaggaaggaataataacactg
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acatggatacatccacttaatctacatttgcttattcctatcttgactatatctatatcc
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[etc.]
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</code></pre>
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<h4 id="fig2">Figure 2: Feature table format</h4>
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<p>This mock example of a feature table file includes:</p>
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<ul>
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<li>Genes whose 5' and 3' UTRs are known (eg, <a href="#Ngs_17131">Ngs_17131</a> and <a href="#Ngs_3038">Ngs_3038</a> ).</li>
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<li>Gene with no UTR information ( <a href="#Ngs_2945">Ngs_2945</a> ).</li>
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<li>Features on the complementary strand (eg, <a href="#Ngs_3038">Ngs_3038</a> and <a href="#Ngs_11232">Ngs_11232</a> ).</li>
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<li>Pseudogene ( <a href="#Ngs_10112">Ngs_10112</a> ).</li>
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<li>Gene that is alternatively spliced ( <a href="#Ngs_3038">Ngs_3038</a> ).</li>
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<li>Gene for a bifunctional protein ( <a href="#Ngs_2945">Ngs_2945</a> ).</li>
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<li>RNAs (eg, <a href="#Ngs_10111">Ngs_10111</a> and <a href="#Ngs_11232">Ngs_11232</a> )</li>
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<li>Transposable elements and AT-rich sequences ( <a href="#repeat_region">repeat_region features</a> )</li>
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<li>Features that are partial (eg, <a href="#Ngs_2945">Ngs_2945</a> ).</li>
|
|
<li>A <a href="#misc_feature">misc_feature</a> .</li>
|
|
<li>Experiment and inference evidence qualifiers (CDS of <a href="#Ngs_17131">Ngs_17131</a> and <a href="#Ngs_2945">Ngs_2945</a> )</li>
|
|
</ul>
|
|
|
|
|
|
<p>Note that the relative order of the features in the file does not matter, and that the misc_feature and repeat_region features do not have a corresponding gene feature, and so do not have a locus_tag.</p>
|
|
|
|
|
|
<p>See the flatfile view of this file in <a href="#fig3">Figure 3</a> .</p>
|
|
|
|
|
|
<pre><code>>Feature HTE831
|
|
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|Ngs_mrna17131
|
|
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|Ngs_mrna17131
|
|
inference similar to RNA sequence, mRNA:INSD:AY123455.2
|
|
102664 100872 gene
|
|
locus_tag Ngs_3038
|
|
gene TpnI
|
|
102664 102502 mRNA
|
|
102400 102234
|
|
102168 100872
|
|
product troponin isoform B
|
|
protein_id gnl|ncbi|Ngs_3038B
|
|
transcript_id gnl|ncbi|Ngs_mrna3038B
|
|
note transcript variant B; alternatively spliced
|
|
102655 102234 mRNA
|
|
102168 100872
|
|
product troponin isoform A
|
|
protein_id gnl|ncbi|Ngs_3038A
|
|
transcript_id gnl|ncbi|Ngs_mrna3038A
|
|
note transcript variant A; alternatively spliced
|
|
102503 102502 CDS
|
|
102400 102234
|
|
102168 101261
|
|
product troponin isoform B
|
|
protein_id gnl|ncbi|Ngs_3038B
|
|
transcript_id gnl|ncbi|Ngs_mrna3038B
|
|
note encoded by transcript variant B; alternatively spliced
|
|
102492 102234 CDS
|
|
102168 101261
|
|
product troponin isoform A
|
|
protein_id gnl|ncbi|Ngs_3038A
|
|
transcript_id gnl|ncbi|Ngs_mrna3038A
|
|
note encoded by transcript variant A; alternatively spliced
|
|
<112616 >115107 gene
|
|
locus_tag Ngs_2945
|
|
<112616 112646 mRNA
|
|
112703 113463
|
|
113584 113762
|
|
113821 114249
|
|
114302 114464
|
|
114804 114902
|
|
114964 >115107
|
|
product bifunctional methylenetetrahydrofolate dehydrogenase (NADP+)/methenyltetrahydrofolate cyclohydrolase
|
|
protein_id gnl|ncbi|Ngs_2945
|
|
transcript_id gnl|ncbi|Ngs_mrna2945
|
|
112616 112646 CDS
|
|
112703 113463
|
|
113584 113762
|
|
113821 114249
|
|
114302 114464
|
|
114804 114902
|
|
114964 115107
|
|
product bifunctional methylenetetrahydrofolate dehydrogenase (NADP+)/methenyltetrahydrofolate cyclohydrolase
|
|
EC_number 1.5.1.5
|
|
EC_number 3.5.4.9
|
|
note bifunctional
|
|
experiment Western blot
|
|
protein_id gnl|ncbi|Ngs_2945
|
|
transcript_id gnl|ncbi|Ngs_mrna2945
|
|
101 180 gene
|
|
locus_tag Ngs_10111
|
|
gene trnL
|
|
101 180 tRNA
|
|
product Leu
|
|
45111 45190 gene
|
|
locus_tag Ngs_10112
|
|
pseudo
|
|
45111 45190 tRNA
|
|
product Xxx
|
|
2103 400 gene
|
|
locus_tag Ngs_11232
|
|
2103 400 rRNA
|
|
product 18S ribosomal RNA
|
|
60101 60567 misc_feature
|
|
note similar to ABC transporters
|
|
43027 43136 repeat_region
|
|
mobile_element retrotransposon:mini-me-Dpse-like{}4773
|
|
56408 56558 repeat_region
|
|
mobile_element retrotransposon:INE-1{}4674
|
|
62077 62147 repeat_region
|
|
mobile_element retrotransposon:P-T-Damb-like{}4769
|
|
63111 63154 repeat_region
|
|
note at-rich
|
|
</code></pre>
|
|
|
|
|
|
<h4 id="id378887">Figure 3: GenBank flatfile</h4>
|
|
|
|
|
|
<p>This is part of the flatfile view of the .sqn file made from the .fsa file ( <a href="#fig1">Fig. 1</a> ) and .tbl file ( <a href="#fig2">Fig. 2</a> ).</p>
|
|
|
|
|
|
<pre><code>source 1..116100
|
|
/organism="Drosophila yakuba"
|
|
/mol_type="genomic DNA"
|
|
/strain="HTE831"
|
|
/db_xref="taxon:7245"
|
|
gene 101..180
|
|
/gene="trnL"
|
|
/locus_tag="Ngs_10111"
|
|
tRNA 101..180
|
|
/gene="trnL"
|
|
/locus_tag="Ngs_10111"
|
|
/product="tRNA-Leu"
|
|
gene complement(400..2103)
|
|
/locus_tag="Ngs_11232"
|
|
rRNA complement(400..2103)
|
|
/locus_tag="Ngs_11232"
|
|
/product="18S ribosomal RNA"
|
|
repeat_region 43027..43136
|
|
/mobile_element="retrotransposon:mini-me-Dpse-like{}4773"
|
|
gene 45111..45190
|
|
/locus_tag="Ngs_10112"
|
|
/pseudo
|
|
tRNA 45111..45190
|
|
/locus_tag="Ngs_10112"
|
|
/product="tRNA-OTHER"
|
|
/pseudo
|
|
repeat_region 56408..56558
|
|
/mobile_element="retrotransposon:INE-1{}4674"
|
|
misc_feature 60101..60567
|
|
/note="similar to ABC transporters"
|
|
repeat_region 62077..62147
|
|
/mobile_element="retrotransposon:P-T-Damb-like{}4769"
|
|
repeat_region 63111..63154
|
|
/note="at-rich"
|
|
gene 63574..87173
|
|
/locus_tag="Ngs_17131"
|
|
mRNA join(63574..63907,75690..75730,84396..85536,85598..85773,
|
|
85836..86109,86173..86467,86555..86670,86731..87173)
|
|
/locus_tag="Ngs_17131"
|
|
/product="hypothetical protein"
|
|
CDS join(84402..85536,85598..85773,85836..86109,86173..86467,
|
|
86555..86670,86731..86882)
|
|
/locus_tag="Ngs_17131"
|
|
/inference="similar to RNA sequence, mRNA:INSD:AY123455.2"
|
|
/codon_start=1
|
|
/product="hypothetical protein"
|
|
/translation="MQSTQSKSDRSSMHRGPLLLCAVMVVLVTLPEQINARMAFEKLT
|
|
DFDFPGNTYYSVKNLSLYECQGWCREEADCQAAAFSFVVNPLSPSQETHCQLQNDSSA
|
|
ANPSAAPQRSANMYYMIKLQLRSENVCHRPWSFERVPNKVIRGLDNALIYTSTKEACL
|
|
SACLNERRFVCRSVEYDYNNMKCVLSDSDRRSSGQFVQLVDAQGTDYFENLCLKPAQA
|
|
CKNNRSFGNSQKMGVSEEKVAQYVGLHYYTDKELQVTSESACRLACEIESEFLCRSFL
|
|
YLGQPQGSQYNCRLYHLDHKTLPDGPSTYLNHERPLIDHGEPIGQYFENQCEKAAGLG
|
|
AGSPPGTLDKIDTLPVSLDTIEDPNLTNLTRNDVNCDKTGTCYDVSVHCKDTRIAVQV
|
|
RTNKPFNGRIYALGRSETCNIDVINSDAFRLDLTMAGQDCNTQSVTGVYSNTVVLQHH
|
|
SVVMTKADKIYKVKCTYDMSSKNITFGMMPIRDPEMIHINSSPEAPPPRIRILDTRQR
|
|
EVETVRIGDRLNFRIEIPEDTPYGIFARSCVAMAKDARTSFKIIDDDGCPTDPTIFPG
|
|
FTADGNALQSTYEAFRFTESYGVIFQCNVKYCLGPCEPAVCEWNMDSFESLGRRRRRS
|
|
IESNDTKSEDDMNISQEILVLDFGDEKREFFKADPSTDFAKDKTVTIIEPCPTKTSVL
|
|
ALAVTCALMILLYISTLFCYYMKKWMQPHKIVA"
|
|
gene complement(100872..102664)
|
|
/gene="TpnI"
|
|
/locus_tag="Ngs_3038"
|
|
mRNA complement(join(100872..102168,102234..102400,
|
|
102502..102664))
|
|
/gene="TpnI"
|
|
/locus_tag="Ngs_3038"
|
|
/product="troponin isoform B"
|
|
/note="transcript variant B; alternatively spliced"
|
|
mRNA complement(join(100872..102168,102234..102655))
|
|
/gene="TpnI"
|
|
/locus_tag="Ngs_3038"
|
|
/product="troponin isoform A"
|
|
/note="transcript variant A; alternatively spliced"
|
|
CDS complement(join(101261..102168,102234..102400,
|
|
102502..102503))
|
|
/gene="TpnI"
|
|
/locus_tag="Ngs_3038"
|
|
/note="encoded by transcript variant B; alternatively spliced"
|
|
/codon_start=1
|
|
/product="troponin isoform B"
|
|
/translation="MDSSQSRKNGFLLHLPLETKRNPSNPNTPLSNLLNLTDFHYLLA
|
|
SNVCRKAKRELLAVLIVTSYAGHDALRSAHRQAIPQSKLEEMGLRRVFLLAALPSREH
|
|
FISQDQLASEQNRFGDLLQGNFIEDYRNLSYKHVMGLKWVSEECKKQAKFIIKLDDDI
|
|
IYDVFHLRRYLETLEVREPGLATSSTLLSGYVLDAKPPIRLRANKWYVSKKEYPQALY
|
|
PAYLSGWLYVTNVPTAERIVAEAERMSFFWIDDTWLTGVVRTRLGIPLERHNDWFSAN
|
|
AEFIDCCVRDLKKHNYECEYSVGPNGGDDRLLVEFLHNVEKCYFDECVKRPVGKSLKE
|
|
TCLAAAKSRPPKHGFPEIKALRLR"
|
|
CDS complement(join(101261..102168,102234..102492))
|
|
/gene="TpnI"
|
|
/locus_tag="Ngs_3038"
|
|
/note="encoded by transcript variant A; alternatively spliced"
|
|
/codon_start=1
|
|
/product="troponin isoform A"
|
|
/translation="MRMRGRRLLPIILSLLLIVLLSLCYFSNHLRDSSQSRKNGFLLH
|
|
LPLETKRNPSNPNTPLSNLLNLTDFHYLLASNVCRKAKRELLAVLIVTSYAGHDALRS
|
|
AHRQAIPQSKLEEMGLRRVFLLAALPSREHFISQDQLASEQNRFGDLLQGNFIEDYRN
|
|
LSYKHVMGLKWVSEECKKQAKFIIKLDDDIIYDVFHLRRYLETLEVREPGLATSSTLL
|
|
SGYVLDAKPPIRLRANKWYVSKKEYPQALYPAYLSGWLYVTNVPTAERIVAEAERMSF
|
|
FWIDDTWLTGVVRTRLGIPLERHNDWFSANAEFIDCCVRDLKKHNYECEYSVGPNGGD
|
|
DRLLVEFLHNVEKCYFDECVKRPVGKSLKETCLAAAKSRPPKHGFPEIKALRLR"
|
|
gene <112616..>115107
|
|
/locus_tag="Ngs_2945"
|
|
mRNA join(<112616..112646,112703..113463,113584..113762,
|
|
113821..114249,114302..114464,114804..114902,
|
|
114964..>115107)
|
|
/locus_tag="Ngs_2945"
|
|
/product="bifunctional methylenetetrahydrofolate dehydrogenase (NADP+)/methenyltetrahydrofolate cyclohydrolase"
|
|
CDS join(112616..112646,112703..113463,113584..113762,
|
|
113821..114249,114302..114464,114804..114902,
|
|
114964..115107)
|
|
/locus_tag="Ngs_2945"
|
|
/EC_number="3.5.4.9"
|
|
/EC_number="1.5.1.5"
|
|
/experiment="Western blot"
|
|
/codon_start=1
|
|
/product="bifunctional methylenetetrahydrofolate dehydrogenase (NADP+)/methenyltetrahydrofolate cyclohydrolase"
|
|
/translation="MESITFGVLTISDTCWQEPEKDTSGPILRQLIGETFANTQVIGN
|
|
IVPDEKDIIQQELRKWIDREELRVILTTGGTGFAPRDVTPEATRQLLEKECPQLSMYI
|
|
TLESIKQTQYAALSRGLCGIAGNTLILNLPGSEKAVKECFQTISALLPHAVHLIGDDV
|
|
SLVRKTHAEVQGSAQKSHICPHKTGTGTDSDRNSPYPMLPVQEVLSIIFNTVQKTANL
|
|
NKILLEMNAPVNIPPFRASIKDGYAMKSTGFSGTKRVLGCIAAGDSPNSLPLAEDECY
|
|
KINTGAPLPLEADCVVQVEDTKLLQLDKNGQESLVDILVEPQAGLDVRPVGYDLSTND
|
|
RIFPALDPSPVVVKSLLASVGNRLILSKPKVAIVSTGSELCSPRNQLTPGKIFDSNTT
|
|
MLTELLVYFGFNCMHTCVLSDSFQRTKESLLELFEVVDFVICSGGVSMGDKDFVKSVL
|
|
EDLQFRIHCGRVNIKPGKPMTFASRKDKYFFGLPGNPVSAFVTFHLFALPAIRFAAGW
|
|
DRCKCSLSVLNVKLLNDFSLDSRPEFVRASVISKSGELYASVNGNQISSRLQSIVGAD
|
|
VLINLPARTSDRPLAKAGEIFPASVLRFDFISKYE"
|
|
ORIGIN
|
|
1 tagagcaaaa aatagacatt ttaatggcgc taatcataca aggaaggaat aataacactg
|
|
61 acatggatac atccacttaa tctacatttg cttattccta tcttgactat atctatatcc
|
|
[etc.]
|
|
</code></pre>
|
|
</div>
|
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|
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