Eukaryotic Genome Submission Examples
Figure 1: Sample FASTA-formatted sequence
>HTE831 [organism=Drosophila yakuba] [strain=HTE831] tagagcaaaaaatagacattttaatggcgctaatcatacaaggaaggaataataacactg acatggatacatccacttaatctacatttgcttattcctatcttgactatatctatatcc [etc.]
Figure 2: Feature table format
This mock example of a feature table file includes:
- Genes whose 5' and 3' UTRs are known (eg, Ngs_17131 and Ngs_3038).
- Gene with no UTR information (Ngs_2945).
- Features on the complementary strand (eg, Ngs_3038 and Ngs_11232).
- Pseudogene (Ngs_10112).
- Gene that is alternatively spliced (Ngs_3038).
- Gene for a bifunctional protein (Ngs_2945).
- RNAs (eg, Ngs_10111 and Ngs_11232)
- Transposable elements and AT-rich sequences (repeat_region features)
- Features that are partial (eg, Ngs_2945).
- A misc_feature.
- Experiment and inference evidence qualifiers (CDS of Ngs_17131 and Ngs_2945)
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.
See the flatfile view of this file in Figure 3.
>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
Figure 3: GenBank flatfile
This is part of the flatfile view of the .sqn file made from the .fsa file (Fig. 1) and .tbl file (Fig. 2).
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.]
Revised October 16, 2007