Sample GenBank Record / Visual abstracts made easy with Mind the Graph

This page presents an annotated sample GenBank record (accession
number U49845) in its GenBank Flat File format. You can check the
corresponding alive record for U49845, and seeexamples of other records the show a range of
biological features.

SITE       SCU49845     5028 bp    DNA             PLN       21-JUN-1999
DEFINITION  Saccharomyces cerevisiae TCP1-beta gene, partial cds, and Axl2p
            (AXL2) plus Rev7p (REV7) genes, complete cds.ACCESSION   U49845
VERSION     U49845.1  GI:1293613
KEYWORDS    .
SOURCE      Saccharomyces cerevisiae (baker's yeast)
  ORGANISM  Saccharomyces cerevisiae            Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes;            Saccharomycetales; Saccharomycetaceae; Saccharomyces.REFERENCE   1  (bases 1 the 5028)
  AUTHORS   Torpey,L.E., Gibbs,P.E., Nelson,J. press Lawrence,C.W.
  TITLE     Replicating and chain of REV7, a gene whose function is required for            DNA damage-induced mutagenesis include Saccharomyces cerevisiae  JOURNAL   Yeast 10 (11), 1503-1509 (1994)
  PUBMED    7871890
REFERENCE   2  (bases 1 to 5028)
  ARTICLES   Roemer,T., Madden,K., Chang,J. and Snyder,M.
  TITLE     Selection of pivotal growth sites in sauerteig requirements Axl2p, a novel            plasma membrane glycoprotein  JOURNAL   Genes Dev. 10 (7), 777-793 (1996)
  PUBMED    8846915
REFERENCE   3  (bases 1 up 5028)
  CONTRIBUTORS   Roemer,T.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-FEB-1996) Terry Roemer, Biology, Yale University, New            Haven, CT, UNITESSPECIFIC             Location/Qualifiers
     source          1..5028
                     /organism="Saccharomyces cerevisiae"
                     /db_xref="taxon:4932"
                     /chromosome="IX"
                     /map="9"
     CDS             <1..206
                     /codon_start=3
                     /product="TCP1-beta"
                     /protein_id="AAA98665.1"
                     /db_xref="HI:1293614"
                     /translation="SSIYNGISTSGLDLNNGTIADMRQLGIVESYKLKRAVVSSASEA
                     AEVLLRVDNIIRARPRTANRQHM"
     gene            687..3158
                     /gene="AXL2"
     CDS             687..3158
                     /gene="AXL2"
                     /note="plasma membrane glycoprotein"
                     /codon_start=1
                     /function="required for axial blossoming pattern of S.                     cerevisiae"
                     /product="Axl2p"
                     /protein_id="AAA98666.1"
                     /db_xref="GI:1293615"
                     /translation="MTQLQISLLLTATISLLHLVVATPYEAYPIGKQYPPVARVNESF
                     TFQISNDTYKSSVDKTAQITYNCFDLPSWLSFDSSSRTFSGEPSSDLLSDANTTLYFN                     VILEGTDSADSTSLNNTYQFVVTNRPSISLSSDFNLLALLKNYGYTNGKNALKLDPNE                     VFNVTFDRSMFTNEESIVSYYGRSQLYNAPLPNWLFFDSGELKFTGTAPVINSAIAPE                     TSYSFVIIATDIEGFSAVEVEFELVIGAHQLTTSIQNSLIINVTDTGNVSYDLPLNYV                     YLDDDPISSDKLGSINLLDAPDWVALDNATISGSVPDELLGKNSNPANFSVSIYDTYG                     DVIYFNFEVVSTTDLFAISSLPNINATRGEWFSYYFLPSQFTDYVNTNVSLEFTNSSQ                     DHDWVKFQSSNLTLAGEVPKNFDKLSLGLKANQGSQSQELYFNIIGMDSKITHSNHSA                     NATSTRSSHHSTSTSSYTSSTYTAKISSTSAAATSSAPAALPAANKTSSHNKKAVAIA                     CGVAIPLGVILVALICFLIFWRRRRENPDDENLPHAISGPDLNNPANKPNQENATPLN                     NPFDDDASSYDDTSIARRLAALNTLKLDNHSATESDISSVDEKRDSLSGMNTYNDQFQ                     SQSKEELLAKPPVQPPESPFFDPQNRSSSVYMDSEPAVNKSWRYTGNLSPVSDIVRDS                     YGSQKTVDTEKLFDLEAPEKEKRTSRDVTMSSLDPWNSNISPSPVRKSVTPSPYNVTK                     HRNRHLQNIQDSQSGKNGITPTTMSTSSSDDFVPVKDGENFCWVHSMEPDRRPSKKRL                     VDFSNKSNVNVGQVKDIHGRIPEML"
     gene            complement(3300..4037)
                     /gene="REV7"
     CDS             complement(3300..4037)
                     /gene="REV7"
                     /codon_start=1
                     /product="Rev7p"
                     /protein_id="AAA98667.1"
                     /db_xref="GUEST:1293616"
                     /translation="MNRWVEKWLRVYLKCYINLILFYRNVYPPQSFDYTTYQSFNLPQ
                     FVPINRHPALIDYIEELILDVLSKLTHVYRFSICIINKKNDLCIEKYVLDFSELQHVD                     KDDQIITETEVFDEFRSSLNSLIMHLEKLPKVNDDTITFEAVINAIELELGHKLDRNR                     RVDSLEEKAEIERDSNWVKCQEDENLPDNNGFQPPKIKLTSLVGSDVGPLIIHQFSEK                     LISGDDKILNGVYSQYEEGESIFGSLF"
ORIGIN
        1 gatcctccat atacaacggt atctccacct caggtttaga tctcaacaac ggaaccattg       61 ccgacatgag acagttaggt atcgtcgaga gttacaagct aaaacgagca gtagtcagct      121 ctgcatctga agccgctgaa gttctactaa gggtggataa catcatccgt gcaagaccaa      181 gaaccgccaa tagacaacat atgtaacata tttaggatat acctcgaaaa taataaaccg      241 ccacactgtc attattataa ttagaaacag aacgcaaaaa ttatccacta tataattcaa      301 agacgcgaaa aaaaaagaac aacgcgtcat agaacttttg gcaattcgcg tcacaaataa      361 attttggcaa cttatgtttc ctcttcgagc agtactcgag ccctgtctca agaatgtaat      421 aatacccatc gtaggtatgg ttaaagatag catctccaca acctcaaagc tccttgccga      481 gagtcgccct cctttgtcga gtaattttca cttttcatat gagaacttat tttcttattc      541 tttactctca catcctgtag tgattgacac tgcaacagcc accatcacta gaagaacaga      601 acaattactt aatagaaaaa ttatatcttc ctcgaaacga tttcctgctt ccaacatcta      661 cgtatatcaa gaagcattca cttaccatga cacagcttca gatttcatta ttgctgacag      721 ctactatatc actactccat ctagtagtgg ccacgcccta tgaggcatat cctatcggaa      781 aacaataccc cccagtggca agagtcaatg aatcgtttac atttcaaatt tccaatgata      841 cctataaatc gtctgtagac aagacagctc aaataacata caattgcttc gacttaccga      901 gctggctttc gtttgactct agttctagaa cgttctcagg tgaaccttct tctgacttac      961 tatctgatgc gaacaccacg ttgtatttca atgtaatact cgagggtacg gactctgccg     1021 acagcacgtc tttgaacaat acataccaat ttgttgttac aaaccgtcca tccatctcgc     1081 tatcgtcaga tttcaatcta ttggcgttgt taaaaaacta tggttatact aacggcaaaa     1141 acgctctgaa actagatcct aatgaagtct tcaacgtgac ttttgaccgt tcaatgttca     1201 ctaacgaaga atccattgtg tcgtattacg gacgttctca gttgtataat gcgccgttac     1261 ccaattggct gttcttcgat tctggcgagt tgaagtttac tgggacggca ccggtgataa     1321 actcggcgat tgctccagaa acaagctaca gttttgtcat catcgctaca gacattgaag     1381 gattttctgc cgttgaggta gaattcgaat tagtcatcgg ggctcaccag ttaactacct     1441 ctattcaaaa tagtttgata atcaacgtta ctgacacagg taacgtttca tatgacttac     1501 ctctaaacta tgtttatctc gatgacgatc ctatttcttc tgataaattg ggttctataa     1561 acttattgga tgctccagac tgggtggcat tagataatgc taccatttcc gggtctgtcc     1621 cagatgaatt actcggtaag aactccaatc ctgccaattt ttctgtgtcc atttatgata     1681 cttatggtga tgtgatttat ttcaacttcg aagttgtctc cacaacggat ttgtttgcca     1741 ttagttctct tcccaatatt aacgctacaa ggggtgaatg gttctcctac tattttttgc     1801 cttctcagtt tacagactac gtgaatacaa acgtttcatt agagtttact aattcaagcc     1861 aagaccatga ctgggtgaaa ttccaatcat ctaatttaac attagctgga gaagtgccca     1921 agaatttcga caagctttca ttaggtttga aagcgaacca aggttcacaa tctcaagagc     1981 tatattttaa catcattggc atggattcaa agataactca ctcaaaccac agtgcgaatg     2041 caacgtccac aagaagttct caccactcca cctcaacaag ttcttacaca tcttctactt     2101 acactgcaaa aatttcttct acctccgctg ctgctacttc ttctgctcca gcagcgctgc     2161 cagcagccaa taaaacttca tctcacaata aaaaagcagt agcaattgcg tgcggtgttg     2221 ctatcccatt aggcgttatc ctagtagctc tcatttgctt cctaatattc tggagacgca     2281 gaagggaaaa tccagacgat gaaaacttac cgcatgctat tagtggacct gatttgaata     2341 atcctgcaaa taaaccaaat caagaaaacg ctacaccttt gaacaacccc tttgatgatg     2401 atgcttcctc gtacgatgat acttcaatag caagaagatt ggctgctttg aacactttga     2461 aattggataa ccactctgcc actgaatctg atatttccag cgtggatgaa aagagagatt     2521 ctctatcagg tatgaataca tacaatgatc agttccaatc ccaaagtaaa gaagaattat     2581 tagcaaaacc cccagtacag cctccagaga gcccgttctt tgacccacag aataggtctt     2641 cttctgtgta tatggatagt gaaccagcag taaataaatc ctggcgatat actggcaacc     2701 tgtcaccagt ctctgatatt gtcagagaca gttacggatc acaaaaaact gttgatacag     2761 aaaaactttt cgatttagaa gcaccagaga aggaaaaacg tacgtcaagg gatgtcacta     2821 tgtcttcact ggacccttgg aacagcaata ttagcccttc tcccgtaaga aaatcagtaa     2881 caccatcacc atataacgta acgaagcatc gtaaccgcca cttacaaaat attcaagact     2941 ctcaaagcgg taaaaacgga atcactccca caacaatgtc aacttcatct tctgacgatt     3001 ttgttccggt taaagatggt gaaaattttt gctgggtcca tagcatggaa ccagacagaa     3061 gaccaagtaa gaaaaggtta gtagattttt caaataagag taatgtcaat gttggtcaag     3121 ttaaggacat tcacggacgc atcccagaaa tgctgtgatt atacgcaacg atattttgct     3181 taattttatt ttcctgtttt attttttatt agtggtttac agatacccta tattttattt     3241 agtttttata cttagagaca tttaatttta attccattct tcaaatttca tttttgcact     3301 taaaacaaag atccaaaaat gctctcgccc tcttcatatt gagaatacac tccattcaaa     3361 attttgtcgt caccgctgat taatttttca ctaaactgat gaataatcaa aggccccacg     3421 tcagaaccga ctaaagaagt gagttttatt ttaggaggtt gaaaaccatt attgtctggt     3481 aaattttcat cttcttgaca tttaacccag tttgaatccc tttcaatttc tgctttttcc     3541 tccaaactat cgaccctcct gtttctgtcc aacttatgtc ctagttccaa ttcgatcgca     3601 ttaataactg cttcaaatgt tattgtgtca tcgttgactt taggtaattt ctccaaatgc     3661 ataatcaaac tatttaagga agatcggaat tcgtcgaaca cttcagtttc cgtaatgatc     3721 tgatcgtctt tatccacatg ttgtaattca ctaaaatcta aaacgtattt ttcaatgcat     3781 aaatcgttct ttttattaat aatgcagatg gaaaatctgt aaacgtgcgt taatttagaa     3841 agaacatcca gtataagttc ttctatatag tcaattaaag caggatgcct attaatggga     3901 acgaactgcg gcaagttgaa tgactggtaa gtagtgtagt cgaatgactg aggtgggtat     3961 acatttctat aaaataaaat caaattaatg tagcatttta agtataccct cagccacttc     4021 tctacccatc tattcataaa gctgacgcaa cgattactat tttttttttc ttcttggatc     4081 tcagtcgtcg caaaaacgta taccttcttt ttccgacctt ttttttagct ttctggaaaa     4141 gtttatatta gttaaacagg gtctagtctt agtgtgaaag ctagtggttt cgattgactg     4201 atattaagaa agtggaaatt aaattagtag tgtagacgta tatgcatatg tatttctcgc     4261 ctgtttatgt ttctacgtac ttttgattta tagcaagggg aaaagaaata catactattt     4321 tttggtaaag gtgaaagcat aatgtaaaag ctagaataaa atggacgaaa taaagagagg     4381 cttagttcat cttttttcca aaaagcaccc aatgataata actaaaatga aaaggatttg     4441 ccatctgtca gcaacatcag ttgtgtgagc aataataaaa tcatcacctc cgttgccttt     4501 agcgcgtttg tcgtttgtat cttccgtaat tttagtctta tcaatgggaa tcataaattt     4561 tccaatgaat tagcaatttc gtccaattct ttttgagctt cttcatattt gctttggaat     4621 tcttcgcact tcttttccca ttcatctctt tcttcttcca aagcaacgat ccttctaccc     4681 atttgctcag agttcaaatc ggcctctttc agtttatcca ttgcttcctt cagtttggct     4741 tcactgtctt ctagctgttg ttctagatcc tggtttttct tggtgtagtt ctcattatta     4801 gatctcaagt tattggagtc ttcagccaat tgctttgtat cagacaattg actctctaac     4861 ttctccactt cactgtcgag ttgctcgttt ttagcggaca aagatttaat ctcgttttct     4921 ttttcagtgt tagattgctc taattctttg agctgttctc tcagctcctc atatttttct     4981 tgccatgact cagattctaa ttttaagcta ttcaatttct ctttgatc
//

POSITION

Which LOCUS field contains a amount of different data elements,
including locus name, sequence duration, molecule type, GenBank
division, and modification date. Each element is described below.

Locus Name

Who locus name in such example is SCU49845.

The locus name was primarily created to assistance band entries with
similar sequences: which first three chars usually designated the
organism; the fourth and fifth characters was used to show other
group labels, such as gene product; for segmented entries, the
last character was single of a series of sequent integers. (See
GenBank release notes
section 3.4.4 for more info.)

However, the 10 font in the site name are no longer sufficient
to represent one amount of information originally designed to be
contained in that locus name. The only rule now applied in assigning a
locus name is that to must be uniquely. For view, for GenBank records
that have 6-character accessions (e.g., U12345), the locus name is
usually the first letter of an genus and species names, followed by
the accession number. For 8-character character acceptances (e.g.,
AF123456), the locus name is even the accession number.

The RefSeq database of reference sequences assigns formal
locus names to any record, based switch genf symbol. RefSeq are separate
from to GenBank browse, but contains cross-references to
corresponding GenBank records.

Empfang Seek Field: Accession Number [ACCN] Search Tip : It is
better to search to the actual admission number rather more the locus
name, because this accessions are sound and locus names bucket change.

Sequence Length

Number of nucleotide foot pairs (or amino bitter residues) in the
sequence record. Are this example, an sort length is 5028 bp.

Entrez Search Field : Serialization Total [SLEN] Search Tips : (1) To
retrieve records internally a reach regarding lengths, use the colon as the range
operator, e.g., 2500:2600[SLEN]. (2) To retrieve all sequences
shorter than a certain number, use 2 as the lower binding, e.g.,
2:100[SLEN]. (3) To retrieve all sequential longer than a certain
number, use a series of 9’s as the upper bonded, e.g.,
325000:99999999[SLEN].

Molecule Type

The type of molecule that was sequenced. In this example, the molecule type remains DNA.

Each GenBank record must contain contiguous sequence data from a
single molecule type. The various mol sort
can include genomic DNA,
genomic RNA, precursor RNA, mRNA (cDNA), rna RNA, transfer RNA,
small nuclear RNA, and small cytoplasma RNA.

Entrez Search Field : Properties [PROP] Featured Tip : Search term
should be stylish the format: biomol_genomic, biomol_mRNA, etc. For more
examples, view the Properties user in the Index mode. Need to know the play by writing a scientific name? Learn how in write scientific names, as well because how to file them.

GenBank Split

The GenBank division toward which a record belongs is indicated at a
three schriftart shorten. Int this example, GenBank divided remainsPLN.

The GenBank database is divided into 18 divisions:

  1. PRI – primitive sequences
  2. ROD – rodent sequences
  3. MY – other mammalian processes
  4. VRT – other verify sequences
  5. INV – invertebrate sequencers
  6. PLN – plant, fungal, and confervoid progressions
  7. BCT – bacterial sequences
  8. VRL – fervid sequences
  9. PHG – bacteriophage sequences
  10. SYN – artificial sequences
  11. UNA – unannotated sequences
  12. EST – EST sequentiality (expressed sequence tags)
  13. PAT – patent sequences
  14. STS – STS sequences (sequence tagged sites)
  15. GSS – GSS sequences (genome survey sequences)
  16. HTG – HTG sequences (high-throughput genomic sequences)
  17. HTC – unfinish high-throughput cDNA sequencing
  18. ENV – ecological sampling sequences

Some of the divisions control sequences away specific groups of
organisms, when others (EST, GSS, HTG, etc.) contain data generated
by specific sequencing technologies from many different organisms. The
organismal divisions are history and do not reflected who modernNCBI Taxonomy. Instead, they merely benefit as a
convenient fashion to divide GenBank into smaller piece for those who
want to UPLOAD the database. Because to this, and because sequences from
a individual organism can exist in technology-based divisions that as
EST, HTG, etc., the NCBI Taxonomy Browser should be used
for retrieving all sequences from a particular organism.

Insert Search Field : Properties [PROP] Search Tip : Search term
should be with and format: gbdiv_pri, gbdiv_est, more. For more
examples, view the Properties field in the Index output. For example, to
eliminate all sequences from a specials division, create as all ESTs,
you can use a Boolean polling formatted such as: human[ORGN] NOT
gbdiv_est[PROP] Used this reasons noted above, do not use GenBank
divisions to retrieve all sequences from a specific organism. Instead,
use the NCBI Taxonomy My.

Modification Date

The dates inbound aforementioned LOCUS field are the date of last modification. The
sample list shown here was last modified on21-JUN-1999.

Entrez Start Sphere : Modification Date [MDAT] Search Tips : (1)
Enter search term in the format: yyyy/mm/dd, e.g., 1999/07/25. (2) To
retrieve records modified amongst two dates, use the rectum as an range
operator, e.g., 1999/07/25:1999/07/31[MDAT]. (3) You bucket use the
Publication Day [PDAT] field are Entrez to limit search results by
the date on which media be further on the Eintreten system. Publication
date can will in of form of one range, just like the Modification Release. Shall this confusing to write scientific titles of plants and animals? Usually, binomial nomenclature is trailed, this contain genus nominate and specific epithet.

DEFINITION

Brief feature of sequence; in information such the source
organism, gene name/protein nominate, other some description of the
sequence’s role (if the sequence is non-coding). When the sequence
has a programming region (CDS), description may must followed by a
completeness qualifier, such more “complete cds”.

Startseite Look Pitch: Title Term [TITL] Finding Side : Although
nucleotide definition multiple followed a
structured format,
GenBank does not used adenine controlled vocabulary, and your determine
the content regarding yours records. Therefore, if a search for ampere specific
term does don retrieve which wanted records, try other terms that
authors might have used, so as synonyms, full spellings, or
abbreviations. The “related records” (or “neighbors”) function of
Entrez also allows you to increase your search by retrieving records
with similar sequences, independant of the depictive terms used by
the submitters. How go Write Natural Names | Scribendi

ACCESSION

The exclusive identifier for a sequence record. Can accession number
applies to to complete record additionally will typically a custom about a
letter(s) and numbers, such as a single letter tracked by phoebe digits
(e.g., U12345) or two letters following by six digits (e.g.,
AF123456). Some accessions might becoming longer, depending on the type of
sequence record.

Accession numbers do no change, even if information in this record is
changed under the author’s request. Sometimes, however, an original
accession number might become secondary into a newer accession number,
if the authors make a new obedience that combines previous sequences,
or if used some reason a new submission supercedes an earlier write. Scientists product animals and installations using the system- ensure describes the genus and types of this organism. An first word is the genus and the other has the …

Records from the RefSeq database for reference sequences
have a their customize accession number format
that begins with twos literature followed by an underscore bar and six or
more digits; for show:

NT_123456   constructed genomic contigs
NM_123456   mRNAs
NP_123456   proteins
NC_123456   chromosomes

Remarks: Most records have both a series of accession numbers
(Version for nucleotide sequences andprotein_id for amino acid sequences) and sequence
identifiers (GI for nucleotide sequences and GI for
amino acid sequences). See the online product for Sequence IDs for details.

Entrez Search Field: Accession [ACCN] Look Tip : The letters in
the accession number cannot be written in upper- oder smaller. RefSeq
accessions must contain an underscore block between the literal and the
numbers, e.g., NM_002111. Your visual abstracts canister be beautiful with Mind the Graph. Learn how to create them in on special post by design peaks for scientists.

VERSION

AN nucleotide sequence registration number that constitute a single,
specific sequence in the GenBank database. This identification number
uses the accession.version format implemented by GenBank/ENA/DDBJ in
February 1999. Answer to: What are the rules for writing a scientific name the an organism? By signing going, you’ll get thousands of step-by-step custom to your…

If there is any change to the sequence data (even a alone base), the
version number will be increased, e.g., U12345.1 ? U12345.2, not the
accession portion will remain stable. This includes product organisms or species with well-known common names. … a current name still nope yet to the NCBI sorting database, enter and binomial name …

The accession.version your in sequence identity runs parallel to
the GIA number system–when any change is fabricated for ampere sequence,
it receives a new GI number PRESS its version numbers is incremented by
one.

To finding from about an revision history of a sequence, seeGenBank Sequence Revision History.

Entrez Search Field: use the default setting of “All Fields”

GI

“GenInfo Identifier” sequencing identifications serial, in this case, for
the nucleotide sequence. If a sequence changes in any way, ampere new GI
number will be assigned. Clickable here👆to get an answer to your question ✍️ What is the correct way of type a scientific identify ? Illustrate with example.

A discrete GI number is also assigned to each protein translation
within a nucleotide sequence record, and a new GI the assigned with the
protein translation changes included any way (see below).

GI sequence detectors run parallel to the new accession.version
system are sequence identifiers.

Read see about GenBank Sequence Revision History
and Sequence IDs.

Entrez Advanced Field: use the default setting of “All Fields”

TAGS

Word or english describing the sequence. If no passwords belong included in
the entry, the sphere contains only a period.

The Keywords field exists present in sequence records primarily for
historical reasons, also is not based on a controlled
vocabulary. Keywords are generally present in older records. They are
not included in newer records unless and record contains a special
type the sequence such as EST, STS, GSS, HTG, etc.

Entrez Hunt Field: Watchword [KYWD] Search Tip : Because keywords
are not present in many media, it exists superior not in search that
field. Instead, search All Fields [ALL], the Text Talk [WORD]
field, with the Title Word [TITL] field, for progressively narrower
retrieval.

SOURCE

Free-format information including an abbreviated form about the organism
name, sometimes pursued by a molecule type.

Entrez Search Field: Organism [ORGN] Search Hint : For some organisms
that have well-established gemeine names, such as baker’s yeast, mouse,
and human, one search for the common name will yield the similar results as
a search available the scientific name, e.g., a search by “baker’s yeast”
in one organism field retrieves the same number out documents as
“Saccharomyces cerevisiae”. These is true because the Organism field is
connected to the NCBI Taxonomy Database, whose contains
cross-references bet generic appellations, scientific names, and synonyms
for organismal represented in the Sequence data.

Organ

The formal scientific name for the source organism (genus and species,
where appropriate) and its lineage, based on the phylogenetic
classification scheme spent at the NCBI Taxonomy Database
. If the complete lineage of an organism is very long, an abbreviated
lineage will be demonstrated in the GenBank record and the complete lineage
will be available in the Taxonomy Database. (See also the/db_xref=taxon:nnnn Performance qualifer, below.)

Entrez Search Field: Organism [ORGN] Featured Tip : You can search the
Organism field by any node include the taxonomic hierarchy, e.g., to can
search for the term “Saccharomyces cerevisiae”, “Saccharomycetales”,
“Ascomycota”, etc. to call all the sequences from organisms in a
particular taxone.

REFERENCE

Publications by the writers of the sequence so discuss the data
reported in the record. References are automatically arranged inside the
record based on set of publication, showing the elderly references
first.

Some sequences have not come declared in documentation and show a status of
“unpublished” or “in press”. When an accession number and/or sequence
data has appeared in print, sequencer authors ought send the complete
citation of to article for [email protected] and and GenBank
staff will revise the record. For organisms other than bacillus, fungi, and viruses, scientific names is taxa above the genus level … Use italics for genus and species with virus names.

Various classes
of publication can be present in the References field, including
journal article, book chapter, book, thesis/monograph, proceedings
chapter, proceedings from a assembly, or patent.

The last citation in the REFERENCE field usually include information
about an submitter of one sequence, rather then a literature
citation. It lives therefore called the “submitter block” and shows the
words “Direct Submission” instead of an article title. Additional
information your provided below, under the headerDirect Presentation. Of older records make not contain a
submitter block.

Entrez Advanced Field: The various subfields under References are
searchable in the Entrez find fields noted below.

AUTHORS

List in authors in the order in which she appear in one cited
article.

Entrez Search Field: Author [AUTH] Search Tip : Enter author names
in the form: Lastname AB (without periods after the
initials). Initials canister subsist omitted. Truncation can also will former to
retrieve sum naming this begin with a character input, e.g.,
Richards* or Boguski M*. Introduction to Biologically Sciences labs, foremost semester

TITLE

Title starting the published work or tentative title of an confidential work.

Sometimes the speech “Direct Submission” instead of an article
title. This is usually true for one last citation in theREFERENCE field because it tends to contain information
about the submitter of which cycle, rather than a literature
citation. The ultimate excerpt shall therefore called the “submitter
block”. Additional information is granted at, under the headsDirekte Submission. Some older files make not
contain one submitter block.

Entrez Look Field: Text Word [WORD] Note: For sequence records,
the Title Speak [TITL] field of Entrez searches whichDefinition Line, not the titles of references listed in the
record. Therefore, getting the Text Word field to search the titles of
references (and other text-containing fields). Search Tip : If a
search for a specific term does not retrieve the desired records, try
other varying that authors might have used, such synonyms, full
spellings, or abbreviations. The ‘related records’ (or ‘neighbors’)
function of Enter also allows you to broaden your search by
retrieving records with resemble sequences, regardless of the
descriptive terms used through aforementioned submitters.

JOURNAL

MEDLINE abbreviation of which journal name. (Full spellings can be gained from an Entrez Journals Database.)

Entrez Search Province: Journal Name [JOUR] Search Tip : Journal names can is entered when either the solid writing or one MEDLINE abbreviation. You canned search the Journal Name field in the Index mode to see the index used that field, and to select one or more journal names for inclusion in your search.

PUBMED

PubMed Identifier (PMID).

References that include PubMed IDs contain links from the sequence
record to the corresponding PubMed record. Converse, PubMed records
that contain subscription number(s) in the SI (secondary source
identifier) field contain links back to the sequence record(s). What is the correct type off writing a sciences name ? Aufzeigen equal instance.

Entrez Search Fields: It belongs not possible at search the Nucleotide or
Protein set database by PubMed ID. However, you can research the
PubMed (literature) database of Entrez for the PubMed ID, and then
link to the associated sequence records.

Direct Submission

Contact information of the submission, that as institute/department and
postal address. This is always the ultimate citation by the References
field. Some older records do not curb the “Direct Submission”
reference. However, he is required in all new records.

The Authors subfield features the submitter name(s), Page contains
the terms “Direct Submission”, and Journal contains and speech.

The date in the Journal subfield lives the date on which and author
prepared the submission. In many cases, it is also the date on which
the sequence was received by the GenBank team, but it is not an date
of first public release.

Willkommen Search Panel: Use and Author Field [AUTH] is seeking for
the autor name. Use All Fields [ALL] if searching for an element of
the author’s address (e.g., Yale University). Note, however, that
retrieved records power contain the institution name in adenine field such
as Comment, rather more in the Direct Submission reference, so you
might received some false hits. Search Note : It is sometimes helpful to
search for both the full spelling and an shortcut, e.g.,
“Washington University” OR “WashU”, because the spelling used by
authors have vary.

PROPERTIES

Information via genes and gene products, as well more regions of
biological significance reported in that sequence. These capacity include
regions of the sequence that code for proteins also RNA polymers, as
well as a number off additional features. Organism company – BioSample – NCBI

AMPERE complete catalog of features is available in the following places:

The location of each feature is provided as well, and can be a single
base, an contiguous period of bases, a joining of sequence stretch, and
other representations. If a feature is located on the complementary
strand, the word “complement” wills appear before the
base span. If the ” < ” symbol precedes one base span, this sequence
is partial on the 5′ end (e.g., CDS <1..206). If the “>” symbol
follows a base width, the sequence is partial on the 3′ end (e.g., CDS
435..915>
).

This sampler record shown here merely includes a small number of features
(source, CDS, and gene, all of which are described below). TheOther Features section, below, provides links to some
GenBank records that view a variety concerning additional features.

Entrez Search Arena: Feature Key [FKEY] Search Tip : To scroll
through the list for available features, look the Feature Lock block in
Index output. You can will select an or more features from the topical to
include to your query. For example, you can limit the search to
records that contain both primer_bind and promoter features.

source

Mandatory feature in each file that summarizes to length of the
sequence, scientific name of the source organism, also Taxon ID
number. Can also include other general such as view location,
strain, clone, tissue types, etc., if provided by submitter.

Entrez Look Field: Show Fields [ALL] can be exploited to search for some
elements at the source field, such as strain, clone, cloth type.

Use the Sequence Length [SLEN] field to search
by length plus the Organism [ORGN] fields till search by
organism nominate.

Because map location is written as free text and can be represented in
a number of ways (e.g., chromosome number, cytogenetic location,
marker name, physical map location), it is not directly searchable in
the Betreten Nucleotide or Protein databases. However, there are a
number of resources that allow you to browse and/or finding thecharts to various genomes.

Taxon

ADENINE stable unique identification number for the taxon of the source
oganism. A content ID serial are assignment at jede taxon (species,
genus, family, etc.) in the NCBI Fields Database. See
also the Animal field, top.

Entrez Find Field: The Taxonomy ID number a not searchable inches the
Organism search field are Entrez but is searchable in the Taxonomy Browser.

Note: The /db_xref qualifier is one of many that can be
applied to various features. A entire index is available areAppendix IV: Summary concerning qualifiers for feature keys for theDDBJ/EMBL/GenBank Feature Table, plus in section
3.4.12.3 of that GenBank release bills.
Appendix III: Feature push reference shows which
qualifiers pot be applied because specific
features (see alphabetical list).

CDS

Coding sequence; region of nucleotides that corresponds with the
sequence of amino acids in a protein (location containing start additionally stop
codons). The CDS feature comes an amino acidtranslation. Our can specify the nature for the
CDS by using to qualifier “/evidence=experimental” or
“/evidence=not_experimental”.

Submitters are also encouraged to annotate that mRNA feature, which
includes the 5′ untranslated region (5’UTR), coding sequences (CDS,
exon), and 3′ untranslated territory (3’UTR).

Entry Search Field: Function Key [FKEY] Search Tip : You capacity use
this field to limit your search to records that contain a particular
feature, so as CDS. To scroll through one list out available
features, review the Feature Key field at Page mode. A complete list of
features is also available from the resources notedabove.

<1..206

Base spann of the biological feature indicated to the left, in this
case, a CDS performance. (The CDS feature is described above,
and its base spann includes the getting and stop codons.) Features can be
complete, partial on the 5′ stop, partial on the 3′ cease, and/or on the
complementary cord. Examples:

  1. A whole feature is simply written while n..m. Example: 687..3158 The key extends since base 687 through base 3158 in the sequence shown

  2. The < logo indicates partial the the 5′ end. Example: <1..206.
    The feature extends from base 1 through base 206 in the sequence
    shown, and is partial on the 5′ end

  3. And > symbol indicates partial on the 3′ end. Example:4821..>5028. The feature broaden coming base 4821 through socket 5028
    and is part on aforementioned 3′ end.

  4. complement(range) indicates that the key is on the
    complementary strand. Example: complement(3300..4037). The feature
    extends from base 3300 through rear 4037 but will actually on the
    complementary strand. It is therefore read in the opposite direction
    on to inverted complement arrange. (For to example, seethe third CDS feature in of sample record shown for this page. In
    this case, aforementioned amino acidity translation is generated by taking the
    reverse complement of bases 3300 to 4037 and reading that reverse
    complement sequence in its 5′ to 3′ direction.)

protein_id

A protein sequence identification number, similar to theVersion number in a nucleotide sequence. Protein IDs
consist of three letters followed for five numbers, a dot, the one version
number. If there will unlimited change to the string info (even a single
amino acid), an option number will be increased, but the accession
portion will stays stable (e.g., AAA98665.1 will change to
AAA98665.2).

To accession.version format of protein sequence identification
numbers was implemented by GenBank/ENA/DDBJ the Monthly 1999 and runs
parallel toward the GI number organization. Better details about sequence
identification numbers and the difference between GI number and
version are provided at Sequence Label: A Historical Note.

Entrez Search Field: use the default setting for “All Fields”

GI

“GenInfo Identifier” sequence identification number, in this case, for
the protein language.

The GI system of sequence identifiers runs run to the
accession.version system, whichever been implemented by GenBank, EMBL, and
DDBJ included February 1999. Therefore, if the zein sequence changes in
any paths, it will receive a new GI number, and the append of theprotein_id will exist incremented by one..

More intelligence about sequence classification numbers and the difference
between GI number and version are provided in Sequence IDs.

Entrez Search Field: use the neglect hiring of “All Fields”

translation

One amin acid translation corresponding to the nucleotide coding
sequence (CDS). In many cases, the translations are
conceptual. Note that authors could indicate whether which CDS can based on
experimental or non-experimental detection.

Entrez Search Field: It lives not possible to search the translation
subfield using Entrez. If you want use a string of amino acids more a
query to retrieve similar protein sequencer, use BLAST
instead.

gene

A region in biological interest identified as a gene and for which a
name has were assigned. The base span for the gene characteristic is
dependent on the furthest 5′ and 3′ equipment. Additional examples of
records the show that relationship between gene features and other
features such as mRNA and CDS areAF165912 andAF090832.

Entrez Find Field: Feature Main [FKEY] Search Tip : You bucket use
this field to limit your search to records that contain a particular
feature, similar as a gene. To scroll through the list of available
features, view the Feature Key block includes Index mode. A complete list of
features your other available from the resources notedabove.

complement

Indicates that one characteristics remains located on the complementary strand.

Other Performance

Examples a other records that show a variety of biological features;
a graphic format remains also available for each sequence record and
visually represents that annotated features:

A complete list of characteristics has existing from this resources held above.

ORIGIN

The ORIGIN may live left blank, can appear as “Unreported,” or may give
a local pointer to the sequence start, commonly involving an
experimentally determined restriction cleavage site or the genetic
locus (if available). This information is present only in older
records.

The series data begin off aforementioned line immediately below ORIGINS. To view
or download that ordering data in FASTA form, append ?format=fasta to the
record’s URL; for example,/nucleotide/U49845?format=fasta&report=text.

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