Sequence Databases. April 28, 2005
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conflict Separate determinations of the same seq. differ
rep_origin Origin of replication
protein_bind Protein binding site on DNA
CDS (Protein) coding sequence
Feature Key Location/Qualifiers
The feature CDS is a coding sequence beginning at base 23 and ending at base 400 that has a product called “alcohol dehydrogenase” and corresponds to the gene called “adhI”.
Feat. Key Location/Qualifiers
CDS join (544..589,688..1032)
/product=“T-cell recep. B-ch.”
The feature CDS is a partial coding sequence formed by joining the indicated elements to form one contiguous sequence encoding a product called T-cell receptor beta-chain.
GenBank division (plant, fungal and algal)
LOCUS SCU49845 5028 bp DNA PLN 21-JUN-1999
DEFINITION Saccharomyces cerevisiae TCP1-beta gene, partial cds, and
Axl2p (AXL2) and Rev7p (REV7) genes, complete cds.
VERSION U49845.1 GI:1293613
SOURCE baker's yeast.
ORGANISM Saccharomyces cerevisiae
Eukaryota; Fungi; Ascomycota; Hemiascomycetes; Saccharomycetales;
Unique identifier (never changes)
GeneInfo identifier (changes whenever there is a change)
Nucleotide sequence identifier (changes when there is a change
in sequence (accession.version))
Word or phrase describing the sequence (not based on controlled vocabulary).
Not used in newer records.
Common name for organism
Formal scientific name for the source organism and its lineage
based on NCBI Taxonomy Database
Oldest reference first
REFERENCE 1 (bases 1 to 5028)
AUTHORS Torpey,L.E., Gibbs,P.E., Nelson,J. and Lawrence,C.W.
TITLE Cloning and sequence of REV7, a gene whose function is required
for DNA damage-induced mutagenesis in Saccharomyces cerevisiae
JOURNAL Yeast 10 (11), 1503-1509 (1994)
REFERENCE 2 (bases 1 to 5028)
AUTHORS Roemer,T., Madden,K., Chang,J. and Snyder,M.
TITLE Selection of axial growth sites in yeast requires Axl2p, a
novel plasma membrane glycoprotein
JOURNAL Genes Dev. 10 (7), 777-793 (1996)
REFERENCE 3 (bases 1 to 5028)
TITLE Direct Submission
JOURNAL Submitted (22-FEB-1996) Terry Roemer, Biology, Yale University,
New Haven, CT, USA
Submitter of sequence (always the last reference)
There are three parts to the feature key: a keyword (indicates functional group), a location
(instruction for finding the feature), and a qualifier (auxiliary information about a feature)
Partial sequence on the 5’ end. The 3’ end is complete.
Start of open reading frame
Descriptive free text must be in quotations
Protein sequence ID #
Note: only a partial sequence
/note="plasma membrane glycoprotein"
/function="required for axial budding pattern of S.
/db_xref="GI:1293615" /translation="MTQLQISLLLTATISLLHLVVATPYEAYPIGKQYPPVARVN. . . “
/db_xref="GI:1293616" /translation="MNRWVEKWLRVYLKCYINLILFYRNVYPPQSFDYTTYQSFNLPQ . . . “
BASE COUNT 1510 a 1074 c 835 g 1609 t
1 gatcctccat atacaacggt atctccacct caggtttaga tctcaacaac ggaaccattg
61 ccgacatgag acagttaggt atcgtcgaga gttacaagct aaaacgagca gtagtcagct . . .//
Parts of the record are parsed into separate database files
from GenBank containing
data for a single gene
DNA databases derived from GenBank
containing data for a single gene
RNA (cDNA) databases derived
containing data for a single gene
dbEST-expressed sequence tags-single pass cDNA sequences (high error freq.)
It is non-redundant
HTGS-high-throughput genomic sequence database (errors!)
PDB-Three-dimensional structure coordinates of biological molecules
PROSITE-database of protein domain/function relationships.Types of primary databases carrying biological infomation
Genome databases-(there are over 20 genome databases that can be searched
EPD:eukaryotic promoter database
NR-non-redundant GenBank+EMBL+DDBJ+PDB. Entries with 100% sequence identity are merged as one.
Vector: A subset of GenBank containing vector DNA
BLOCKSTypes of secondary databases carrying biological infomation