References:
Ch.2 :The GenBank Sequence Database.
website: http://www.ncbi.nlm.nih.gov The NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research 2000 Jan 1;28(1):15-8).
Genbank Flat File Format3 Parts:
Features Sequence Header:
Features:
Sequence:
FASTA FORMATThe most simple and widely used by all softwares designed for molecular biology. >Description Line ASN.1 (Abstract Syntax Notation 1) FormatOne can download the entire GenBank database in this format GenBank Submission ToolsSequin : A stand alone sequence submission tool that runs on PC, MAC and Unix. Anyone can submit any sequence to GenBank. Archival database vs. Curated Database
Basic Local Alignment Search ToolProgram also determines the statistical significance of the output. Since the size of the database increases frequently, the statistical significance of one match may change in time. Some databases that are available to Blast against:
GenBank Retrieval Methods
Entrez
|
LOCUS AF067844 218336 bp DNA PRI 08-FEB-1999
DEFINITION Homo sapiens chromosome 10 clone PTEN, complete sequence.
ACCESSION AF067844
VERSION AF067844.1 GI:4240386
KEYWORDS HTG.
SOURCE human.
ORGANISM Homo sapiens
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia;
Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE 1 (bases 1 to 218336)
AUTHORS Jensen,K., de la Bastide,M., Parsons,R., Parnell,L.D., Dedhia,N.,
Gottesman,T., Gnoj,L., Kaplan,N., Lodhi,M., Johnson,A.F.,
Shohdy,N., Hasegawa,A., Haberman,K., Huang,E.N., Schutz,K.,
Calma,C., Granat,S., Wigler,M. and McCombie,W.R.
TITLE Genomic sequence of PTEN/MMAC1
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 218336)
AUTHORS Jensen,K., de la Bastide,M., Parsons,R., Parnell,L.D., Dedhia,N.,
Gottesman,T., Gnoj,L., Kaplan,N., Lodhi,M., Johnson,A.F.,
Shohdy,N., Hasegawa,A., Haberman,K., Huang,E.N., Schutz,K.,
Calma,C., Granat,S., Wigler,M. and McCombie,W.R.
TITLE Direct Submission
JOURNAL Submitted (18-MAY-1998) Lita Annenberg Hazen Genome Sequencing
Center, Cold Spring Harbor Laboratory, 1 Bungtown Rd., Cold Spring
Harbor, NY 11724, USA
FEATURES Location/Qualifiers
source 1..218336
/organism="Homo sapiens"
/db_xref="taxon:9606"
/chromosome="10"
/clone="PTEN"
source 1..106991
/organism="Homo sapiens"
/db_xref="taxon:9606"
/chromosome="10"
/clone="BAC 265N13"
5'UTR 22308..23338
/gene="PTEN"
/note="5'-UTR defined by comparison to PTEN cDNA U93051"
mRNA join(22308..23417,51995..52079,83482..83526,89015..89058,
90987..91225,110086..110227,115821..115987,118862..119086,
123258..124345)
/gene="PTEN"
/note="mRNA coordinates delineated by comparison to PTEN
cDNA U93051"
gene 22308..124345
/gene="PTEN"
/note="the coding region of PTEN, as defined by the cDNA,
identifies 9 exons within this region; identical to MMAC1
(U92346) and PTEN (U93051)"
/evidence=experimental
exon 22308..23417
/gene="PTEN"
/function="5'-UTR and initial segment of the CDS"
/number=1
CDS join(23339..23417,51995..52079,83482..83526,89015..89058,
90987..91225,110086..110227,115821..115987,118862..119086,
123258..123443)
/gene="PTEN"
/note="coding regions delineated by comparison to PTEN
cDNA"
/codon_start=1
/product="PTEN"
/protein_id="AAD13528.1"
/db_xref="GI:4240387"
/translation="MTAIIKEIVSRNKRRYQEDGFDLDLTYIYPNIIAMGFPAERLEG
VYRNNIDDVVRFLDSKHKNHYKIYNLCAERHYDTAKFNCRVAQYPFEDHNPPQLELIK
PFCEDLDQWLSEDDNHVAAIHCKAGKGRTGVMICAYLLHRGKFLKAQEALDFYGEVRT
RDKKGVTIPSQRRYVYYYSYLLKNHLDYRPVALLFHKMMFETIPMFSGGTCNPQFVVC
QLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVN
TFFIPGPEETSEKVENGSLCDQEIDSICSIERADNDKEYLVLTLTKNDLDKANKDKAN
RYFSPNFKVKLYFTKTVEEPSNPEASSSTSVTPDVSDNEPDHYRYSDTTDSDPENEPF
DEDQHTQITKV"
exon 51995..52079
/gene="PTEN"
/number=2
source 58169..218336
/organism="Homo sapiens"
/db_xref="taxon:9606"
/chromosome="10"
/clone="BAC 60C5"
exon 83482..83526
/gene="PTEN"
/number=3
exon 89015..89058
/gene="PTEN"
/number=4
exon 90987..91225
/gene="PTEN"
/number=5
exon 110086..110227
/gene="PTEN"
/number=6
exon 115821..115987
/gene="PTEN"
/number=7
exon 118862..119086
/gene="PTEN"
/number=8
exon 123258..124345
/gene="PTEN"
/function="terminal segment of the CDS and 3'-UTR"
/number=9
3'UTR 123444..124345
/gene="PTEN"
/note="3'-UTR defined by comparison to PTEN cDNA U93051"
/evidence=experimental
BASE COUNT 64194 a 39437 c 43295 g 71406 t 4 others
ORIGIN
1 caagctttac actagagcct atatgaagtt ttgattctaa gtgttaatgt accttctgac
61 aactgtgaaa tgaaccttgt tcctggggag cgcgttctgg ttttctcttt gcacagttaa
121 gctgagacta gcatcattct agtttgcagg tgacattctc tgggaagcta gtctatgggg
181 gagatgacat cttctgaacc tagtccccac agagaacttt gaatgagtgg aatcaagagg
241 ttgcctgcat tcttgctcat gtcacaatgc tggacatgtg acttcagaga agcatgtgcc
301 aggtcaatat gattgggctg ttctcacaat acaaggcctt gaccatagag tgattcagag
361 gcaaatgcag ccttcttaga ctcttaacca aaacattggc atgacataaa attataatta
421 ataaaagata tacagttatt tcaaaagtac cgttttattg ggacatctca aaggactaag
481 aaaatgttta ttttcttatc tcctatcttt tgttaatagc tgttcatcgc tcatcagcct
541 ttactgaaag cttatcatgt atcaaacaat atgccaggtg tcagagaggg cagcaaagag
601 agtacaattg agttagatag agtacctgca ctcaataata ataacagcta acacttacat
661 agtgctttct gcgtgccagg cttgtcctaa gtgattttac acacacacac acacacacac
721 acacacacac acacacactc cctcactcag tccttataaa aacccactga taggccgggt
781 gcggtggctc atacctgtaa tcccagcaac tttgggaggc tgaagcaggc agatcacttg
841 aggtcaggag ttcgagatca ccctggccaa catggtgaaa cctcatctct actaaaaata
901 caaaaattaa ccaagcatgg tggcaggtgc ctgtaatcct agctactcaa gaggctgaga
961 caggaaaatc acttgaacct ggtaggtgga tgttgcagtg tgccgagatc gtgccaccac
1021 actccagcct gagcaacaga gtgagactct atctaaaaaa aaaaaaaaaa aaattaaaaa
217861 ggatacggtg gtgtaaaagg caaaacatat acctgatttc atggaactca cattctaggg
217921 gtggtttgtg tatatatgag aacagtaact agaaaaaaat aatgaacaag gtattttatg
217981 taacgataag agctatgaag aaaatcagac atgacgattt tcagctagag ctacccaaag
218041 catgatcttt gagtcaacaa caacatatga gcaatcagtt tgttaaaaat gcagaatctc
218101 agaagacggc ctagacctac tgattcagaa tcatcattgt aacaggatcc ccttgtcatt
218161 tctttgcatg ctaatgtttg agaagcactg agctagacag tgggaaatgg aaggtttctc
218221 tgcctaggtg acatctgagc tgagacttga atgaagaaaa gctgtccatg taaagatctg
218281 ggagcagaag gatccaggca gaggaaatgg aaagtacaag gggctggatg agagaa
//
>gi|4240386|gb|AF067844.1|AF067844 Homo sapiens chromosome 10 clone PTEN, complete sequence CAAGCTTTACACTAGAGCCTATATGAAGTTTTGATTCTAAGTGTTAATGTACCTTCTGACAACTGTGAAA TGAACCTTGTTCCTGGGGAGCGCGTTCTGGTTTTCTCTTTGCACAGTTAAGCTGAGACTAGCATCATTCT AGTTTGCAGGTGACATTCTCTGGGAAGCTAGTCTATGGGGGAGATGACATCTTCTGAACCTAGTCCCCAC AGAGAACTTTGAATGAGTGGAATCAAGAGGTTGCCTGCATTCTTGCTCATGTCACAATGCTGGACATGTG ACTTCAGAGAAGCATGTGCCAGGTCAATATGATTGGGCTGTTCTCACAATACAAGGCCTTGACCATAGAG TGATTCAGAGGCAAATGCAGCCTTCTTAGACTCTTAACCAAAACATTGGCATGACATAAAATTATAATTA ATAAAAGATATACAGTTATTTCAAAAGTACCGTTTTATTGGGACATCTCAAAGGACTAAGAAAATGTTTA TTTTCTTATCTCCTATCTTTTGTTAATAGCTGTTCATCGCTCATCAGCCTTTACTGAAAGCTTATCATGT ATCAAACAATATGCCAGGTGTCAGAGAGGGCAGCAAAGAGAGTACAATTGAGTTAGATAGAGTACCTGCA CTCAATAATAATAACAGCTAACACTTACATAGTGCTTTCTGCGTGCCAGGCTTGTCCTAAGTGATTTTAC ACACACACACACACACACACACACACACACACACACACTCCCTCACTCAGTCCTTATAAAAACCCACTGA TAGGCCGGGTGCGGTGGCTCATACCTGTAATCCCAGCAACTTTGGGAGGCTGAAGCAGGCAGATCACTTG AGGTCAGGAGTTCGAGATCACCCTGGCCAACATGGTGAAACCTCATCTCTACTAAAAATACAAAAATTAA CCAAGCATGGTGGCAGGTGCCTGTAATCCTAGCTACTCAAGAGGCTGAGACAGGAAAATCACTTGAACCT GGTAGGTGGATGTTGCAGTGTGCCGAGATCGTGCCACCACACTCCAGCCTGAGCAACAGAGTGAGACTCT ATCTAAAAAAAAAAAAAAAAAAATTAAAAACCCAATGAGGTGGCTACTGTTATCATCCCCATTTTACGGA TGAGGACATGGGTACATAGAGATTAAGTAACTTGCCAAAGATCTCACAACTGGTAAGTGGCAGAGCAAAA TTTGAAAACAAACAATCTGGTTCCAGAAACTGTACTTTTAACCTCATGATAGCTTCCTGAGGAATTTATG ATCTGAGTATATATAGTAAGTACCTCCCCTTTCAGGGTAAGGCAGTAGGTAATGGTGAACAGGGAAGCAA AAGGTGACTCAGGTTGAGTAAACAACACCAAGCATATCTGACTCAAGGAATGCTTCAGAGGCCAGGGGTG CATGCCTGTAATCCCAGCACCTTGGAAGGCTGACACAGGAGGATCACTGGAGCCCAAGTTCAAGACCAGC
Seq-entry ::= set {
class nuc-prot ,
descr {
source {
genome genomic ,
org {
taxname "Homo sapiens" ,
common "human" ,
db {
{
db "taxon" ,
tag
id 9606 } } ,
orgname {
name
binomial {
genus "Homo" ,
species "sapiens" } ,
lineage "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo" ,
gcode 1 ,
mgcode 2 ,
div "PRI" } } ,
subtype {
{
subtype chromosome ,
name "10" } ,
{
subtype clone ,
name "PTEN" } } } ,
pub {
pub {
sub {
authors {
names
std {
{
name
name {
last "Jensen" ,
first "Kendall" ,
initials "K." } } ,
{
name
name {
last "de la Bastide" ,
first "Melissa" ,
initials "M." } } ,
{
name
name {
last "Parsons" ,
first "Ramon" ,
initials "R." } } ,
{
name
name {
last "Parnell" ,
first "Laurence" ,
initials "L.D." } } ,
{
name
name {
last "Dedhia" ,
first "Neilay" ,
initials "N." } } ,
{
name
name {
last "Gottesman" ,
first "Tina" ,
initials "T." } } ,
{
name
name {
last "Gnoj" ,
first "Lidia" ,
initials "L." } } ,
{
name
name {
last "Kaplan" ,
first "Nancy" ,
initials "N." } } ,
{
name
name {
last "Lodhi" ,
first "Muhammad" ,
initials "M." } } ,
{
name
name {
last "Johnson" ,
first "Arthur" ,
initials "A.F." } } ,
{
name
name {
last "Shohdy" ,
first "Nadim" ,
initials "N." } } ,
{
name
name {
last "Hasegawa" ,
first "Amy" ,
initials "A." } } ,
{
name
name {
last "Haberman" ,
first "Kristina" ,
initials "K." } } ,
{
name
name {
last "Huang" ,
first "Emily" ,
initials "E.N." } } ,
{
name
name {
last "Schutz" ,
first "Kristin" ,
initials "K." } } ,
{
name
name {
last "Calma" ,
first "Christopher" ,
initials "C." } } ,
{
name
name {
last "Granat" ,
first "Susan" ,
initials "S." } } ,
{
name
name {
last "Wigler" ,
first "Michael" ,
initials "M." } } ,
{
name
name {
last "McCombie" ,
first "W Richard" ,
initials "W.R." } } } ,
affil
std {
affil "Cold Spring Harbor Laboratory" ,
div "Lita Annenberg Hazen Genome Sequencing Center" ,
city "Cold Spring Harbor" ,
sub "NY" ,
country "USA" ,
street "1 Bungtown Rd." ,
postal-code "11724" } } ,
medium other ,
date
std {
year 1998 ,
month 5 ,
day 18 } } } } ,
pub {
pub {
gen {
cit "unpublished" ,
authors {
names
std {
{
name
name {
last "Jensen" ,
first "Kendall" ,
initials "K." } } ,
{
name
name {
last "de la Bastide" ,
first "Melissa" ,
initials "M." } } ,
{
name
name {
last "Parsons" ,
first "Ramon" ,
initials "R." } } ,
{
name
name {
last "Parnell" ,
first "Laurence" ,
initials "L.D." } } ,
{
name
name {
last "Dedhia" ,
first "Neilay" ,
initials "N." } } ,
{
name
name {
last "Gottesman" ,
first "Tina" ,
initials "T." } } ,
{
name
name {
last "Gnoj" ,
first "Lidia" ,
initials "L." } } ,
{
name
name {
last "Kaplan" ,
first "Nancy" ,
initials "N." } } ,
{
name
name {
last "Lodhi" ,
first "Muhammad" ,
initials "M." } } ,
{
name
name {
last "Johnson" ,
first "Arthur" ,
initials "A.F." } } ,
{
name
name {
last "Shohdy" ,
first "Nadim" ,
initials "N." } } ,
{
name
name {
last "Hasegawa" ,
first "Amy" ,
initials "A." } } ,
{
name
name {
last "Haberman" ,
first "Kristina" ,
initials "K." } } ,
{
name
name {
last "Huang" ,
first "Emily" ,
initials "E.N." } } ,
{
name
name {
last "Schutz" ,
first "Kristin" ,
initials "K." } } ,
{
name
name {
last "Calma" ,
first "Christopher" ,
initials "C." } } ,
{
name
name {
last "Granat" ,
first "Susan" ,
initials "S." } } ,
{
name
name {
last "Wigler" ,
first "Michael" ,
initials "M." } } ,
{
name
name {
last "McCombie" ,
first "W Richard" ,
initials "W.R." } } } ,
affil
std {
affil "Cold Spring Harbor Laboratory" ,
div "Lita Annenberg Hazen Genome Sequencing Center" ,
city "Cold Spring Harbor" ,
sub "NY" ,
country "USA" ,
street "1 Bungtown Rd" ,
postal-code "11724" } } ,
title "Genomic sequence of PTEN/MMAC1" } } } ,
update-date
std {
year 1998 ,
month 6 ,
day 18 } ,
create-date
std {
year 1999 ,
month 2 ,
day 8 } } ,
seq-set {
seq {
id {
local
str "HsPTEN.genomic" ,
genbank {
name "AF067844" ,
accession "AF067844" ,
version 1 } ,
gi 4240386 } ,
descr {
molinfo {
biomol genomic ,
tech htgs-3 ,
completeness complete } } ,
inst {
repr raw ,
mol dna ,
length 218336 ,
seq-data