(Q33942621)

30 July 2017

title

Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species (English)

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Andrew Jackson O'Shaughnessy

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Andrew O'Shaughnessy

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Teresa Utterback

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Pat Minx

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Mihaela Pertea

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Tamara Feldblyum

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Richard Wilson

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Lori Spiegel

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Lidia Nascimento

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Theresa Zutavern

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Jiming Jiang

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Kristi Collura

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Melissa de la Bastide

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Melissa de la Bastide

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Meizhong Luo

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Jetty Siva S Ammiraju

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Jetty Siva S Ammiraju

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Carol Soderlund

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Lance Palmer

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Sujit Dike

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Aihui Wang

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Teri Rambo

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C Robin Buell

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Brian Haas

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Owen White

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Susan Van Aken

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Luke Tallon

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Qiaoping Yuan

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Shu Ouyang

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Jia Liu

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Wei Zhu

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Rama Maiti

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Kristine M Jones

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Mary Kim

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Larry Overton

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Tamara Tsitrin

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Douglas Fadrosh

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Jayati Bera

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Bruce Weaver

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Shaohua Jin

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Shivani Johri

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Matt Reardon

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Kristen Webb

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Jessica Hill

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Kelly Moffat

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Matthew Lewis

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Victoria Zismann

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Stacey Iobst

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Joseph Hsiao

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Aymeric R de Vazeille

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Yeisoo Yu

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HeyRan Kim

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Jennifer Currie

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Shelly Kernodle-Thompson

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Fusheng Wei

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Kudrna Kudrna

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Jose Luis Goicoechea

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David Henry

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Ryan Oates

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Michael Palmer

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Gina Pries

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Christopher Saski

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Jessica Simmons

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William Nelson

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Emily Huang

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Raymond Preston

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Holly Cordum

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Weiwei Jin

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Hye-Ran Lee

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Scott Jackson

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30 July 2017

Rice Chromosome 3 Sequencing Consortium

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30 July 2017

publication date

18 August 2005

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30 July 2017

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30 July 2017

volume

15

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30 July 2017

issue

9

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30 July 2017

page(s)

1284-1291

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The oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species

30 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

The Genomes of Oryza sativa: a history of duplications

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

Role of transposable elements in heterochromatin and epigenetic control

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

High throughput T-DNA insertion mutagenesis in rice: a first step towards in silico reverse genetics.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

Rapid recent growth and divergence of rice nuclear genomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

Enrichment of gene-coding sequences in maize by genome filtration

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

The Pfam protein families database

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

High-throughput fingerprinting of bacterial artificial chromosomes using the snapshot labeling kit and sizing of restriction fragments by capillary electrophoresis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

Comparative DNA sequence analysis of wheat and rice genomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. japonica)

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

An integrated physical and genetic map of the rice genome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

A comprehensive rice transcript map containing 6591 expressed sequence tag sites

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

Toward a cytological characterization of the rice genome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

Contigs built with fingerprints, markers, and FPC V4.7.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

Ab initio gene finding in Drosophila genomic DNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

High gene density is conserved at syntenic loci of small and large grass genomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

Comparative genetics in the grasses

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

A high-density rice genetic linkage map with 2275 markers using a single F2 population.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

Cereal Genome Evolution: Grasses, line up and form a circle

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

Basic local alignment search tool

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

Toward a cytogenetically based physical map of the wheat genome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

Rapid, large-scale generation of Ds transposant lines and analysis of the Ds insertion sites in rice

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

Annotation of the Arabidopsis genome

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

Sequence and analysis of rice chromosome 4.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

The genome sequence and structure of rice chromosome 1.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

Genome sequencing of a 239-kb region of rice chromosome 10L reveals a high frequency of gene duplication and a large chloroplast DNA insertion

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

Functional rice centromeres are marked by a satellite repeat and a centromere-specific retrotransposon

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

Early and multiple Ac transpositions in rice suitable for efficient insertional mutagenesis.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

In-Depth View of Structure, Activity, and Evolution of Rice Chromosome 10

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1199543

The complete sequence of a heterochromatic island from a higher eukaryote. The Cold Spring Harbor Laboratory, Washington University Genome Sequencing Center, and PE Biosystems Arabidopsis Sequencing Consortium

29 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16109971

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Access to the maize genome: an integrated physical and genetic map

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16109971

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Homoeologous relationships of rice, wheat and maize chromosomes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16109971

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GR.3869505

1 reference

30 July 2017

1 reference

30 July 2017

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