(Q33268608)

24 July 2017

title

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana (English)

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Oryza sativa

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10

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45

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86

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79

Tatiana Tatusova

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Claire O'Donovan

54

Claire O'Donovan

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Tsuyoshi Tanaka

Tsuyoshi Tanaka

3

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Yao-Cheng Lin

Yao-Cheng Lin

41

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Kanako O Koyanagi

Kanako O Koyanagi

38

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Takeshi Itoh

Takeshi Itoh

2

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Tadashi Imanishi

Tadashi Imanishi

28

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Joachim Messing

Joachim Messing

46

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Nicola Mulder

Nicola Mulder

48

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Richard Bruskiewich

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Richard Bruskiewich

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Mika Tsugane

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Akio Miyao

Akio Miyao

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Tetsuya Sakurai

Tetsuya Sakurai

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Takashi Gojobori

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Takashi Gojobori

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Kazuho Ikeo

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David Lonsdale

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Pankaj Jaiswal

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Chisato Yamasaki

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Katsumi Sakata

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Phillip B Hilton

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Roberto A Barrero

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Takuya Habara

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Masako Kanno

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Akihiro Matsuya

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Shin Nurimoto

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Naomi Saichi

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Fusano Todokoro

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Hajime Ohyanagi

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Naoki Osato

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Motohiko Tanino

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Satoshi Oota

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Hiroaki Sakai

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Antonio Baltazar-Raigosa

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Baltazar A Antonio

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49

Yoshiaki Nagamura

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Takuji Sasaki

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Rice Annotation Project

1

Rice Annotation Project

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15

Galina Fuks

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Georg Haberer

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Erimi Harada

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Aiko T Hiraki

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Douglas Hoen

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Satomi Hosokawa

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Yue-Ie Caroline Hsing

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Yue-ie Hsing

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Hiroshi Ikawa

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Yukiyo Ito

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Hiroaki Kawashima

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Jitendra P Khurana

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Shoshi Kikuchi

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Hiromi Kubooka

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Damien Lieberherr

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Nobukazu Namiki

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Hisataka Numa

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Toshihisa Okido

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Saurabh Raghuvanshi

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Yasumichi Sakai

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Michie Shibata

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Yuji Shinso

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Brian Smith-White

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Jun-ichi Takeda

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Akhilesh K Tyagi

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Yasuyuki Fujii

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Lance E Palmer

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Francis Quetier

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Aihui Wang

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Kazuo Shinozaki

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Hirohiko Hirochika

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Hideo Aono

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Thomas Bureau

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Frances Burr

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Antonio Costa de Oliveira

14

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Bin Han

18

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Hiroki Hokari

23

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Yoshihiro Kawahara

32

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Toshiyuki Kawamura

33

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Setsuko Komatsu

37

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Takashi Matsumoto

43

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Jongmin Nam

50

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Fumihiko Sato

67

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Yoshiharu Sato

68

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Heiko Schoof

69

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Motoaki Seki

70

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Yuji Shimizu

72

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Nagendra K Singh

75

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Supat Thongjuea

80

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Apichart Vanavichit

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Kaori Yamaguchi

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Mayu Yamamoto

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Naoyuki Yamamoto

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Yeisoo Yu

90

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Hao Zhang

91

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Qiang Zhao

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Kenichi Higo

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Benjamin Burr

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24 July 2017

publication date

8 January 2007

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volume

17

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24 July 2017

issue

2

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24 July 2017

page(s)

175-183

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The Rice Annotation Project Database (RAP-DB): hub for Oryza sativa ssp. japonica genome information

24 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=1781349

Functional diversification of the two C-class MADS box genes OSMADS3 and OSMADS58 in Oryza sativa

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

The transcriptional landscape of the mammalian genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

The map-based sequence of the rice genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

InterProScan: protein domains identifier

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Large-scale identification of expressed sequence tags involved in rice and rice blast fungus interaction

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Non-coding RNAs: hope or hype?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Cloning and characterization of microRNAs from rice

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

The Genomes of Oryza sativa: a history of duplications

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Rice proteome analysis: a step toward functional analysis of the rice genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Construction and evaluation of cDNA libraries for large-scale expressed sequence tag sequencing in wheat (Triticum aestivum L.).

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Consistent over-estimation of gene number in complex plant genomes.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Characterization of the maize endosperm transcriptome and its comparison to the rice genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Rice mutant resources for gene discovery

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

The new genes of rice: a closer look.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Integrative annotation of 21,037 human genes validated by full-length cDNA clones

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Anchoring 9,371 maize expressed sequence tagged unigenes to the bacterial artificial chromosome contig map by two-dimensional overgo hybridization

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis: its status in 2003.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Bioverse: Functional, structural and contextual annotation of proteins and proteomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Comparative biology comes into bloom: genomic and genetic comparison of flowering pathways in rice and Arabidopsis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Comparison of rice and Arabidopsis annotation.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

A comprehensive rice transcript map containing 6591 expressed sequence tag sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Comparison of RNA expression profiles based on maize expressed sequence tag frequency analysis and micro-array hybridization

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

InterProScan--an integration platform for the signature-recognition methods in InterPro

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Microbial genes in the human genome: lateral transfer or gene loss?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Initial sequencing and analysis of the human genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

The evolutionary fate and consequences of duplicate genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Biology's new Rosetta stone

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Codon catalog usage and the genome hypothesis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Sequences of four tRNA genes from Caenorhabditis elegans and the expression of C. elegans tRNALeu (anticodon IAG) in Xenopus oocytes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Codon usage and tRNA content in unicellular and multicellular organisms

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for arabidopsis lateral root development

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

The genome sequence and structure of rice chromosome 1.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Genome-wide transcription analyses in rice using tiling microarrays

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Evaluation of five ab initio gene prediction programs for the discovery of maize genes

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1781349

Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17210932

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17210932

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1101/GR.5509507

1 reference

release_ifpovjyd6nbzvba43hr2r4ugci

24 July 2017

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/ifpovjyd6nbzvba43hr2r4ugci

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMC publication ID

1781349

1 reference

24 July 2017

1 reference