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Pubmed ID :27862469
Publication Date : //

Araport11: a complete reannotation of the Arabidopsis thaliana reference genome.


The flowering plant Arabidopsis thaliana is a dicot model organism for research in many aspects of plant biology. A comprehensive annotation of its genome paves the way for understanding the functions and activities of all types of transcripts, including mRNA, the various classes of non-coding RNA, and small RNA. The TAIR10 annotation update had a profound impact on Arabidopsis research but was released more than 5 years ago. Maintaining the accuracy of the annotation continues to be a prerequisite for future progress. Using an integrative annotation pipeline, we assembled tissue-specific RNA-Seq libraries from 113 datasets and constructed 48 359 transcript models of protein-coding genes in eleven tissues. In addition, we annotated various classes of non-coding RNA including microRNA, long intergenic RNA, small nucleolar RNA, natural antisense transcript, small nuclear RNA, and small RNA using published datasets and in-house analytic results. Altogether, we identified 635 novel protein-coding genes, 508 novel transcribed regions, 5178 non-coding RNAs, and 35 846 small RNA loci that were formerly unannotated. Analysis of the splicing events and RNA-Seq based expression profiles revealed the landscapes of gene structures, untranslated regions, and splicing activities to be more intricate than previously appreciated. Furthermore, we present 692 uniformly expressed housekeeping genes, 43% of whose human orthologs are also housekeeping genes. This updated Arabidopsis genome annotation with a substantially increased resolution of gene models will not only further our understanding of the biological processes of this plant model but also of other species.

Authors : Cheng Chia-Yi , Krishnakumar Vivek , Chan Agnes P , Thibaud-Nissen Françoise , Schobel Seth , Town Christopher D ,

Related products :

Catalog number Product name Quantity
AS07 258 Antibody: LOX-C | chloroplastic lipoxygenase, Immunogen: recombinant Arabidopsis thaliana protein, loop (aa 257-450) P38418, Host: rabbit, polyclonal, Confirmed reactivity: Arabidopsis thaliana 100
AS11 1783 Antibody: Acd1 | accelerated cell death 1 , Immunogen: recombinant PaO from Arabidopsis thaliana Q9FYC2, Host: rabbit, polyclonal, Confirmed reactivity: Arabidopsis thaliana 100
AS09 476 Antibody: AtArf2 | ADP ribosylation factor 2, Immunogen: synthetic peptide derived from Arabidopsis thaliana Q9SRC3, Host: rabbit, polyclonal, Confirmed reactivity: Arabidopsis thaliana 100
AS09 477 Antibody: S14 | 40S ribosomal protein S14-1, Immunogen: KLH-conjugated synthetic peptide derived from Arabidopsis thaliana Q9SIH0, Host: rabbit, polyclonal, Confirmed reactivity: Arabidopsis thaliana 100
AS09 515 Antibody: KC1 | potassium channel KAT3 , Immunogen: KLH-conjugated peptide derived from Arabidopsis thaliana KC1 protein P92960, Host: rabbit, polyclonal, Confirmed reactivity: Arabidopsis thaliana 200
AS09 474 Antibody: AtMTP4 | metal tolerance protein B, Immunogen: synthetic peptide derived from Arabidopsis thaliana Q9SRC3, Host: rabbit, polyclonal, Confirmed reactivity: Arabidopsis thaliana 100
AS09 475 Antibody: Ligand-gated ion channel 1.3, Immunogen: KLH-conjugated synthetic peptide derived from Arabidopsis thaliana Q9FH75, Host: rabbit, polyclonal, Confirmed reactivity: Arabidopsis thaliana, Raph 100
AS10 931 Antibody: AtPCaP1 | Arabidopsis thaliana plasma membrane cation-binding protein-1, Immunogen: KLH-conjugated peptide derived from Arabidopsis thaliana PCaP1 sequence Q96262, Host: rabbit, polyclonal, 100
AS10 651 Antibody: Enolase, Immunogen: recombinant Arabidopsis thaliana enolase At2g36530, Host: rabbit, polyclonal, Confirmed reactivity: Arabidopsis thaliana 200
AS10 937 Antibody: CPLD11 , Immunogen: overexpressed fragment of recombinant Arabidopsis thaliana CPLD11 NP_566650, Host: rabbit, polyclonal, Confirmed reactivity: Arabidopsis thaliana 200
AS10 671 Antibody: AGO5 | argonaute 5, Immunogen: peptide of Arabidopsis thaliana AGO5 Q9SJK3, AT2G27880, Host: rabbit, polyclonal, Confirmed reactivity: Arabidopsis thaliana 200
AS09 459 Antibody: ClpB-P | ClpB3, Immunogen: KLH-conjugated peptide derived from ClpB-P of Arabidopsis thaliana Q9LF37, Host: rabbit, polyclonal, Confirmed reactivity: Arabidopsis thaliana 200
AS10 672 Antibody: AGO6 | argonaute 6, Immunogen: KLH-conjugated peptide derived from Arabidopsis thaliana AGO6 At2g32940, Host: rabbit, polyclonal, Confirmed reactivity: Arabidopsis thaliana 100
AS10 721 Antibody: PHOT2 | phototropin-2, Immunogen: KLH-conjugated synthetic peptide derived from known Arabidopsis thaliana PHOT2 P93025, Host: rabbit, polyclonal, Confirmed reactivity: Arabidopsis thaliana 100
AS11 1628 Antibody: HSP18.5 | class IV heat shock protein, Immunogen: recombinant Arabidopsis thaliana Hsp18.5 , Host: rabbit, polyclonal, Confirmed reactivity: Arabidopsis thaliana 200
AS11 1753 Antibody: HDT3 | histone deacetylase, Immunogen: recombinant part of Arabidopsis thaliana HDT3 Q9LZR5, Host: rabbit, polyclonal, Confirmed reactivity: Arabidopsis thaliana 100
AS10 720 Antibody: PHOT1 | phototropin-1, Immunogen: KLH-conjugated synthetic peptide derived from known Arabidopsis thaliana PHOT1 O48963, Host: rabbit, polyclonal, Confirmed reactivity: Arabidopsis thaliana 100
AS06 116 Antibody: PGL35 | plastoglobulin 35, Immunogen: recombinant Arabidopsis thaliana PGL35 protein O81439 , Host: rabbit, polyclonal, Confirmed reactivity: Arabidopsis thaliana, Gossypium hirsutum cv. Del 200
AS11 1629 Antibody: HSP90-2 | heat shock protein 90-2, Immunogen: full length recombinant Hsp90-2 from Arabidopsis thaliana, Host: rabbit, polyclonal, Confirmed reactivity: Arabidopsis thaliana 100
AS09 481 Antibody: BiP | lumenal-binding protein , Immunogen: KLH-conjugated synthetic peptide derived from Arabidopsis thaliana BiP2 Q39043. Chosen peptide is also conserved in Arabidopsis thaliana BiP1 prote 200
AS09 527 Antibody: AGO1 | argonaute 1, Immunogen: N-terminal peptide of Arabidopsis thaliana AGO1 O04379, Host: rabbit, polyclonal, Confirmed reactivity: Arabidopsis thaliana, Hyacinthus orientalis, Nicotiana 100
AS05 059 Antibody: PsbR | 10 kDa protein of PSII, Immunogen: KLH-conjugated synthetic peptide chosen from Arabidopsis thaliana PsbR P27202, Host: rabbit, polyclonal, Confirmed reactivity: Arabidopsis thaliana, 100
AS09 615 Antibody: BiP | lumenal-binding protein , Immunogen: KLH-conjugated synthetic peptide derived from Arabidopsis thaliana BiP2 Q39043. Chosen peptide is also conserved in Arabidopsis thaliana BiP1 prote 100
AS09 614 Antibody: BiP | lumenal-binding protein , Immunogen: KLH-conjugated synthetic peptide derived from Arabidopsis thaliana BiP2 Q39043. Chosen peptide is also conserved in Arabidopsis thaliana BiP1 prote 100
AS10 711 Antibody: DEG15 | endopeptidase, peroxisomal marker , Immunogen: synthetic peptide derived from Arabidopsis thaliana DEG15, Q8VZD4, Host: rabbit, polyclonal, Confirmed reactivity: Arabidopsis thaliana 100


 

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