Reference health
AtRTD2: A Reference Transcript Dataset for accurate quantification of alternative splicing and expression changes in <i>Arabidopsis thaliana</i> RNA-seq data
57/57 checkable references clean · checked 2026-07-22
Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.
4 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
The 57 checked references that resolve
resolves10.1146/annurev-biochem-060614-034316
Mechanisms and Regulation of Alternative Pre-mRNA Splicing
resolves10.1093/nar/gkr932
Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis
resolves10.1016/j.bbagrm.2013.02.005
Nonsense-mediated mRNA decay — Mechanisms of substrate mRNA recognition and degradation in mammalian cells
resolves10.1016/j.plantsci.2011.09.006
Alternative splicing: Enhancing ability to cope with stress via transcriptome plasticity
resolves10.1007/s00709-012-0448-9
On the physiological significance of alternative splicing events in higher plants
resolves10.1105/tpc.113.113803
Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses
resolves10.1016/j.pbi.2015.02.008
Alternative splicing in plants: directing traffic at the crossroads of adaptation and environmental stress
resolves10.1101/gr.134106.111
Transcriptome survey reveals increased complexity of the alternative splicing landscape in <i>Arabidopsis</i>
resolves10.1038/nature09470
A methyl transferase links the circadian clock to the regulation of alternative splicing
resolves10.1105/tpc.112.104828
Mutation of
<i>Arabidopsis SPLICEOSOMAL TIMEKEEPER LOCUS1</i>
Causes Circadian Clock Defects
resolves10.1038/nature12633
Temperature-dependent regulation of flowering by antagonistic FLM variants
resolves10.1126/science.1250322
A Chloroplast Retrograde Signal Regulates Nuclear Alternative Splicing
resolves10.1371/journal.pgen.1004375
Intron Retention in the 5′UTR of the Novel ZIF2 Transporter Enhances Translation to Promote Zinc Tolerance in Arabidopsis
resolves10.1073/pnas.1407147112
Phytochrome controls alternative splicing to mediate light responses in
<i>Arabidopsis</i>
resolves10.1371/journal.pgen.1005737
Seed Dormancy in Arabidopsis Requires Self-Binding Ability of DOG1 Protein and the Presence of Multiple Isoforms Generated by Alternative Splicing
resolves10.1101/gr.186585.114
Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity
resolves10.1105/tpc.111.093948
Alternative Splicing Mediates Responses of the <i>Arabidopsis</i> Circadian Clock to Temperature Changes
resolves10.1104/pp.107.108720
Alternative Splicing and mRNA Levels of the Disease Resistance Gene <i>RPS4</i> Are Induced during Defense Responses
resolves10.1104/pp.109.138180
Two Alternatively Spliced Isoforms of the Arabidopsis SR45 Protein Have Distinct Roles during Normal Plant Development
resolves10.1371/journal.pone.0126516
MAF2 Is Regulated by Temperature-Dependent Splicing and Represses Flowering at Low Temperatures in Parallel with FLM
resolves10.1073/pnas.1009050107
Single amino acid change alters the ability to specify male or female organ identity
resolves10.1038/nbt.2450
Differential analysis of gene regulation at transcript resolution with RNA-seq
resolves10.1038/nbt.1621
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
resolves10.1093/bioinformatics/btr355
Identification of novel transcripts in annotated genomes using RNA-Seq
resolves10.1186/gb-2013-14-4-r36
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
resolves10.1186/1471-2105-12-323
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
resolves10.1038/nmeth.2251
Streaming fragment assignment for real-time analysis of sequencing experiments
resolves10.1038/nbt.3122
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
resolves10.1093/bioinformatics/btv488
Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data
resolves10.1038/nbt.2862
Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms
resolves10.1111/nph.13545
At<scp>RTD</scp> – a comprehensive reference transcript dataset resource for accurate quantification of transcript‐specific expression in <i>Arabidopsis thaliana</i>
resolves10.1002/dvg.22877
The arabidopsis information resource: Making and mining the “gold standard” annotated reference plant genome
resolves10.1101/047308
Araport11: a complete reannotation of the
<i>Arabidopsis thaliana</i>
reference genome
resolves10.1261/rna.051557.115
Leveraging transcript quantification for fast computation of alternative splicing profiles
resolves10.1101/gad.258814.115
Phenotypic evolution through variation in splicing of the noncoding RNA<i>COOLAIR</i>
resolves10.1093/nar/gkp189
Gene structures and processing of Arabidopsis thaliana HYL1-dependent pri-miRNAs
resolves10.1111/j.1365-313X.2007.03392.x
Monitoring changes in alternative precursor messenger RNA splicing in multiple gene transcripts
resolves10.1105/tpc.114.125617
Paired-End Analysis of Transcription Start Sites in <i>Arabidopsis</i> Reveals Plant-Specific Promoter Signatures
resolves10.1038/nsmb.2345
Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation
resolves10.1371/journal.pone.0066511
Genome-Wide Survey of Cold Stress Regulated Alternative Splicing in Arabidopsis thaliana with Tiling Microarray
resolves10.1186/gb-2011-12-3-r22
Improving RNA-Seq expression estimates by correcting for fragment bias
resolves10.1105/tpc.15.00572
Lost in Translation: Pitfalls in Deciphering Plant Alternative Splicing Transcripts
resolves10.1093/nar/gkp869
Involvement of the nuclear cap-binding protein complex in alternative splicing in Arabidopsis thaliana
resolves10.1093/nar/gks873
An hnRNP-like RNA-binding protein affects alternative splicing by in vivo interaction with transcripts in Arabidopsis thaliana
resolves10.1186/s12859-014-0364-4
Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems
The 4 references without a DOI — listed, not checked
no DOI — not checkedGenome-wide identification of evolutionarily conserved alternative splicing events in flowering plants
no DOI — not checkedPatro R , Duggal G , Kingsford C : Accurate, fast, and model-aware transcript expression quantification with Salmon. bioRxiv 2015, dx.doi.org/10.1101/021592.
no DOI — not checkedBray N , Pimentel H , Melsted P , Pachter L : Near-optimal RNA-Seq quantification. arXivorg 2015, arXiv:1505.02710v2.
no DOI — not checkedAraport: Arabidopsis Information Portal www.araport.org. Accessed 12 April 2016 .
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