Arabidopsis thaliana (TAIR10) ▼ 
Summary
Splice variantsTranscript comparisonGene allelesSequenceSecondary StructureGene familiesLiteraturePlant ComparaPan-taxonomic ComparaOntologiesPhenotypesGenetic VariationVariant tableVariant imageStructural variantsGene expressionPathwayRegulationExternal referencesSupporting evidenceID HistoryGene historyGramene Search.
phytochrome D [Source:NCBI gene (formerly Entrezgene);Acc:827319]
DL4165C, FCAALL.323, PHYTOCHROME D
Chromosome 4: 9,195,247-9,199,840 reverse strand.
This gene has 1 transcript (splice variant), 160 orthologues and 15 paralogues.
| Name | Transcript ID | bp | Protein | Translation ID | Biotype | UniProt | RefSeq | Flags |
|---|---|---|---|---|---|---|---|---|
| PHYD-201 | AT4G16250.1 | 4204 | 1164aa | AT4G16250.1 | Protein coding | A0A654FPT9 P42497 | - | Ensembl Canonical, |
.
Showing the top 50 hits from Europe PubMed Central
| PubMed ID | Title | Authors | Journal |
|---|---|---|---|
| PMC10706466 | Effect of Red Light on the Expression of the Phytochrome Gene Family and the Accumulation of Glycoside Alkaloids in Potatoes | Zhang X, Jiang H, Liu W, Wang Y, Zeng F. | Foods 12 (23) 2023 |
| 37810087 | Photobiotechnology for abiotic stress resilient crops: Recent advances and prospects. | Gururani MA. | Heliyon 9 (9) 2023 |
| 35687579 | Photoreceptors' gene expression of Arabidopsis thaliana grown with biophilic LED-sourced lighting systems. | Beatrice P, Chiatante D, Scippa GS, Montagnoli A. | PLoS One 17 (6) 2022 |
| 38545394 | Phytochrome phosphorylation in plant light signaling. | Han YJ, Kim SH, Kim JI. | Front Plant Sci 15 2024 |
| 36430613 | Phytochromes and Their Role in Diurnal Variations of ROS Metabolism and Plant Proteome. | Luklová M, Novák J, Kopecká R, Kameniarová M, Gibasová V, Brzobohatý B, Černý M. | Int J Mol Sci 23 (22) 2022 |
| 38247523 | Application of Multi-Omics Technologies to the Study of Phytochromes in Plants. | Wu S, Gao Y, Zhang Q, Liu F, Hu W. | Antioxidants (Basel) 13 (1) 2024 |
| 38275750 | Phytochrome-Interacting Proteins. | Kaeser G, Krauß N, Roughan C, Sauthof L, Scheerer P, Lamparter T. | Biomolecules 14 (1) 2023 |
| 37887291 | Role of Phytochromes in Red Light-Regulated Alternative Splicing in Arabidopsis thaliana: Impactful but Not Indispensable. | Careno DA, Assaf CH, Eggermont EDC, Canelo M, Cerdán PD, Yanovsky MJ. | Cells 12 (20) 2023 |
| 33668919 | Network Analysis of Gene Transcriptions of Arabidopsis thaliana in Spaceflight Microgravity. | Manian V, Orozco J, Gangapuram H, Janwa H, Agrinsoni C. | Genes (Basel) 12 (3) 2021 |
| 37514360 | The Role of Light Quality in Regulating Early Seedling Development. | Wei Y, Wang S, Yu D. | Plants (Basel) 12 (14) 2023 |
| 36140734 | Transcriptomic Analysis Reveals the Correlation between End-of-Day Far Red Light and Chilling Stress in Setaria viridis. | Sun S, Liu Q, Dai X, Wang X. | Genes (Basel) 13 (9) 2022 |
| 36882415 | The Arabidopsis endosperm is a temperature-sensing tissue that implements seed thermoinhibition through phyB. | Piskurewicz U, Sentandreu M, Iwasaki M, Glauser G, Lopez-Molina L. | Nat Commun 14 (1) 2023 |
| 35856037 | Recent transcriptomic studies to elucidate the plant adaptive response to spaceflight and to simulated space environments. | Manzano A, Carnero-Diaz E, Herranz R, Medina FJ. | iScience 25 (8) 2022 |
| 38143485 | The red/far-red light photoreceptor FvePhyB regulates tissue elongation and anthocyanin accumulation in woodland strawberry. | Gao Q, Hu S, Wang X, Han F, Luo H, Liu Z, Kang C. | Hortic Res 10 (12) 2023 |
| 36941263 | Meta-analysis of the space flight and microgravity response of the Arabidopsis plant transcriptome. | Barker R, Kruse CPS, Johnson C, Saravia-Butler A, Fogle H, Chang HS, Trane RM, Kinscherf N, Villacampa A, Manzano A, Herranz R, Davin LB, Lewis NG, Perera I, Wolverton C, Gupta P, Jaiswal P, Reinsch SS, Wyatt S, Gilroy S. | NPJ Microgravity 9 (1) 2023 |
| 37017001 | COLD REGULATED GENE 27 and 28 antagonize the transcriptional activity of the RVE8/LNK1/LNK2 circadian complex. | Sorkin ML, Tzeng SC, King S, Romanowski A, Kahle N, Bindbeutel R, Hiltbrunner A, Yanovsky MJ, Evans BS, Nusinow DA. | Plant Physiol 192 (3) 2023 |
| 36982350 | The Role of Light-Regulated Auxin Signaling in Root Development. | Yun F, Liu H, Deng Y, Hou X, Liao W. | Int J Mol Sci 24 (6) 2023 |
| 36161012 | Functional analysis of PHYB polymorphisms in Arabidopsis thaliana collected in Patagonia. | Ruiz-Diaz MJ, Matsusaka D, Cascales J, Sánchez DH, Sánchez-Lamas M, Cerdán PD, Botto JF. | Front Plant Sci 13 2022 |
| 38139141 | Two-Component System Genes in Brassica napus: Identification, Analysis, and Expression Patterns in Response to Abiotic and Biotic Stresses. | Liu H, Liu N, Peng C, Huang J, Hua W, Fu Z, Liu J. | Int J Mol Sci 24 (24) 2023 |
| 37333861 | Machine learning classification of plant genotypes grown under different light conditions through the integration of multi-scale time-series data. | Sakeef N, Scandola S, Kennedy C, Lummer C, Chang J, Uhrig RG, Lin G. | Comput Struct Biotechnol J 21 2023 |
| 36340397 | Divergence of flowering-related genes to control flowering in five Euphorbiaceae genomes. | Jiang L, Fan T, Wang L, Zhang L, Xu J. | Front Plant Sci 13 2022 |
| 35024973 | Phylogenetic analysis of phytochrome A gene from Lablab purpureus (L.) Sweet. | Krishna S, Modha K, Parekh V, Patel R, Chauhan D. | J Genet Eng Biotechnol 20 (1) 2022 |
| 35955826 | Phylogenomics-Based Reconstruction and Molecular Evolutionary Histories of Brassica Photoreceptor Gene Families. | Muthusamy M, Kim JA, Lee SI. | Int J Mol Sci 23 (15) 2022 |
| 35955637 | Underlying Biochemical and Molecular Mechanisms for Seed Germination. | Farooq MA, Ma W, Shen S, Gu A. | Int J Mol Sci 23 (15) 2022 |
| 31596952 | Differential phosphorylation of the N-terminal extension regulates phytochrome B signaling. | Viczián A, Ádám É, Staudt AM, Lambert D, Klement E, Romero Montepaone S, Hiltbrunner A, Casal J, Schäfer E, Nagy F, Klose C. | New Phytol 225 (4) 2020 |
| 36670526 | Phytochrome F mediates red light responsiveness additively with phytochromes B1 and B2 in tomato. | Balderrama D, Barnwell S, Carlson KD, Salido E, Guevara R, Nguyen C, Madlung A. | Plant Physiol 191 (4) 2023 |
| 36617439 | Shade avoidance in the context of climate change. | Casal JJ, Fankhauser C. | Plant Physiol 191 (3) 2023 |
| 38000896 | Improved super-resolution ribosome profiling reveals prevalent translation of upstream ORFs and small ORFs in Arabidopsis. | Wu HL, Ai Q, Teixeira RT, Nguyen PHT, Song G, Montes C, Elmore JM, Walley JW, Hsu PY. | Plant Cell 36 (3) 2024 |
| 35574141 | Candidate Genes Modulating Reproductive Timing in Elite US Soybean Lines Identified in Soybean Alleles of Arabidopsis Flowering Orthologs With Divergent Latitude Distribution. | Dietz N, Chan YO, Scaboo A, Graef G, Hyten D, Happ M, Diers B, Lorenz A, Wang D, Joshi T, Bilyeu K. | Front Plant Sci 13 2022 |
| 36967993 | RNA sequencing-based exploration of the effects of far-red light on microRNAs involved in the shade-avoidance response of D. officinale. | Yang Y, Qiu Y, Ye W, Sun G, Li H. | PeerJ 11 2023 |
| 29648603 | PHYD prevents secondary dormancy establishment of seeds exposed to high temperature and is associated with lower PIL5 accumulation. | Martel C, Blair LK, Donohue K. | J Exp Bot 69 (12) 2018 |
| 33888582 | ARABIDOPSIS THALIANA HOMEOBOX GENE 1 controls plant architecture by locally restricting environmental responses. | Ejaz M, Bencivenga S, Tavares R, Bush M, Sablowski R. | Proc Natl Acad Sci U S A 118 (17) 2021 |
| 35008892 | Molecular Genetic Understanding of Photoperiodic Regulation of Flowering Time in Arabidopsis and Soybean. | Luo X, Yin M, He Y. | Int J Mol Sci 23 (1) 2021 |
| 34290729 | Genome-Wide Comparative Analysis of Flowering-Time Genes; Insights on the Gene Family Expansion and Evolutionary Perspective. | Hong S, Lim YP, Kwon SY, Shin AY, Kim YM. | Front Plant Sci 12 2021 |
| 35106435 | Arabidopsis CIA2 and CIL have distinct and overlapping functions in regulating chloroplast and flower development. | Yang CY, Yan WY, Chang HY, Sun CW. | Plant Direct 6 (1) 2022 |
| 36979120 | Generation of High-Value Genomic Resource in Rice: A "Subgenomic Library" of Low-Light Tolerant Rice Cultivar Swarnaprabha. | Sahu S, Gupta P, Gowtham TP, Yogesh KS, Sanjay TD, Singh A, Duong HV, Pradhan SK, Bisht DS, Singh NK, Baig MJ, Rai R, Dash PK. | Biology (Basel) 12 (3) 2023 |
| 37063177 | Omics-assisted characterization of two-component system genes from Gossypium Raimondii in response to salinity and molecular interaction with abscisic acid. | Rasool A, Azeem F, Ur-Rahman M, Rizwan M, Hussnain Siddique M, Bay DH, Binothman N, Al Kashgry NAT, Qari SH. | Front Plant Sci 14 2023 |
| 32351535 | Progress of Research on the Regulatory Pathway of the Plant Shade-Avoidance Syndrome. | Wang X, Gao X, Liu Y, Fan S, Ma Q. | Front Plant Sci 11 2020 |
| 34899869 | Two-Component System Genes in Sorghum bicolor: Genome-Wide Identification and Expression Profiling in Response to Environmental Stresses. | Zameer R, Zameer R, Sadaqat M, Fatima K, Fiaz S, Rasul S, Zafar H, Qayyum A, Nashat N, Raza A, Shah AN, Batool R, Azeem F, Sun S, Chung G. | Front Genet 12 2021 |
| 29049346 | Biological activity and dimerization state of modified phytochrome A proteins. | Liu P, Sharrock RA. | PLoS One 12 (10) 2017 |
| 31420516 | Large-effect flowering time mutations reveal conditionally adaptive paths through fitness landscapes in Arabidopsis thaliana. | Taylor MA, Wilczek AM, Roe JL, Welch SM, Runcie DE, Cooper MD, Schmitt J. | Proc Natl Acad Sci U S A 116 (36) 2019 |
| 36340409 | Bifunctional regulators of photoperiodic flowering in short day plant rice. | Sun C, He C, Zhong C, Liu S, Liu H, Luo X, Li J, Zhang Y, Guo Y, Yang B, Wang P, Deng X. | Front Plant Sci 13 2022 |
| 33530294 | Carotenoid Biosynthesis and Plastid Development in Plants: The Role of Light. | Quian-Ulloa R, Stange C. | Int J Mol Sci 22 (3) 2021 |
| 27820825 | Bottom-up Assembly of the Phytochrome Network. | Sánchez-Lamas M, Lorenzo CD, Cerdán PD. | PLoS Genet 12 (11) 2016 |
| 32265943 | Test of Arabidopsis Space Transcriptome: A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments. | Barker R, Lombardino J, Rasmussen K, Gilroy S. | Front Plant Sci 11 2020 |
| 36768431 | Regulation of Plant Photoresponses by Protein Kinase Activity of Phytochrome A. | Choi DM, Kim SH, Han YJ, Kim JI. | Int J Mol Sci 24 (3) 2023 |
| 34039713 | Differing biophysical properties underpin the unique signaling potentials within the plant phytochrome photoreceptor families. | Burgie ES, Gannam ZTK, McLoughlin KE, Sherman CD, Holehouse AS, Stankey RJ, Vierstra RD. | Proc Natl Acad Sci U S A 118 (22) 2021 |
| 28662188 | Genetic dissection of the Arabidopsis spaceflight transcriptome: Are some responses dispensable for the physiological adaptation of plants to spaceflight? | Paul AL, Sng NJ, Zupanska AK, Krishnamurthy A, Schultz ER, Ferl RJ. | PLoS One 12 (6) 2017 |
| 34205326 | Detection of Genes in Arabidopsis thaliana L. Responding to DNA Damage from Radiation and Other Stressors in Spaceflight. | Manian V, Orozco-Sandoval J, Diaz-Martinez V. | Genes (Basel) 12 (6) 2021 |
| 35645991 | Arabidopsis Circadian Clock Repress Phytochrome a Signaling. | Liu Y, Sun Y, Yao H, Zheng Y, Cao S, Wang H. | Front Plant Sci 13 2022 |
.
Gramene release 68 - Nov 2023 © EMBL-EBI EMBL-EBI
.
.
![[RSS logo]](/i/rss_icon_16.png "Gramene blog"){kind=icon}
![[twitter logo]](/i/twitter.png "Follow us on Twitter!")
