Family Search for PF03478 (DUF295)
PF03478 hits 69 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
Q2QXK7 F-box domain containing protein from Oryza sativa subsp. japonica
Aligns to 327:384 / 419 (13.8%), covers 94.5% of PF03478, 57.6 bits
- Genomic approach to study floral development genes in Rosa sp.
Dubois, PloS one 2011 - “...0,00 1,27 0,03 0,71 0,44 BI978115 (Q84W81) Hypothetical protein At5g49800 1,27 0,34 1,85 0,57 EC586690 Q2QXK7) F-box domain, putative 1,31 0,91 1,36 0,02 EC588294 (Q1S0D0) Glyoxalase/bleomycin resistance protein 1,32 0,46 0,77 1,19 EC588783 (Q9LUC1) Putative protein At3g14740 1,34 0,27 1,19 0,31 RoAP1a (Q283Q1) APETALA1 protein 1,38...”
AT1G27580 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 285:339 / 364 (15.1%), covers 98.2% of PF03478, 55.3 bits
AT4G25920 hypothetical protein (RefSeq) from Arabidopsis thaliana
Aligns to 309:354 / 390 (11.8%), covers 96.4% of PF03478, 52.3 bits
- Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants
Lama, Molecular biology and evolution 2019 - “...Land Vir AT4G14260 AtDOA7 + + nu Brass Eud AT4G16080 AtDOA8 + + mito mito AT4G25920 AtDOA9 + + mito Eud AT4G25930 AtDOA10 + + mito + Ang Eud AT5G03390 AtDOA11 + + mito plastid Land AT5G46130 AtDOA12 + + mito AT5G46140 AtDOA13 + + cyt...”
- “...as an annotated domain ( fig.1 ). Yeast two-hybrid interactions have been reported only for At4g25920 ( Arabidopsis Interactome Mapping Consortium 2011 ) ( supplementary table 1 , Supplementary Material online). A fourth group (indicated in orange in fig.1 ), including At1g57790 and At5g55150 , contains...”
- Comparative analysis of plant immune receptor architectures uncovers host proteins likely targeted by pathogens
Sarris, BMC biology 2016 - “...DNA-binding domain HARXL16 AT4G32570 tify tify domain HARXL21 AT1G15750 WD40 WD domain, G-beta repeat HARXL44 AT4G25920 DUF295 Protein of unknown function (DUF295) HARXL44 AT4G16380 HMA Heavy metal-associated domain HARXL45_group AT4G02550 Myb_DNA-bind_3 Myb/SANT-like DNA-binding domain HARXL68 AT1G45145 Thioredoxin Thioredoxin HARXL68 AT5G42980 Thioredoxin Thioredoxin HARXL73 AT4G39050 Kinesin Kinesin...”
- Conserved versatile master regulators in signalling pathways in response to stress in plants
Balderas-Hernández, AoB PLANTS 2013 - “...Sip1p/Sip2p/Gal83p family member); activates glucose-repressed genes, represses glucose-induced genes; role in sporulation and peroxisome biogenesis AT4G25920 828698 Hypothetical protein AT1G07310 837242 Calcium-dependent lipid-binding domain GDU4 817013 Glutamine dumper 4 ATERDJ2A 844334 Translocation protein SEC63 AT1G19450 8838529 Sugar transporter ERD6-like 4 CNGC18 831339 Cyclic nucleotide-gated channel 18...”
- Regulation of ABCB1/PGP1-catalysed auxin transport by linker phosphorylation
Henrichs, The EMBO journal 2012 - “...protein (At3G48830) and an unknown protein (At4G25920). In addition, two protein kinases, the histidinelike kinase AHK5/CYTOKININ INDEPENDENT2 (At5G10720)...”
- “...AT3G48830 61 3.2 Similar to unknown protein 1.1 AT4G25920 38 AHK5 (CYTOKININ INDEPENDENT 2) AT5G10720 34 1.2 PID (PINOID) AT2G34650 32 3.0 Protein phosphatase...”
AT5G46140 hypothetical protein (RefSeq) from Arabidopsis thaliana
Aligns to 212:257 / 289 (15.9%), covers 94.5% of PF03478, 51.2 bits
AT2G45940 hypothetical protein (RefSeq) from Arabidopsis thaliana
Aligns to 264:312 / 352 (13.9%), covers 92.7% of PF03478, 50.9 bits
AT1G30170 hypothetical protein (RefSeq) from Arabidopsis thaliana
Aligns to 293:337 / 366 (12.3%), covers 96.4% of PF03478, 50.4 bits
- A novel seed plants gene regulates oxidative stress tolerance in Arabidopsis thaliana
Sujeeth, Cellular and molecular life sciences : CMLS 2020 - “...HSFA2, ZAT10 ), chromatin remodelers ( CHR34 ), and unknown or uncharacterized proteins ( AT5G59390, AT1G30170, AT1G21520 ) are elevated in atr7 . This indicates that atr7 is primed for an upcoming oxidative stress via pathways involving genes of unknown functions. Collectively, the data reveal ATR7...”
- “...remodelers ( CHR34 ), and many genes encoding uncharacterized proteins ( ANAC085 , AT5G59390 , AT1G30170 , AT1G21520 ), were constantly upregulated in atr7 in the absence of stress (Table 1 , Supplementary Table3). Among the proteins encoded by the 100 most upregulated genes, 32% are...”
- Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants
Lama, Molecular biology and evolution 2019 - “...Land AT1G05550 AtDOA2 + + pm Land Ang AT1G30160 AtDOA3 + + cyt + Eud AT1G30170 AtDOA4 + + mito Ang AT1G68960 AtDOA5 + + mito Ang Eud AT2G45940 AtDOA6 + + cyt Land Vir AT4G14260 AtDOA7 + + nu Brass Eud AT4G16080 AtDOA8 + +...”
AT2G04830 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 9:73 / 100 (65.0%), covers 98.2% of PF03478, 49.9 bits
AT1G27540 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 304:358 / 383 (14.4%), covers 98.2% of PF03478, 49.1 bits
AT5G46130 hypothetical protein (RefSeq) from Arabidopsis thaliana
Aligns to 300:344 / 376 (12.0%), covers 94.5% of PF03478, 48.8 bits
AT1G68960 hypothetical protein (RefSeq) from Arabidopsis thaliana
Aligns to 303:349 / 376 (12.5%), covers 96.4% of PF03478, 48.6 bits
FB111_ARATH / Q3EBY8 F-box protein At2g17690; Protein SUPPRESSOR OF DRM1 DRM2 CMT3 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
NP_179360 ascorbic acid mannose pathway regulator, putative (DUF295) from Arabidopsis thaliana
AT2G17690 SDC (SUPPRESSOR OF DRM1 DRM2 CMT3) (RefSeq) from Arabidopsis thaliana
Aligns to 349:404 / 421 (13.3%), covers 96.4% of PF03478, 48.2 bits
- function: Involved in heat stress response. Contributes to recovery from heat stress.
- SDC mediates DNA methylation-controlled clock pace by interacting with ZTL in Arabidopsis.
Tian, Nucleic acids research 2021 - GeneRIF: SDC mediates DNA methylation-controlled clock pace by interacting with ZTL in Arabidopsis.
- Heat-induced release of epigenetic silencing reveals the concealed role of an imprinted plant gene.
Sanchez, PLoS genetics 2014 - GeneRIF: We propose that transcriptional gene silencing, known to be involved in gene imprinting, is also co-opted in the specific tuning of SDC expression upon heat stress and subsequent recovery
- Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading.
Henderson, Genes & development 2008 - GeneRIF: SDC has important implications for how plant genomes utilize gene silencing to repress endogenous genes. [Suppressor of drm1 drm2 cmt3] [SDC]
- SDC mediates DNA methylation-controlled clock pace by interacting with ZTL in Arabidopsis
Tian, Nucleic acids research 2021 - “...ddc3 mutant and found that the transcript levels of AT3G30720 ( Qua-Quine Starch, QQS ), AT2G17690 ( SDC ) and AT2G34655 were elevated in both met1 and ddc3 mutants ( Supplementary Figure S6B ). Among these, AT2G34655 encodes a hypothetical protein composed of only 22 amino...”
- Epigenetic regulation of spurious transcription initiation in Arabidopsis
Le, Nature communications 2020 - “...showing the ectopic activation of the TSSs at FWA ( AT4G25530 ) and SDC ( AT2G17690 ) gene loci in the met1 and ddm1 backgrounds (indicated by orange windows). Their dominant CTSSs (red arrows) were aligned to the upstream sequences, indicating the presence of TATA-box motifs...”
- The Pol IV largest subunit CTD quantitatively affects siRNA levels guiding RNA-directed DNA methylation
Wendte, Nucleic acids research 2019 - “...and siRNA levels. ( A ) AtSN1 ( AT3TE63860 ); ( B ) SDC ( AT2G17690 ); ( C ) AT3TE63155 ; ( D ) AT5TE47755 ; ( E ) AT3TE47840 ; ( F ) ERT14 (AT2G01422) ; ( G ) soloLTR (AT5TE35950) ; ( H...”
- Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants
Lama, Molecular biology and evolution 2019 - “...Vir AT2G17030 AtFDA11/SKIP23 + + + golgi + Vir AT2G17036 AtFDA12 + + + cyt AT2G17690 AtFDA13 + + + cyt cyto + Ang Eud Brass AT2G24250 AtFDA14 + + + cyt + Land AT2G24255 AtFDA15 + + + pm Ang Eud AT2G26160 AtFDA16 + +...”
- DNA sequence properties that predict susceptibility to epiallelic switching
Catoni, The EMBO journal 2017 - “...represent unmethylated cytosine and closed circles methylated. DNA methylation analyses at two RTELs (AT3TE46565Copia28 and AT2G17690 SDC promoter). General marking as in (A). Transcript levels in met11 and in reciprocal F1 hybrids of met11 and wild type (colour code above the graphs) of transposons assigned to...”
- A two-step process for epigenetic inheritance in Arabidopsis
Blevins, Molecular cell 2014 - “...or the indicated mutants (see also Figure S2 ). (C) Diagram of the SDC locus (At2g17690), showing upstream tandem repeats (purple arrows), the Pol II transcription start site (+1), and PolyA+ RNA-seq data plotted on a log 2 scale (black). PCR amplicons for chromatin immunoprecipitation (ChIP)...”
- Heat-induced release of epigenetic silencing reveals the concealed role of an imprinted plant gene
Sanchez, PLoS genetics 2014 - “...[16] , [18] [20] . We tested the heat stress entrainment of the genes SDC (AT2G17690), SQN (AT2G15790), and APUM9 (AT1G35730). Of these three candidates, only SDC showed a response pattern similar to L5-GUS ( Figure 1B and S 1). We hypothesized that for both L5-GUS...”
- RNA-directed DNA methylation regulates parental genomic imprinting at several loci in Arabidopsis
Vu, Development (Cambridge, England) 2013 - “...pSDC-H2B-RFP contains 2731 bp promoter sequences of SDC (At2g17690) locus in order to drive the expression of HISTONE2B-RFP in the plasmid pGnk-GW-H2B-RFP...”
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AT4G16080 hypothetical protein (RefSeq) from Arabidopsis thaliana
Aligns to 278:322 / 354 (12.7%), covers 94.5% of PF03478, 48.1 bits
- Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants
Lama, Molecular biology and evolution 2019 - “...Eud AT2G45940 AtDOA6 + + cyt Land Vir AT4G14260 AtDOA7 + + nu Brass Eud AT4G16080 AtDOA8 + + mito mito AT4G25920 AtDOA9 + + mito Eud AT4G25930 AtDOA10 + + mito + Ang Eud AT5G03390 AtDOA11 + + mito plastid Land AT5G46130 AtDOA12 + +...”
- “...evidence for organellar location of the DOA and DOB proteins was very limited. AtDOA8 ( At4g16080 ) was identified in purified mitochondria by mass spectrometry (MS) ( Senkler etal. 2017 ), whereas AtDOA11 ( AT5G03390 ) was identified by MS in purified chloroplasts ( Zybailov etal....”
AT5G25290 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 320:374 / 397 (13.9%), covers 98.2% of PF03478, 47.9 bits
AT2G24080 F-box family protein-related (RefSeq) from Arabidopsis thaliana
Aligns to 292:349 / 374 (15.5%), covers 98.2% of PF03478, 47.3 bits
AT4G14260 hypothetical protein (RefSeq) from Arabidopsis thaliana
Aligns to 305:349 / 379 (11.9%), covers 94.5% of PF03478, 46.8 bits
LOC106438264 uncharacterized protein LOC106438264 from Brassica napus
Aligns to 301:349 / 383 (12.8%), covers 94.5% of PF03478, 45.7 bits
AT5G03390 hypothetical protein (RefSeq) from Arabidopsis thaliana
Aligns to 305:352 / 373 (12.9%), covers 96.4% of PF03478, 45.4 bits
- Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants
Lama, Molecular biology and evolution 2019 - “...mito AT4G25920 AtDOA9 + + mito Eud AT4G25930 AtDOA10 + + mito + Ang Eud AT5G03390 AtDOA11 + + mito plastid Land AT5G46130 AtDOA12 + + mito AT5G46140 AtDOA13 + + cyt AT5G53780 AtDOA14 + + cyt Eud Brass AT5G53790 AtDOA15 + + pm Brass AT5G55440...”
- “...in purified mitochondria by mass spectrometry (MS) ( Senkler etal. 2017 ), whereas AtDOA11 ( AT5G03390 ) was identified by MS in purified chloroplasts ( Zybailov etal. 2008 ). As no green fluorescent protein (GFP) localization data were published for any of the predicted mitochondrial isoforms,...”
AT5G53790 hypothetical protein (RefSeq) from Arabidopsis thaliana
Aligns to 296:341 / 380 (12.1%), covers 94.5% of PF03478, 45.3 bits
LOC107418241 F-box protein At2g26160-like from Ziziphus jujuba var. spinosa
Aligns to 312:373 / 396 (15.7%), covers 92.7% of PF03478, 44.2 bits
- Construction of a highly saturated genetic map and identification of quantitative trait loci for leaf traits in jujube
Yan, Frontiers in plant science 2022 - “...genes were identified within the QTLs cluster regions. Annotation information showed that 4 genes (LOC107418196, LOC107418241, LOC107417968, and LOC112492570) in these QTLs are related to cell division and cell wall integrity. This research will provide a valuable tool for further QTL analysis, candidate gene identification, map-based...”
- “...cell wall biosynthesis (LOC107433386, LOC107417968, LOC112492570, LOC112491602, LOC107418569, and LOC107418597) and cell division (LOC107418196 and LOC107418241). Table8 Markers and genes in the associated regions by comparing the data bases. LG Coincidence interval (cM) QTL loci Gene number Gene withEff variation KEGG GO comments Eff SNP Eff...”
AT2G26160 hypothetical protein (RefSeq) from Arabidopsis thaliana
Aligns to 283:328 / 331 (13.9%), covers 72.7% of PF03478, 43.6 bits
AT4G17565 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 297:348 / 378 (13.8%), covers 100.0% of PF03478, 43.1 bits
AT5G67040 hypothetical protein (RefSeq) from Arabidopsis thaliana
Aligns to 93:138 / 165 (27.9%), covers 96.4% of PF03478, 42.7 bits
AT4G35733 hypothetical protein (RefSeq) from Arabidopsis thaliana
Aligns to 287:338 / 358 (14.5%), covers 96.4% of PF03478, 42.3 bits
AT3G25750 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 270:321 / 348 (14.9%), covers 98.2% of PF03478, 42.2 bits
AT4G25930 hypothetical protein (RefSeq) from Arabidopsis thaliana
Aligns to 293:344 / 367 (14.2%), covers 90.9% of PF03478, 41.6 bits
- Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants
Lama, Molecular biology and evolution 2019 - “...nu Brass Eud AT4G16080 AtDOA8 + + mito mito AT4G25920 AtDOA9 + + mito Eud AT4G25930 AtDOA10 + + mito + Ang Eud AT5G03390 AtDOA11 + + mito plastid Land AT5G46130 AtDOA12 + + mito AT5G46140 AtDOA13 + + cyt AT5G53780 AtDOA14 + + cyt Eud...”
- “...were published for any of the predicted mitochondrial isoforms, we cloned three representatives AtDOA10 ( At4g25930 ), AtDOB5 ( At5g52940 ), and AtDOB12 ( At5g54550 ) into C-terminal GFP-fusion vectors (see below for more information on why these were selected). The localization of the fusion proteins...”
SKI23_ARATH / Q3EBZ2 F-box protein SKIP23; SKP1-interacting partner 23 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT2G17030 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 306:365 / 407 (14.7%), covers 96.4% of PF03478, 40.1 bits
- function: Component of SCF(ASK-cullin-F-box) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins.
subunit: Part of a SCF (ASK-cullin-F-box) protein ligase complex (By similarity). Interacts with SKP1A/ASK1. - Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants
Lama, Molecular biology and evolution 2019 - “...AtFDA9 + + (+) pm Ang Eud Brass AT2G16365 AtFDA10 + + (+) nu Vir AT2G17030 AtFDA11/SKIP23 + + + golgi + Vir AT2G17036 AtFDA12 + + + cyt AT2G17690 AtFDA13 + + + cyt cyto + Ang Eud Brass AT2G24250 AtFDA14 + + + cyt...”
- “...2008 ). The Arabidopsis genome contains 20 ancestral-type F-box/DUF295 proteins. The SKP1-interacting Protein SKIP23 ( At2g17030 ) is part of this group and was previously found to interact with ASK1 ( Risseeuw etal. 2003 ), a component of, for example, the strigolactone SCF MAX2 receptor complex...”
- iRefIndex: a consolidated protein interaction database with provenance.
Razick, BMC bioinformatics 2008 - “...For example, Q7XJL8 was found to be a secondary accession in three separate UniProt records (Q3EBZ2, Q6DR20, and Q8GWA9). 2) The secondary references supplied by the interaction record point to more than one unique protein sequence. 3) An EntrezGene identifier is provided in the interaction record...”
AT5G55440 hypothetical protein (RefSeq) from Arabidopsis thaliana
Aligns to 288:343 / 365 (15.3%), covers 94.5% of PF03478, 39.9 bits
AT2G04840 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 302:362 / 389 (15.7%), covers 98.2% of PF03478, 39.4 bits
AT1G44080 F-box protein-related / C-type lectin-related (RefSeq) from Arabidopsis thaliana
Aligns to 271:323 / 347 (15.3%), covers 98.2% of PF03478, 38.4 bits
AT1G65760 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 288:346 / 362 (16.3%), covers 78.2% of PF03478, 38.1 bits
- Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants
Lama, Molecular biology and evolution 2019 - “...Vir At1g65375 AtFDA4 + + + AT1G65740 AtFDA5/UCL1 + + + cyt + Eud Brass AT1G65760 AtFDA6 + + + pm AT1G65770 AtFDA7 + + + mito + Eud Brass AT2G16290 AtFDA8 + + + pm Ang Eud Brass AT2G16300 AtFDA9 + + (+) pm Ang...”
- Control of Paternally Expressed Imprinted UPWARD CURLY LEAF1, a Gene Encoding an F-Box Protein That Regulates CURLY LEAF Polycomb Protein, in the Arabidopsis Endosperm
Jeong, PloS one 2015 - “...per well. Samples were normalized against 2 tubulin or actin levels. Sequencing of At1g65750 and At1g65760 in different Arabidopsis ecotypes To amplify At1g65750 and At1g65760 in different Arabidopsis ecotypes, the primer sets JCW637/638 and JCW639/640 ( S2 Table ) were used. Agarose gel electrophoresis revealed that...”
- Expression-based and co-localization detection of arabinogalactan protein 6 and arabinogalactan protein 11 interactors in Arabidopsis pollen and pollen tubes
Costa, BMC plant biology 2013 - “...(Pathogenesis-related protein, putative) At2g19970 +23.34 + C2 domain-containing protein At3g57880 +16.93 + F-box family protein At1g65760 +11.8 + Beta glucosidase 36 At1g51490 +4.95 + CAP (allergen V5) At2g19980 +4.79 + Hypothetical protein At2g22340 -141.79 - Pentatricopeptide (PPR) At5g28380 -44.55 - Avirulence-responsive family protein At4g09950 -25.77 -...”
- “...AGI locus LBFC a Gene annotation b 29.5.11.4.3.2: protein. degradation. ubiquitin. E3. SCF. F-box Up-regulated At1g65760 11.8 Protein of unknown function (DUF295) At2g27520 6.63 F-box and associated interaction domains-containing protein At5g38390 5.43 F-box/RNI-like superfamily protein At3g52030 3.92 F-box family protein with WD40/YVTN repeat domain At2g24080 3.52...”
- An E3 ligase complex regulates SET-domain polycomb group protein activity in Arabidopsis thaliana
Jeong, Proceedings of the National Academy of Sciences of the United States of America 2011 - “...RT-PCR (qRT-PCR) showed that expression of At1g65740, At1g65760, and At1g65770 was elevated in ucl1-D homozygous plants (Fig. S1B). Among these three...”
AT2G04810 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 311:370 / 397 (15.1%), covers 98.2% of PF03478, 37.5 bits
AT1G69090 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 318:370 / 401 (13.2%), covers 100.0% of PF03478, 37.0 bits
AT1G65740 F-box family protein (RefSeq) from Arabidopsis thaliana
NP_176751 ascorbic acid mannose pathway regulator (DUF295) from Arabidopsis thaliana
Aligns to 298:353 / 371 (15.1%), covers 70.9% of PF03478, 36.9 bits
- Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants
Lama, Molecular biology and evolution 2019 - “...cyt AT1G64840 AtFDA3 + + + cyt, pm + Vir At1g65375 AtFDA4 + + + AT1G65740 AtFDA5/UCL1 + + + cyt + Eud Brass AT1G65760 AtFDA6 + + + pm AT1G65770 AtFDA7 + + + mito + Eud Brass AT2G16290 AtFDA8 + + + pm Ang...”
- “...interact with Arabidopsis 14-3-3 proteins ( Hong etal. 2017 ). Upward Curly Leaf 1 (UCL1, At1g65740 ) was found to be a nuclear protein interacting with Curly Leaf Polycomb proteins and ASK1 ( Jeong etal. 2011 ). This indicates that ASK1 binding is a common feature...”
- Control of Paternally Expressed Imprinted UPWARD CURLY LEAF1, a Gene Encoding an F-Box Protein That Regulates CURLY LEAF Polycomb Protein, in the Arabidopsis Endosperm
Jeong, PloS one 2015 - “...According to the TAIR annotation, At1g65750 , which is located upstream of the UCL1 ( At1g65740 ) locus, encodes a non-LTR retrotransposon (LINE). Using the RepeatMasker program ( http://www.repeatmasker.org/cgi-bin/WEBRepeatMasker ), we identified two ATLINE1_1 transposable elements (TEs) in the Col-0 ecotype, namely 1) a long one...”
- “...that At1g65750 has a single non-LTR retrotransposon (LINE), which is located upstream of UCL1 ( At1g65740 ), At1g65750 is likely composed of two ATLINE1_1 transposable elements (TEs), according to the RepeatMasker program. Interestingly, the number of ATLINE1_1 TEs is not identical in different ecotypes. While both...”
- An E3 ligase complex regulates SET-domain polycomb group protein activity in Arabidopsis thaliana
Jeong, Proceedings of the National Academy of Sciences of the United States of America 2011 - “...had inserted in the intergenic region between At1g65740 and At1g65750 (Fig. 1B). Real-time quantitative RT-PCR (qRT-PCR) showed that expression of At1g65740,...”
- “...observed the curly leaf phenotype only when overexpressing At1g65740 in transgenic plants using the Cauliflower Mosaic Virus (CaMV) promoter (Figs. S1 C and D...”
- Control of Paternally Expressed Imprinted UPWARD CURLY LEAF1, a Gene Encoding an F-Box Protein That Regulates CURLY LEAF Polycomb Protein, in the Arabidopsis Endosperm.
Jeong, PloS one 2015 - GeneRIF: UPWARD CURLY LEAF1 (UCL1), a gene encoding an E3 ligase that degrades the CURLY LEAF (CLF) polycomb protein, is a paternally expressed imprinted gene(PEG). [UCL1]
AT1G65770 F-box family protein (RefSeq) from Arabidopsis thaliana
NP_176753 ascorbic acid mannose pathway regulator 1 from Arabidopsis thaliana
Aligns to 286:340 / 360 (15.3%), covers 94.5% of PF03478, 36.8 bits
- Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants
Lama, Molecular biology and evolution 2019 - “...AT1G65740 AtFDA5/UCL1 + + + cyt + Eud Brass AT1G65760 AtFDA6 + + + pm AT1G65770 AtFDA7 + + + mito + Eud Brass AT2G16290 AtFDA8 + + + pm Ang Eud Brass AT2G16300 AtFDA9 + + (+) pm Ang Eud Brass AT2G16365 AtFDA10 + +...”
- Key changes in gene expression identified for different stages of C4 evolution in Alloteropsis semialata
Dunning, Journal of experimental botany 2019 - “...complex AT3G52200 0 13 20 ASEM_AUS1_38810 UDP-glycosyltransferase AT1G05680 0 35 17 ASEM_AUS1_24427 Putative F-box protein AT1G65770 0 19 16 ASEM_AUS1_43609 a Flavin-containing monooxygenase FMO GS-OX-like 9 AT5G07800 0 7 13 ASEM_AUS1_40960 Cysteine-rich receptor-like protein kinase 26 AT4G23240 1 18 13 ASEM_AUS1_16960 a Valine-tRNA ligase AT1G14610 0...”
- An E3 ligase complex regulates SET-domain polycomb group protein activity in Arabidopsis thaliana
Jeong, Proceedings of the National Academy of Sciences of the United States of America 2011 - “...(qRT-PCR) showed that expression of At1g65740, At1g65760, and At1g65770 was elevated in ucl1-D homozygous plants (Fig. S1B). Among these three genes, we...”
- “...UCL1 overexpression (Fig. 2A). Likewise, overexpression of the At1g65770 gene, which is adjacent to UCL1, did not activate CLF-target genes (Fig. S4A). These...”
- AMR1, an Arabidopsis gene that coordinately and negatively regulates the mannose/l-galactose ascorbic acid biosynthetic pathway.
Zhang, Plant physiology 2009 - GeneRIF: AMR1 appears to play an important role in modulating ascorbic acid levels in Arabidopsis by regulating the expression of major pathway genes in response to developmental and environmental cues. [AMR1]
AT1G05540 hypothetical protein (RefSeq) from Arabidopsis thaliana
Aligns to 293:337 / 367 (12.3%), covers 96.4% of PF03478, 36.6 bits
AT5G53780 hypothetical protein (RefSeq) from Arabidopsis thaliana
Aligns to 307:351 / 376 (12.0%), covers 96.4% of PF03478, 36.3 bits
AT2G05970 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 293:344 / 377 (13.8%), covers 100.0% of PF03478, 36.3 bits
AT4G22170 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 280:332 / 363 (14.6%), covers 100.0% of PF03478, 36.1 bits
AT2G33190 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 292:353 / 379 (16.4%), covers 96.4% of PF03478, 35.8 bits
AT5G24040 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 289:344 / 373 (15.0%), covers 94.5% of PF03478, 35.4 bits
AT4G22060 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 310:368 / 399 (14.8%), covers 100.0% of PF03478, 35.0 bits
AT1G64840 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 287:347 / 384 (15.9%), covers 72.7% of PF03478, 34.7 bits
- Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants
Lama, Molecular biology and evolution 2019 - “...Phylostratum AT1G44080 AtFDA1 + + + nu Ang Eud AT1G57906 AtFDA2 + + + cyt AT1G64840 AtFDA3 + + + cyt, pm + Vir At1g65375 AtFDA4 + + + AT1G65740 AtFDA5/UCL1 + + + cyt + Eud Brass AT1G65760 AtFDA6 + + + pm AT1G65770 AtFDA7...”
- Identifying stably expressed genes from multiple RNA-Seq data sets
Zhuo, PeerJ 2016 - “...these 10 genes from Czechowski et al. (2005) to the expression profiles of five genes (AT1G64840, AT1G75420, AT2G32910, AT3G51310, AT5G48340) that we randomly selected from the top 100 most stably expressed genes identified from the multi-tissue group RNA-Seq data according the total variance \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym}...”
- “...AT1G75420 0.0012 0.0014 0.0050 5 AT5G48340 0.0042 0.0019 0.0074 46 AT2G32910 0.0007 0.0019 0.0113 53 AT1G64840 0.0051 0.0008 0.0095 72 AT3G51310 0.0028 0.0025 0.0100 73 Microarray AT2G28390 0.0034 0.0000 0.0111 62 AT1G13320 0.0036 0.0003 0.0258 513 AT4G34270 0.0063 0.0000 0.0365 1074 AT1G59830 0.0044 0.0039 0.0370 1211...”
- A comprehensive analysis of interaction and localization of Arabidopsis SKP1-like (ASK) and F-box (FBX) proteins
Kuroda, PloS one 2012 - “...6L ), implying that they were localized in the cytosol or vacuole. Five proteins (At1g23390, At1g64840, At3g03360, At3g24760 and At5g52880) showed a preferential speckled localization in the cytoplasm ( Figure 6C, 6F, 6K, 6M and 6U ). Six (At1g21760, At1g47730, At2g25490, At4g05460, At4g27050 and At5g21040) localized...”
- “...FBX proteins. GFP-fused FBX proteins; At1g21410 (A), At1g21760 (B), At1g23390 (C), At1g30790 (D), At1g47730 (E), At1g64840 (F), At1g67190 (G), At2g24250 (H), At2g25490 (I and J), At3g03360 (K), At3g04660 (L), At3g24760 (M), At4g02440 (N), At4g05460 (O and P), At4g27050 (Q and R), At5g21040 (S and T) and...”
AT5G60060 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 301:357 / 374 (15.2%), covers 98.2% of PF03478, 34.2 bits
AT4G22030 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 541:595 / 626 (8.8%), covers 100.0% of PF03478, 33.9 bits
- Transcriptome analysis and functional validation reveal a novel gene, BcCGF1, that enhances fungal virulence by promoting infection-related development and host penetration
Zhang, Molecular plant pathology 2020 - “...Cytochrome P450 84A1 Solyc01g095080.2 ACS2 161.1 1aminocyclopropane1carboxylate synthase 2 Solyc02g080840.1 LOC101256060 157.3 Probable Fbox protein At4g22030 Solyc09g066400.1 LOC101248046 156.6 Premnaspirodiene oxygenase Solyc02g070110.1 LOC101263972 136.4 Cannabidiolic acid synthase Solyc04g016000.2 LOC101266325 136.4 Heat stress transcription factor B3 Solyc01g101170.2 TPS31 133.2 Probable 5epiaristolochene synthase 4 Solyc07g062370.1 LOC101249107 122.5 Hypothetical...”
- Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants
Lama, Molecular biology and evolution 2019 - “...AT4G17565 AtFDB26 + + + cyt Ang Eud AT4G22035 AtFDB27 + + + Eud Brass AT4G22030 AtFDB28 + + + plastid Ang AT4G22060 AtFDB29 + + + pm, golgi Ang Eud AT4G22165 AtFDB30 + + + cyt Ang Eud AT4G22170 AtFDB31 + + + cyt Ang...”
- “...genes spread over 10 tandems. Also here tandems of up to six genes were found (At4g22030 to At4g22180). Finally, also the ancestral FDA family contained many tandem duplications, with 10 of 20 genes (50%) spread over 4 tandems. In conclusion, it appears that the DUF295 family...”
- Whole genome-wide transcript profiling to identify differentially expressed genes associated with seed field emergence in two soybean low phytate mutants
Yuan, BMC plant biology 2017 - “...down gene43660 polygalacturonase inhibitor-like up gene37153 polyphenol oxidase A1, chloroplastic-like up gene24050 probable F-box protein At4g22030 down gene18907 probable glutathione S-transferase up gene36822 probable glycosyltransferase At5g03795 down gene42818 reticuline oxidase-like protein up gene51756 soyasapogenol B glucuronide galactosyltransferase-like up gene53209 two-component response regulator ARR14-like up gene6319 UDP-glycosyltransferase...”
- Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome
Sani, Genome biology 2013 - “...18 protein Down 600 400 Down AT4G19740 Catalytic/ cation binding/chitinase/ hydrolase Down 1,600 200 Down AT4G22030 F-box family protein Down 200 200 Down AT4G22070 WRKY31; transcription factor Down 200 200 Down AT4G28840 Unknown protein Down 800 200 Down AT4G29033 Encodes a defensin-like (DEFL) family protein. Down...”
Q6DR20 F-box protein At2g17036 from Arabidopsis thaliana
Aligns to 301:359 / 404 (14.6%), covers 98.2% of PF03478, 33.7 bits
- iRefIndex: a consolidated protein interaction database with provenance.
Razick, BMC bioinformatics 2008 - “...example, Q7XJL8 was found to be a secondary accession in three separate UniProt records (Q3EBZ2, Q6DR20, and Q8GWA9). 2) The secondary references supplied by the interaction record point to more than one unique protein sequence. 3) An EntrezGene identifier is provided in the interaction record as...”
AT2G17036 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 300:358 / 428 (13.8%), covers 98.2% of PF03478, 33.6 bits
KIB3_ARATH / Q9ZW91 F-box protein KIB3; Protein KINK SUPPRESSED IN BZR1-1D 3 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT1G67160 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 299:357 / 450 (13.1%), covers 92.7% of PF03478, 33.2 bits
- function: Component of SCF(ASK-cullin-F-box) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. Required for brassinosteroid (BR) signal transduction. Mediates ASK7/BIN2/SK21 inactivation both by competing with substrate binding (e.g. BZR1) and by promoting its ubiquitination and subsequent proteasomal degradation.
disruption phenotype: Abolished brassinosteroid (BR)-induced ASK7/BIN2/SK21 degradation, and BR-insensitivity. Suppression of the constitutive BR-response phenotype in the dominant mutant bzr1-1D, and accumulation of phosphorylated BZR1. - Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants
Lama, Molecular biology and evolution 2019 - “...AT1G27550 AtFDB3 + + + mito Brass AT1G27580 AtFDB4 + + + mito Ang Eud AT1G67160 AtFDB5 + + + cyt Ang Eud AT1G69090 AtFDB6 + + + plastid Brass AT2G03560 AtFDB7 + + + cyt Ang Eud Brass AT2G03610 AtFDB8 + + + cyt Ang...”
AT4G22165 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 279:332 / 363 (14.9%), covers 100.0% of PF03478, 33.2 bits
AT5G66830 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 304:358 / 394 (14.0%), covers 98.2% of PF03478, 32.8 bits
AT2G16290 hypothetical protein (RefSeq) from Arabidopsis thaliana
Aligns to 318:392 / 415 (18.1%), covers 96.4% of PF03478, 32.1 bits
- Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants
Lama, Molecular biology and evolution 2019 - “...AT1G65760 AtFDA6 + + + pm AT1G65770 AtFDA7 + + + mito + Eud Brass AT2G16290 AtFDA8 + + + pm Ang Eud Brass AT2G16300 AtFDA9 + + (+) pm Ang Eud Brass AT2G16365 AtFDA10 + + (+) nu Vir AT2G17030 AtFDA11/SKIP23 + + + golgi...”
- “...). Interestingly, AtFDA9 ( At2g16300 ) is nearly identical to the adjacent gene AtFDA8 ( At2g16290 ), however a frameshift has occurred due to a single base deletion just before the start of the DUF295 domain. This leads to a premature stop codon and truncated AtFDA9...”
- Restriction site extension PCR: a novel method for high-throughput characterization of tagged DNA fragments and genome walking
Ji, PloS one 2010 - “...KINASE 1) 87 2982bp of 5end of AT5G67390 87 562 bp downstream of CD of At2g16290 (F-box family protein) 88 633 bp of 3 end of AT4G36030 (armadillo/beta-catenin repeat family protein) 89 4835bp of upstream of CD of AT5G50910 (located in endomembrane sysytem) 91 7221 bp...”
- “...insertions: one is 2982bp of 5end of AT5G67390, and the other 562 bp downstream of At2g16290 (F-box family protein). 4. Isolating unknown sequence from a particular known gene sequence in different plant species The above work suggests that as long as the sequence of a DNA...”
KIB4_ARATH / Q9SRV0 F-box protein KIB4; Protein KINK SUPPRESSED IN BZR1-1D 4 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT3G03730 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 303:360 / 393 (14.8%), covers 92.7% of PF03478, 32.0 bits
- function: Component of SCF(ASK-cullin-F-box) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. Required for brassinosteroid (BR) signal transduction. Mediates ASK7/BIN2/SK21 inactivation both by competing with substrate binding (e.g. BZR1) and by promoting its ubiquitination and subsequent proteasomal degradation.
disruption phenotype: Abolished brassinosteroid (BR)-induced ASK7/BIN2/SK21 degradation, and BR-insensitivity. Suppression of the constitutive BR-response phenotype in the dominant mutant bzr1-1D, and accumulation of phosphorylated BZR1. - Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants
Lama, Molecular biology and evolution 2019 - “...AtFDB17 + + + cyt Ang Eud AT3G03726 AtFDB18 + + + cyt Ang Eud AT3G03730 AtFDB19 + + + cyt Ang Eud AT3G22333 AtFDB20 + + + Ang Eud AT3G22345 AtFDB21 + + + cyt Ang Eud AT4G10820 AtFDB22 + + + cyt Ang Eud...”
AT2G24250 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 282:345 / 374 (17.1%), covers 94.5% of PF03478, 31.8 bits
AT2G03560 ubiquitin-protein ligase (RefSeq) from Arabidopsis thaliana
Aligns to 318:369 / 453 (11.5%), covers 100.0% of PF03478, 31.0 bits
AT2G14290 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 278:327 / 353 (14.2%), covers 100.0% of PF03478, 30.7 bits
- Functional Insight of Nitric-Oxide Induced DUF Genes in Arabidopsis thaliana
Nabi, Frontiers in plant science 2020 - “...IPR007612); BEST Arabidopsis thaliana protein match is: Protein of unknown function (DUF567) (TAIR : AT2G38640.1) AT2G14290 0.28000 23.59000 84.25000 0.00000 6.37693 CONTAINS InterPro DOMAIN/s: F-box domain, cyclin-like (InterPro : IPR001810), F-box domain, Skp2-like (InterPro : IPR022364), Protein of unknown function DUF295 (InterPro : IPR005174); BEST Arabidopsis...”
- Genes Modulating the Increase in Sexuality in the Facultative Diplosporous Grass Eragrostis curvula under Water Stress Conditions.
Selva, Genes 2020 - “...downregulated under stress conditions are the SNF1-related protein kinase regulatory subunit -1 and F-box proteins (At2g14290, At3g07870, and At5g07610). Regarding genes previously related to apomixis and upregulated under stress, the transcription factor NAC10 should be mentioned. 3.9. Validation by qRT-PCR qRT-PCR assays were used to corroborate...”
- Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants
Lama, Molecular biology and evolution 2019 - “...+ + + cyt Ang Eud AT2G05970 AtFDB12 + + + cyt Ang Eud Brass AT2G14290 AtFDB13 + + + cyt Land AT2G14500 AtFDB14 + + + cyt Ang Eud AT2G24080 AtFDB15 + + + cyt Eud AT2G33190 AtFDB16 + + + cyt AT2G33200 AtFDB17 +...”
AT5G38270 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 320:378 / 406 (14.5%), covers 100.0% of PF03478, 30.5 bits
NP_565302 F-box only protein (DUF295) from Arabidopsis thaliana
Aligns to 318:369 / 395 (13.2%), covers 100.0% of PF03478, 30.4 bits
AT4G22180 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 319:370 / 402 (12.9%), covers 69.1% of PF03478, 29.9 bits
AT2G33200 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 288:350 / 376 (16.8%), covers 100.0% of PF03478, 28.3 bits
KIB2_ARATH / Q9SU04 F-box protein KIB2; Protein KINK SUPPRESSED IN BZR1-1D 2 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT4G12820 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 353:406 / 442 (12.2%), covers 89.1% of PF03478, 28.1 bits
- function: Component of SCF(ASK-cullin-F-box) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. Required for brassinosteroid (BR) signal transduction. Mediates ASK7/BIN2/SK21 inactivation both by competing with substrate binding (e.g. BZR1) and by promoting its ubiquitination and subsequent proteasomal degradation.
subunit: Interacts with ASK7/BIN2/SK21.
disruption phenotype: Abolished brassinosteroid (BR)-induced ASK7/BIN2/SK21 degradation, and BR-insensitivity. Suppression of the constitutive BR-response phenotype in the dominant mutant bzr1-1D, and accumulation of phosphorylated BZR1. - Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants
Lama, Molecular biology and evolution 2019 - “...AtFDB22 + + + cyt Ang Eud AT4G12810 AtFDB23 + + + cyt Ang Eud AT4G12820 AtFDB24 + + + cyt Ang Eud AT4G14165 AtFDB25 + + + cyt Ang Eud AT4G17565 AtFDB26 + + + cyt Ang Eud AT4G22035 AtFDB27 + + + Eud Brass...”
- The F-box Protein KIB1 Mediates Brassinosteroid-Induced Inactivation and Degradation of GSK3-like Kinases in Arabidopsis
Zhu, Molecular cell 2017 - “...greatly reduced in kib1-1;bzr1-1D , whereas the expression levels of its neighboring genes AT4G12800 and AT4G12820 were not affected ( Figure 1E ). To confirm that loss of AT4G12810 expression is responsible for the kib1-1 phenotype, we obtained another T-DNA insertion mutant kib12 (SAIL_1230_F06), in which...”
GRMZM2G067198 uncharacterized protein LOC100274863 from Zea mays
Aligns to 294:356 / 385 (16.4%), covers 78.2% of PF03478, 27.0 bits
AT5G55150 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 275:333 / 360 (16.4%), covers 94.5% of PF03478, 26.7 bits
- Physiological and Transcriptomic Analysis of Arabidopsis thaliana Responses to Ailanthone, a Potential Bio-Herbicide
Hopson, International journal of molecular sciences 2022 - “...AT2G42065 DnaJ domain protein 6.94 3.95 5.42 UP AT3G54530 hypothetical protein 6.85 4.55 5.52 UP AT5G55150 F-box SKIP23-like protein (DUF295) 6.65 3.82 3.02 UP AT5G54560 hypothetical protein (DUF295) 6.60 6.05 6.05 UP AT2G20800 NAD(P)H dehydrogenase B4 ( NDB4 ) 6.34 3.76 4.46 UP AT5G54450 hypothetical protein...”
- Transcriptome analysis reveals major transcriptional changes during regrowth after mowing of red clover (Trifolium pratense)
Herbert, BMC plant biology 2021 - “...tdn_154158 8,9 General cell functions ( T. pratense, M. truncatula ) Tp57577_TGAC_v2_mRNA39482.v2 Medtr3g114970.2 M. truncatula AT5G55150 13 TPM1 tdn_65187 9,1 Transposon ( T. pratense, Prunus persica A. thaliana ) Tp57577_TGAC_v2_mRNA30115.v2 Prupe.4G011200.1 Prunus persica AT4G29090 14 TPM1 tdn_100956 9,2 Metabolism ( T. pratense, Capsella rubella, A. thaliana...”
- Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants
Lama, Molecular biology and evolution 2019 - “...AT5G66830 AtFDB38 + + + cyt AT1G57790 AtFDR1 + + + Not clear cyt + AT5G55150 AtFDR2 + + + Not clear pm Land AT1G05540 AtDOA1 + + mito Land AT1G05550 AtDOA2 + + pm Land Ang AT1G30160 AtDOA3 + + cyt + Eud AT1G30170 AtDOA4...”
- “...Supplementary Material online). A fourth group (indicated in orange in fig.1 ), including At1g57790 and At5g55150 , contains the F-box domain, but the DUF295 domain mentioned in the TAIR annotation was not identified using the PFAM profile, indicating it has diverged substantially. A yeast two-hybrid interaction...”
- How exposure to ALS-inhibiting gametocide tribenuron-methyl induces male sterility in rapeseed
Lian, BMC plant biology 2019 - “...endoplasmic reticulum-type TC169680 48.78 OPA3-like protein EV166804 48.59 Protein SRG1 TC171321 47.96 Putative F-box protein At5g55150 TC163384 47.93 ABC transporter B family member 4 TC174670 45.16 External alternative NAD(P)H-ubiquinone oxidoreductase B4, mitochondrial TC187508 42.47 Ethylene-responsive transcription factor CRF6 TC165449 41.90 Ubiquinol oxidase 3, mitochondrial TC166236 41.39...”
- “...ABC transporter C family member 3 TC180553 39.97 AAA-ATPase At1g43910 FG565272 39.51 Putative F-box protein At5g55150 TC173139 37.31 Ubiquinol oxidase 1a, mitochondrial EL625815 36.34 UDP-glycosyltransferase 74E2 TC161751 32.55 Cytosolic sulfotransferase 12 FG566389 31.71 UDP-glycosyltransferase 73C4 FG566278 31.50 Probable inactive poly [ADP-ribose] polymerase SRO3 TC163015 30.51 Indole...”
- The IDA-LIKE peptides IDL6 and IDL7 are negative modulators of stress responses in Arabidopsis thaliana
Vie, Journal of experimental botany 2017 - “...a At3g09450 2.136 0.099 0.008 UGT74E2 (UDP-GLUCOSYL TRANSFERASE 74E2) At1g05680 2.151 1.090 0.048 DUF295-domain protein At5g55150 2.202 1.096 0.043 ZAT10/STZ (SALT-TOLERANCE ZINC FINGER) a At1g27730 2.215 0.137 0.008 ZAT12 /RHL41 (RESPONSIVE TO HIGH LIGHT 41) At5g59820 2.359 0.619 0.013 CML38 (CALMODULIN-LIKE PROTEIN 38) a At1g76650 2.456...”
GRMZM2G446921 uncharacterized protein LOC100273748 from Zea mays
Aligns to 341:404 / 431 (14.8%), covers 70.9% of PF03478, 26.3 bits
- Genome wide association analysis for yield related traits in maize
Zeng, BMC plant biology 2022 - “...GRMZM2G049091 GRMZM2G138067 Transcription initiation factor IIF beta subunit Protein LURP-one-related 5 KNR 7_13586175 8.49E-05 7.77 GRMZM2G446921 F-box domain containing protein HKW 2_206427709 2.45E-05 8.72 GRMZM2G418343 GRMZM2G117900 Cell wall protein precursor putative Translation initiation factor family protein HKW 6_67617018 4.05E-04 5.59 GRMZM2G430902 C3HC4-type RING finger family protein...”
AT3G03720 CAT4 (CATIONIC AMINO ACID TRANSPORTER 4); cationic amino acid transmembrane transporter (RefSeq) from Arabidopsis thaliana
Aligns to 131:181 / 801 (6.4%), covers 69.1% of PF03478, 25.3 bits
- Cellular export of sugars and amino acids: role in feeding other cells and organisms
Kim, Plant physiology 2021 - “...-coexpressed UmamiTs , AAP family protein PUT1 (At1g31820), AAP1 (At1g58360), cationic amino acid transporters CAT4 (At3g03720), CAT9 (At1g05940), and CAT2 (At1g58030) is indicated. The logit score for UmamiT45 was 14.2. Figure 4 The role of SWEETs and UmamiTs in Arabidopsis, rice, and maize. A, The role...”
- Transcription of putative tonoplast transporters in response to glyphosate and paraquat stress in Conyza bonariensis and Conyza canadensis and selection of reference genes for qRT-PCR
Moretti, PloS one 2017 - “...amino acid transporter (CAT), [ 22 ]. In Arabidopsis , both CAT2 (AT1G58030) and CAT4 (AT3G03720) encode CATs which are primarily localized to the tonoplast [ 23 ], making them appropriate candidates for the vacuolar sequestration of paraquat. In glyphosate-paraquat-resistant (GPR) Conyza spp ., reduced translocation...”
- “...MRP8 (M11) NM_112148.3 AT3G13090 JSWR01014711.1 67 4e -105 CATIONIC AMINO ACID TRANSPORTER 4 (CAT4) NM_111243.7 AT3G03720 JSWR01002601.1 77 2e -37 NM_179491.2 AT1G58030 83 5-ENOL-PYRUVYLSHIKIMATE-3-PHOSPHATE SYNTHASE (EPSPS) NM_130093.2 AT2G45300 AY545666; JSWR01004464.1 78 7e -41 AY545667; JSWR01002887.1 77 3e -39 AY545668; JSWR01015937.1 71 2e -23 a Gene nomenclature...”
- Transcriptome-wide high-throughput deep m(6)A-seq reveals unique differential m(6)A methylation patterns between three organs in Arabidopsis thaliana
Wan, Genome biology 2015 - “...AT5G53530, AT5G01990, AT3G55320, AT4G13750, AT1G16820, AT1G77140, AT5G05570, AT5G07770, AT2G21340, AT2G27460, AT1G74720, AT1G47550, AT5G66380, AT5G47490, AT5G08470, AT3G03720, AT5G61310, AT5G62600, AT5G11980, AT1G56290, AT2G20840, AT2G15240, AT4G39420, AT5G07980, [ 15 21 ] Defense or stress response AT1G63770, AT1G64790, AT1G67090, AT1G80030, AT2G05580, AT2G27380, AT2G35510, AT2G42560, AT3G20290, AT3G22640, AT3G49600, AT4G01210, AT4G04920, AT4G08230,...”
- The AAP gene family for amino acid permeases contributes to development of the cyst nematode Heterodera schachtii in roots of Arabidopsis
Elashry, Plant physiology and biochemistry : PPB 2013 - “...0.2 0.43 At1g58032 AtCAT2 not available on GeneChip At5g36940 AtCAT3 7.8 6 1.8 a 0.00 At3g03720 AtCAT4 6.7 5.4 1.3 0.03 At2g34960 AtCAT5 3.5 3.1 0.4 0.24 At5g04770 AtCAT6 5.3 5.9 0.6 0.03 At3g10600 AtCAT7 3.3 3 0.3 0.20 At1g17120 AtCAT8 6.5 5.6 0.9 a 0.00...”
- A proteomics dissection of Arabidopsis thaliana vacuoles isolated from cell culture
Jaquinod, Molecular & cellular proteomics : MCP 2007 - “...2d Transp. NF NF At5g40670 At1g05940 At1g58030 At3g03720 At1g17120 At3g30390 At2g41190 At2g39130 At2g40420 At3g28960 At1g70330 31,007 60,138 67,072 63,597...”
AT1G30160 hypothetical protein (RefSeq) from Arabidopsis thaliana
Aligns to 291:344 / 366 (14.8%), covers 58.2% of PF03478, 25.3 bits
- Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants
Lama, Molecular biology and evolution 2019 - “...pm Land AT1G05540 AtDOA1 + + mito Land AT1G05550 AtDOA2 + + pm Land Ang AT1G30160 AtDOA3 + + cyt + Eud AT1G30170 AtDOA4 + + mito Ang AT1G68960 AtDOA5 + + mito Ang Eud AT2G45940 AtDOA6 + + cyt Land Vir AT4G14260 AtDOA7 + +...”
- “...(CTTGnnnnnCAAG or similar) was found ( Kulkarni et al. 2018 ). Only for AtDOA3 ( At1g30160 ) no MDM could be found, which is in line with its ANAC017-independent gene expression ( supplementary table 2 , Supplementary Material online). Furthermore, by using DNA affinity purification sequencing...”
AT2G03610 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 135:190 / 216 (25.9%), covers 87.3% of PF03478, 25.0 bits
AT4G22660 F-box family protein (RefSeq) from Arabidopsis thaliana
Aligns to 315:369 / 396 (13.9%), covers 85.5% of PF03478, 25.0 bits
GRMZM2G062031, LOC100276496 uncharacterized protein LOC100276496 from Zea mays
Aligns to 291:354 / 382 (16.8%), covers 81.8% of PF03478, 24.3 bits
- Identification and Validation of Candidate Genes Conferring Resistance to Downy Mildew in Maize (Zea mays L.).
Kim, Genes 2020 - “...15 ( GRMZM2G128315, AC210003.2_FG004, GRMZM2G045049, GRMZM2G178880, GRMZM2G363066, GRMZM2G028643, GRMZM2G330907, GRMZM2G047677, AC191071.3_FG001, GRMZM2G133707, GRMZM2G020043, GRMZM2G039345, GRMZM2G314171, GRMZM2G062031, and GRMZM2G005984 ) were upregulated by DM in the DM-resistant genotypes ( Figure 4 and Figure S4 ). These 15 upregulated genes were classified as peroxidase (POX), chloroplastic/mitochondrial phosphoribosylformylglycinamidine (PITG)...”
- “...photosystem II repair protein PSB27-H1 chloroplastic, photosystem II protein, and uncharacterized. The uncharacterized genes ( GRMZM2G062031, GRMZM2G133707, GRMZM2G20043, and GRMZM2G314171 ) were highly expressed in DM-infected plants. Of the 45 genes, 30 were partially upregulated and were classified into 20 functional annotations. 4. Discussion DM, caused...”
- “...acid receptor PYL5; abscisic acid receptor PYL3; pyrabactin resistance-like protein GRMZM2G062031 T01 1809 382 Uncharacterized LOC100276496 Uncharacterized LOC100276496 GRMZM2G128315 T01 3343 964 Probable LRR receptor-like serine/threonine-protein kinase IRK Putative leucine-rich repeat receptor-like protein kinase family protein GRMZM2G005984 9 9.05 T01 951 222 Photosystem II 11 kd...”
KIB1_ARATH / Q9SU05 F-box/kelch-repeat protein KIB1; Protein KINK SUPPRESSED IN BZR1-1D 1 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT4G12810 F-box family protein (RefSeq) from Arabidopsis thaliana
NP_193017 F-box family protein from Arabidopsis thaliana
Aligns to 287:342 / 382 (14.7%), covers 94.5% of PF03478, 24.1 bits
- function: Component of SCF(ASK-cullin-F-box) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. Required for brassinosteroid (BR) signal transduction. Mediates ASK7/BIN2/SK21 inactivation both by competing with substrate binding (e.g. BZR1) and by promoting its ubiquitination and subsequent proteasomal degradation.
subunit: Part of a SCF (SKP1-cullin-F-box) protein ligase complex. Binds directly to several GSK3 family proteins such as SKP1A/ASK1, ASK1/SK11, ASK3/SK12, ASK5/SK13, ASK7/BIN2/SK21, ASK9/SK22 and ASK6/SK23. Interacts with ASK7/BIN2/SK21 in a brassinosteroid (BR)- dependent manner.
disruption phenotype: Abolished brassinosteroid (BR)-induced ASK7/BIN2/SK21 degradation, and severe BR-insensitivity. Suppression of the constitutive BR-response phenotype in the dominant mutant bzr1-1D, and accumulation of phosphorylated BZR1. - Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants
Lama, Molecular biology and evolution 2019 - “...AtFDB21 + + + cyt Ang Eud AT4G10820 AtFDB22 + + + cyt Ang Eud AT4G12810 AtFDB23 + + + cyt Ang Eud AT4G12820 AtFDB24 + + + cyt Ang Eud AT4G14165 AtFDB25 + + + cyt Ang Eud AT4G17565 AtFDB26 + + + cyt Ang...”
- The F-box Protein KIB1 Mediates Brassinosteroid-Induced Inactivation and Degradation of GSK3-like Kinases in Arabidopsis
Zhu, Molecular cell 2017 - “...Liu et al., 1995 ), we identified a T-DNA flanking sequence in the promoter of AT4G12810 in the kib1-1;bzr1-1D mutant ( Figure 1D ). Quantitative RT-PCR analysis showed that the expression level of AT4G12810 was greatly reduced in kib1-1;bzr1-1D , whereas the expression levels of its...”
- “...AT4G12800 and AT4G12820 were not affected ( Figure 1E ). To confirm that loss of AT4G12810 expression is responsible for the kib1-1 phenotype, we obtained another T-DNA insertion mutant kib12 (SAIL_1230_F06), in which a T-DNA was inserted in an exon of AT4G12810 ( Figure 1D )....”
- The F-box Protein KIB1 Mediates Brassinosteroid-Induced Inactivation and Degradation of GSK3-like Kinases in Arabidopsis.
Zhu, Molecular cell 2017 - GeneRIF: KIB1 plays an essential role in brassinosteroid signaling by inhibiting BIN2 through dual mechanisms of blocking substrate access and promoting degradation. [KIB1]
AT5G54320 hypothetical protein (RefSeq) from Arabidopsis thaliana
Aligns to 297:348 / 369 (14.1%), covers 72.7% of PF03478, 23.7 bits
- Neofunctionalization of Mitochondrial Proteins and Incorporation into Signaling Networks in Plants
Lama, Molecular biology and evolution 2019 - “...Vir AT5G53230 AtDOB6 + + mito + Ang Eud AT5G53240 AtDOB7 + + mito Brass AT5G54320 AtDOB8 + + mito Ang Eud AT5G54330 AtDOB9 + + mito Ang Eud AT5G54420 AtDOB10 + + pm Land Brass AT5G54450 AtDOB11 + + mito + Ang Eud AT5G54550 AtDOB12...”
- “...of 34 genes (80%) spread over 13 tandems. One tandem even contained six genes spanning At5g54320 to At5g54560 . The F-box/DUF295 FDB group contained 26 of 38 (68%) tandem duplicated genes spread over 10 tandems. Also here tandems of up to six genes were found (At4g22030...”
Or search for genetic data about PF03478 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory