Family Search for PF04859 (DUF641)
April 2024: GapMind for amino acid biosynthesis has been updated to include newly-discovered enzymes and comparative genomics predictions (see details)
PF04859 hits 12 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
AT2G45260 hypothetical protein from Arabidopsis thaliana
Aligns to 31:159 / 425 (30.4%), covers 98.4% of PF04859, 158.9 bits
- Mapping of a novel clubroot disease resistance locus in Brassica napus and related functional identification
Jiang, Frontiers in plant science 2022 - “...AT2G45210 77.87 SAUR-like auxin-responsive protein family LOC106438246 AT2G45220 88.27 Plant invertase/pectin methylesterase inhibitor superfamily LOC106438247 AT2G45260 85.80 myosin-4 protein (DUF641) LOC106438248 AT2G45300 89.35 RNA 3-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta LOC106438249 AT2G45310 85.23 UDP-D-glucuronate 4-epimerase 4 BNAA03G56780D AT2G45320 87.82 polyphosphatidylinositol phosphatase LOC106438251 /AT4G17910 87.25 transferases, transferring acyl...”
- COST1 balances plant growth and stress tolerance via attenuation of autophagy
Bao, Autophagy 2020 (secret) - COST1 regulates autophagy to control plant drought tolerance
Bao, Proceedings of the National Academy of Sciences of the United States of America 2020 (secret) - Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction
Bossi, BMC genomics 2017 - “...Table S1). We found that plants harboring a knockout mutation in a candidate gene (TAIR: AT2G45260), named hereafter as CHIQUITA 1 (CHIQ1 ), was defective in organ size (Fig. 4 ). Adult plants carrying a knockout allele of CHIQ1 ( chiq11 ) were shorter in stature...”
- “...Mendelian locus (Additional file 1 : Table S6). To confirm that a mutation in the AT2G45260 locus ( CHIQ1 ) causes the small size phenotype, we introgressed the mutant allele into wild type to remove unrelated non-linked mutations and performed a linkage analysis, which indicated that...”
- Transcript profiling of crown rootless1 mutant stem base reveals new elements associated with crown root development in rice
Coudert, BMC genomics 2011 - “...- Auxin-responsive SAUR gene family member [ 20 , 61 ] O Os10g23220 2,14 GIL1 At2g45260 unknown protein " O " a gene mentioned in Figure 3. " A " indicates a CRL1- independent auxin responsive gene. " CA " indicates a CRL1- dependent auxin responsive...”
AT4G34080 hypothetical protein from Arabidopsis thaliana
Aligns to 1:124 / 270 (45.9%), covers 95.3% of PF04859, 156.8 bits
- Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction
Bossi, BMC genomics 2017 - “...AT1G53380), CHIQL8 (TAIR: AT2G30380), CHIQL3 (TAIR: AT4G36100), CHIQL2 (TAIR: AT4G33320), CHIQ1 (TAIR: AT2G45260), CHIQL1 (TAIR: AT4G34080), CHIQL9 (TAIR: AT3G60680), CHIQL10 (TAIR: AT5G58960). b - d Physical interaction between CHIQ1, CHIQL6, CHIQL5, and EMF2 based on yeast two-hybrid assays ( b ), pull-down assays in tobacco (...”
- “...To construct the vectors for the yeast two-hybrid assays, we amplified the following genes: AT4G33320, AT4G34080, AT2G32130, AT5G58960, AT1G29300, AT1G53380, AT3G14870, AT5G60680, AT3G23690 ( bHLH077 ), AT1G18040 ( CDKD1;3 ), AT1G76010, AT5G65630 ( GTE7 ), AT3g20740 ( FIE ), AT5G58230 ( MSI1 ), AT5G51230 ( EMF2...”
- Divergent evolutionary and expression patterns between lineage specific new duplicate genes and their parental paralogs in Arabidopsis thaliana
Wang, PloS one 2013 - “...At2g13450 ) showed higher methylation levels in the promoters and two parental genes ( At4g04030, At4g34080 ) showed higher methylation levels in the promoters compared to the common methylation level in the promoters of all the genes (binomial test with correcting multiple testing with FDR <0.05)....”
AT3G14870 hypothetical protein from Arabidopsis thaliana
Aligns to 77:202 / 472 (26.7%), covers 99.2% of PF04859, 154.2 bits
- Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction
Bossi, BMC genomics 2017 - “...in blue and CHIQ1s interactors in red. CHIQL6 (TAIR: AT1G29300), CHIQL7 (TAIR: AT2G32130), CHIQL4 (TAIR: AT3G14870), CHIQL5 (TAIR: AT1G53380), CHIQL8 (TAIR: AT2G30380), CHIQL3 (TAIR: AT4G36100), CHIQL2 (TAIR: AT4G33320), CHIQ1 (TAIR: AT2G45260), CHIQL1 (TAIR: AT4G34080), CHIQL9 (TAIR: AT3G60680), CHIQL10 (TAIR: AT5G58960). b - d Physical interaction between...”
- “...the yeast two-hybrid assays, we amplified the following genes: AT4G33320, AT4G34080, AT2G32130, AT5G58960, AT1G29300, AT1G53380, AT3G14870, AT5G60680, AT3G23690 ( bHLH077 ), AT1G18040 ( CDKD1;3 ), AT1G76010, AT5G65630 ( GTE7 ), AT3g20740 ( FIE ), AT5G58230 ( MSI1 ), AT5G51230 ( EMF2 , full length protein and...”
- Dynamic deposition of histone variant H3.3 accompanies developmental remodeling of the Arabidopsis transcriptome
Wollmann, PLoS genetics 2012 - “...per condition (div/nonDiv): AT3G14820 (0/0), AT3G14830 (18.6/19.7), AT3G14840 (19.8/38.2), AT3G14850 (1.7/1.1), AT3G14855 (0/0), AT3G14860 (12.0/13.9), AT3G14870 (1.4/3.7). Vertical dashed grey lines correspond to the TTS of the genes. (EPS) Click here for additional data file. Figure S2 Genomic distribution of H3.3 and H3.1 enrichment in non-dividing...”
AT1G53380 hypothetical protein from Arabidopsis thaliana
Aligns to 62:187 / 453 (27.8%), covers 99.2% of PF04859, 154.1 bits
- Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction
Bossi, BMC genomics 2017 - “...CHIQ1s interactors in red. CHIQL6 (TAIR: AT1G29300), CHIQL7 (TAIR: AT2G32130), CHIQL4 (TAIR: AT3G14870), CHIQL5 (TAIR: AT1G53380), CHIQL8 (TAIR: AT2G30380), CHIQL3 (TAIR: AT4G36100), CHIQL2 (TAIR: AT4G33320), CHIQ1 (TAIR: AT2G45260), CHIQL1 (TAIR: AT4G34080), CHIQL9 (TAIR: AT3G60680), CHIQL10 (TAIR: AT5G58960). b - d Physical interaction between CHIQ1, CHIQL6, CHIQL5,...”
- “...for the yeast two-hybrid assays, we amplified the following genes: AT4G33320, AT4G34080, AT2G32130, AT5G58960, AT1G29300, AT1G53380, AT3G14870, AT5G60680, AT3G23690 ( bHLH077 ), AT1G18040 ( CDKD1;3 ), AT1G76010, AT5G65630 ( GTE7 ), AT3g20740 ( FIE ), AT5G58230 ( MSI1 ), AT5G51230 ( EMF2 , full length protein...”
LOC106779790 protein GRAVITROPIC IN THE LIGHT 1 from Vigna radiata var. radiata
Aligns to 66:191 / 461 (27.3%), covers 99.2% of PF04859, 149.1 bits
AT4G33320 hypothetical protein from Arabidopsis thaliana
Aligns to 7:136 / 292 (44.5%), covers 99.2% of PF04859, 148.6 bits
- Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction
Bossi, BMC genomics 2017 - “...AT2G32130), CHIQL4 (TAIR: AT3G14870), CHIQL5 (TAIR: AT1G53380), CHIQL8 (TAIR: AT2G30380), CHIQL3 (TAIR: AT4G36100), CHIQL2 (TAIR: AT4G33320), CHIQ1 (TAIR: AT2G45260), CHIQL1 (TAIR: AT4G34080), CHIQL9 (TAIR: AT3G60680), CHIQL10 (TAIR: AT5G58960). b - d Physical interaction between CHIQ1, CHIQL6, CHIQL5, and EMF2 based on yeast two-hybrid assays ( b...”
- “...pGWB3-CHIQ1. To construct the vectors for the yeast two-hybrid assays, we amplified the following genes: AT4G33320, AT4G34080, AT2G32130, AT5G58960, AT1G29300, AT1G53380, AT3G14870, AT5G60680, AT3G23690 ( bHLH077 ), AT1G18040 ( CDKD1;3 ), AT1G76010, AT5G65630 ( GTE7 ), AT3g20740 ( FIE ), AT5G58230 ( MSI1 ), AT5G51230 (...”
AT2G32130 hypothetical protein from Arabidopsis thaliana
Aligns to 29:153 / 157 (79.6%), covers 96.1% of PF04859, 146.1 bits
- Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction
Bossi, BMC genomics 2017 - “...ones. CHIQ1 is in blue and CHIQ1s interactors in red. CHIQL6 (TAIR: AT1G29300), CHIQL7 (TAIR: AT2G32130), CHIQL4 (TAIR: AT3G14870), CHIQL5 (TAIR: AT1G53380), CHIQL8 (TAIR: AT2G30380), CHIQL3 (TAIR: AT4G36100), CHIQL2 (TAIR: AT4G33320), CHIQ1 (TAIR: AT2G45260), CHIQL1 (TAIR: AT4G34080), CHIQL9 (TAIR: AT3G60680), CHIQL10 (TAIR: AT5G58960). b - d...”
- “...construct the vectors for the yeast two-hybrid assays, we amplified the following genes: AT4G33320, AT4G34080, AT2G32130, AT5G58960, AT1G29300, AT1G53380, AT3G14870, AT5G60680, AT3G23690 ( bHLH077 ), AT1G18040 ( CDKD1;3 ), AT1G76010, AT5G65630 ( GTE7 ), AT3g20740 ( FIE ), AT5G58230 ( MSI1 ), AT5G51230 ( EMF2 ,...”
AT1G29300 UNE1 (unfertilized embryo sac 1) from Arabidopsis thaliana
Aligns to 80:205 / 459 (27.5%), covers 99.2% of PF04859, 139.1 bits
- Structural variations in papaya genomes
Liao, BMC genomics 2021 - “...of the ovule, embryogenesis sunup.07G0005810 AT1G06220 GFA1 solo, common female gametophyte development, female fertility sunup.07G0006190 AT1G29300 UNE1 solo defects in pollen tube attraction sunup.07G0010620 AT1G69940 PPME1 common pollen tube elongation sunup.03G0008270 AT1G04880 HMGBD15 common pollen tube growth sunup.01G0016020 AT2G26490 REN4 solo, common negative regulator of pollen...”
- Sound Vibration-Triggered Epigenetic Modulation Induces Plant Root Immunity Against Ralstonia solanacearum
Jung, Frontiers in microbiology 2020 - “...2 FC P -value Description Day 1 miR156g AT2G33810 (SPL3) 0.86 3.55E-04 Metal binding miR4228-3p AT1G29300 (UNE1) 0.64 1.71E-01 Intracellular protein transporter, putative (DUF641) Day 2 miR2936 AT3G12830 (SAUR72) 0.74 3.79E-02 Auxinresponsive protein MIR169d MIR169h AT5G06510 (NF-YA10) 0.95 3.80E-03 Nuclear transcription factor Y subunit A-10 MIR169m...”
- Comparative transcriptome analysis of galls from four different host plants suggests the molecular mechanism of gall development
Takeda, PloS one 2019 - “...protein AT5G62350 7.48 5.69 5.01 2.62 - - - UNE1|Plant protein of unknown function (DUF641) AT1G29300 3.50 3.15 3.05 4.89 - - - GAD4|glutamate decarboxylase 4 AT2G02010 3.15 3.06 1.78 3.93 - - - Protein of unknown function (DUF1635) AT5G22930 2.64 4.18 2.64 2.87 - -...”
- Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction
Bossi, BMC genomics 2017 - “...conserved than shorter ones. CHIQ1 is in blue and CHIQ1s interactors in red. CHIQL6 (TAIR: AT1G29300), CHIQL7 (TAIR: AT2G32130), CHIQL4 (TAIR: AT3G14870), CHIQL5 (TAIR: AT1G53380), CHIQL8 (TAIR: AT2G30380), CHIQL3 (TAIR: AT4G36100), CHIQL2 (TAIR: AT4G33320), CHIQ1 (TAIR: AT2G45260), CHIQL1 (TAIR: AT4G34080), CHIQL9 (TAIR: AT3G60680), CHIQL10 (TAIR: AT5G58960)....”
- “...vectors for the yeast two-hybrid assays, we amplified the following genes: AT4G33320, AT4G34080, AT2G32130, AT5G58960, AT1G29300, AT1G53380, AT3G14870, AT5G60680, AT3G23690 ( bHLH077 ), AT1G18040 ( CDKD1;3 ), AT1G76010, AT5G65630 ( GTE7 ), AT3g20740 ( FIE ), AT5G58230 ( MSI1 ), AT5G51230 ( EMF2 , full length...”
AT4G36100 hypothetical protein from Arabidopsis thaliana
Aligns to 7:159 / 236 (64.8%), covers 81.9% of PF04859, 129.4 bits
- Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction
Bossi, BMC genomics 2017 - “...AT1G29300), CHIQL7 (TAIR: AT2G32130), CHIQL4 (TAIR: AT3G14870), CHIQL5 (TAIR: AT1G53380), CHIQL8 (TAIR: AT2G30380), CHIQL3 (TAIR: AT4G36100), CHIQL2 (TAIR: AT4G33320), CHIQ1 (TAIR: AT2G45260), CHIQL1 (TAIR: AT4G34080), CHIQL9 (TAIR: AT3G60680), CHIQL10 (TAIR: AT5G58960). b - d Physical interaction between CHIQ1, CHIQL6, CHIQL5, and EMF2 based on yeast two-hybrid...”
AT3G60680 hypothetical protein from Arabidopsis thaliana
Aligns to 113:243 / 499 (26.3%), covers 97.6% of PF04859, 128.0 bits
- Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction
Bossi, BMC genomics 2017 - “...AT2G30380), CHIQL3 (TAIR: AT4G36100), CHIQL2 (TAIR: AT4G33320), CHIQ1 (TAIR: AT2G45260), CHIQL1 (TAIR: AT4G34080), CHIQL9 (TAIR: AT3G60680), CHIQL10 (TAIR: AT5G58960). b - d Physical interaction between CHIQ1, CHIQL6, CHIQL5, and EMF2 based on yeast two-hybrid assays ( b ), pull-down assays in tobacco ( c ), and...”
- “...kit according to the manual (ZYMO research). Nine proteins from CHIQ1s family (AT4G33320, AT4G34080, AT2G45260, AT3G60680, AT3G14870, AT1G29300, AT1G53380, AT2G32130, and AT5G58960) in pDEST22 were transformed into yeast strain Y187. To obtain double transformants, single haploid colonies from each transformation were grown overnight, each pair mixed,...”
GIL1_ARATH / F4KGE8 Protein GRAVITROPIC IN THE LIGHT 1 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT5G58960 GIL1 (GRAVITROPIC IN THE LIGHT) from Arabidopsis thaliana
NP_851217 glucose-6-phosphate isomerase, putative (DUF641) from Arabidopsis thaliana
Aligns to 155:280 / 559 (22.5%), covers 99.2% of PF04859, 126.8 bits
- function: Required for red (R) and far red (FR) light-induced and phytochrome-mediated deregulation of negative gravitropism leading to randomization of hypocotyl growth orientation.
disruption phenotype: Maintenance of negative gravitropic hypocotyls grow after exposure of seedlings to red (R) or far red (FR) light. Reduced seedlings viability. - Lasting consequences of psyllid (Bactericera cockerelli L.) infestation on tomato defense, gene expression, and growth
Harrison, BMC plant biology 2021 - “...to 2-Cys peroxiredoxins in chloroplasts." Biochemical and biophysical research communications 348.2 (2006): 478-484. Solyc02g072140.1 GIL1 AT5G58960 -0.44 protein GRAVITROPIC IN THE LIGHT 1 Required for red and far-red light-induced and phytochrome-mediated deregulation of negative gravitropism leading to randomization of hypocotyl growth orientation Impaired gravitropism; Decreased response...”
- Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction
Bossi, BMC genomics 2017 - “...AT4G36100), CHIQL2 (TAIR: AT4G33320), CHIQ1 (TAIR: AT2G45260), CHIQL1 (TAIR: AT4G34080), CHIQL9 (TAIR: AT3G60680), CHIQL10 (TAIR: AT5G58960). b - d Physical interaction between CHIQ1, CHIQL6, CHIQL5, and EMF2 based on yeast two-hybrid assays ( b ), pull-down assays in tobacco ( c ), and bimolecular fluorescence complementation...”
- “...the vectors for the yeast two-hybrid assays, we amplified the following genes: AT4G33320, AT4G34080, AT2G32130, AT5G58960, AT1G29300, AT1G53380, AT3G14870, AT5G60680, AT3G23690 ( bHLH077 ), AT1G18040 ( CDKD1;3 ), AT1G76010, AT5G65630 ( GTE7 ), AT3g20740 ( FIE ), AT5G58230 ( MSI1 ), AT5G51230 ( EMF2 , full...”
- Phytochrome-mediated agravitropism in Arabidopsis hypocotyls requires GIL1 and confers a fitness advantage.
Allen, The Plant journal : for cell and molecular biology 2006 (PubMed)- GeneRIF: GIL1 is necessary for light-dependent randomization of hypocotyl growth orientation in Arabidopsis.
AT2G30380 hypothetical protein from Arabidopsis thaliana
Aligns to 67:192 / 519 (24.3%), covers 93.7% of PF04859, 108.1 bits
- Systematic discovery of novel eukaryotic transcriptional regulators using sequence homology independent prediction
Bossi, BMC genomics 2017 - “...red. CHIQL6 (TAIR: AT1G29300), CHIQL7 (TAIR: AT2G32130), CHIQL4 (TAIR: AT3G14870), CHIQL5 (TAIR: AT1G53380), CHIQL8 (TAIR: AT2G30380), CHIQL3 (TAIR: AT4G36100), CHIQL2 (TAIR: AT4G33320), CHIQ1 (TAIR: AT2G45260), CHIQL1 (TAIR: AT4G34080), CHIQL9 (TAIR: AT3G60680), CHIQL10 (TAIR: AT5G58960). b - d Physical interaction between CHIQ1, CHIQL6, CHIQL5, and EMF2 based...”
Or search for genetic data about PF04859 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory