Family Search for PF06136 (SOK)
April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.
Running HMMer for PF06136
PF06136 hits 14 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
SOK3_ARATH / Q8GYT8 Protein SOSEKI 3; AtSOK3 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT2G28150 hypothetical protein from Arabidopsis thaliana
Aligns to 34:122 / 540 (16.5%), covers 100.0% of PF06136, 169.3 bits
- function: SOSEKI proteins (SOK1-5) locally interpret global polarity cues and can influence cell division orientation to coordinate cell polarization relative to body axes, probably by guiding ANGUSTIFOLIA (AN) polarized localization.
subunit: Homodimer (By similarity). Forms long polymer filaments with other SOKs proteins polymers (e.g. SOK1, SOK2, SOK3 and SOK4) crucial for polar localization and biological activity (PubMed:32004461). Binds to ANGUSTIFOLIA (AN) (PubMed:32004461). - Spatially resolved proteomics of the stomatal lineage: polarity complexes for cell divisions and stomatal pores
Wallner, 2023 - An actin remodeling role for Arabidopsis processing bodies revealed by their proximity interactome
Liu, The EMBO journal 2023 - “...; Labun etal , 2019 ; Ursache etal , 2021 ). To create the SOSEKI3 (AT2G28150) deletion mutant, we used a previously described multiplexed editing approach (Ursache etal , 2021 ). We designed sgRNAs using the CRISPRP 2.0 ( http://crispr.hzau.edu.cn/CRISPR2 ; Liu etal , 2017 )...”
- Comprehensive profiling of alternative splicing landscape during secondary dormancy in oilseed rape (Brassica napus L.)
Liu, Molecular breeding : new strategies in plant improvement 2022 - “...in ABA-mediated stress response (Cruz et al. 2014) At2g28150 At3g50670 JANUS U1-70 K Embryo development Involved in response to osmotic stress (Xiong et al....”
- A SOSEKI-based coordinate system interprets global polarity cues in Arabidopsis
Yoshida, Nature plants 2019 - “...below; SOK1 ; At1g05577). SOK1 has 4 paralogues in the Arabidopsis genome: SOK2 (At5g10150), SOK3 (At2g28150), SOK4 (At3g46110) and SOK5 (At5g59790) ( Fig. 1a ; Extended Fig. 1 ) of which SOK5 was also 2.4-fold down-regulated in embryos with reduced MP function. To determine gene expression...”
SOK5_ARATH / Q9FJF5 Protein SOSEKI 5; AtSOK5 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT5G59790 hypothetical protein from Arabidopsis thaliana
Aligns to 47:135 / 423 (21.0%), covers 100.0% of PF06136, 168.9 bits
- function: SOSEKI proteins (SOK1-5) locally interpret global polarity cues and can influence cell division orientation to coordinate cell polarization relative to body axes.
subunit: Homodimer (By similarity). Forms long polymer filaments with other SOKs proteins polymers (e.g. SOK1, SOK2, SOK3 and SOK4) crucial for polar localization and biological activity (PubMed:32004461). Binds to ANGUSTIFOLIA (AN) (Probable). - A SOSEKI-based coordinate system interprets global polarity cues in Arabidopsis
Yoshida, Nature plants 2019 - “...has 4 paralogues in the Arabidopsis genome: SOK2 (At5g10150), SOK3 (At2g28150), SOK4 (At3g46110) and SOK5 (At5g59790) ( Fig. 1a ; Extended Fig. 1 ) of which SOK5 was also 2.4-fold down-regulated in embryos with reduced MP function. To determine gene expression domains, nuclear-localized triple GFP (n3GFP)...”
- Expression profiling of tomato pre-abscission pedicels provides insights into abscission zone properties including competence to respond to abscission signals
Nakano, BMC plant biology 2013 - “...2.9 0.003 Solyc01g095960 A_96_P129692 AI483484 AT5G53390 unknown protein 3.9 0.022 1.8 0.022 Solyc06g075690 A_96_P235420 AK326143 AT5G59790 unknown protein 2.4 0.049 1.6 0.036 Solyc09g055950 A_96_P108797 BI211136 ATCG00270 PSBD | PSII D2 (PHOTOSYSTEM II REACTION CENTER PROTEIN D2) 4.1 0.019 3.9 0.038 Solyc09g091400 a A_96_P196349 BI204004 AT3G24240 leucine-rich...”
XP_008665220 protein UPSTREAM OF FLC from Zea mays
Aligns to 21:109 / 562 (15.8%), covers 100.0% of PF06136, 164.9 bits
M1BUI4 SOSEKI DIX-like domain-containing protein from Solanum tuberosum
Aligns to 8:96 / 386 (23.1%), covers 100.0% of PF06136, 159.2 bits
- Quantitative Proteomics of Potato Leaves Infected with Phytophthora infestans Provides Insights into Coordinated and Altered Protein Expression during Early and Late Disease Stages
Xiao, International journal of molecular sciences 2019 - “...such as dehydrin, pyruvate dehydrogenase, light-inducible tissue-specific protein, and three uncharacterized proteins, M0ZKB0, M1AM40, and M1BUI4 ( Table S3 ). These proteins have functions related to amino acid metabolism and transport, sterol biosynthesis, and abscisic acid signaling. To put these results into perspective, the increased abundance...”
SOK4_ARATH / Q8GY65 Protein SOSEKI 4; AtSOK4; Auxin-regulated protein 3; AtAuxRP3 from Arabidopsis thaliana (Mouse-ear cress) (see 3 papers)
AT3G46110 hypothetical protein from Arabidopsis thaliana
Aligns to 20:108 / 343 (25.9%), covers 100.0% of PF06136, 157.4 bits
- function: SOSEKI proteins (SOK1-5) locally interpret global polarity cues and can influence cell division orientation to coordinate cell polarization relative to body axes, probably by guiding ANGUSTIFOLIA (AN) polarized localization (PubMed:30737509). Positive regulator of auxin (indole-3-acetic acid, IAA) biosynthesis and signaling pathway leading to the modulation of seedling growth, plant and inflorescence development (PubMed:31207460). Negative regulator of stress responses (e.g. salinity and osmotic stress) (PubMed:31207460).
subunit: Homodimer (By similarity). Forms long polymer filaments with other SOKs proteins polymers (e.g. SOK1, SOK2, SOK3 and SOK4) crucial for polar localization and biological activity (PubMed:32004461). Binds to ANGUSTIFOLIA (AN) (PubMed:32004461). - Mining the Roles of Cucumber DUF966 Genes in Fruit Development and Stress Response
Tian, Plants (Basel, Switzerland) 2022 - “...to abscisic acid (ABA) [ 8 ]. In Arabidopsis , the DUF966 gene AtST39 ( At3g46110 ) was found to strengthen salt and drought tolerance by positively regulating resistance pathways [ 8 ]. Cucumber is one of the most important vegetable crops cultivated worldwide [ 9...”
- Genome-Wide Mining of Wheat DUF966 Gene Family Provides New Insights Into Salt Stress Responses
Zhou, Frontiers in plant science 2020 - “...to abscisic acid (ABA) ( Luo et al., 2014 ). In Arabidopsis, the AtST39 gene (At3g46110) plays a positive regulatory role in salt and drought stress resistance pathways ( Wang, 2014 ). Although the DUF966 genes play vital roles in plants, to the best of our...”
- Characterization the role of a UFC homolog, AtAuxRP3, in the regulation of Arabidopsis seedling growth and stress response
Shen, Journal of plant physiology 2019 (PubMed)- “...characterization of a DUF-966 domain-containing gene, At3g46110, re-named AtAuxRP3. AtAuxRP3 overexpression in Arabidopsis increased the levels of endogenous...”
- “...functional characterization of a DUF-966 domain-containing gene, At3g46110 , re-named AtAuxRP3 . AtAuxRP3 overexpression in Arabidopsis increased the levels of...”
- A SOSEKI-based coordinate system interprets global polarity cues in Arabidopsis
Yoshida, Nature plants 2019 - “...; At1g05577). SOK1 has 4 paralogues in the Arabidopsis genome: SOK2 (At5g10150), SOK3 (At2g28150), SOK4 (At3g46110) and SOK5 (At5g59790) ( Fig. 1a ; Extended Fig. 1 ) of which SOK5 was also 2.4-fold down-regulated in embryos with reduced MP function. To determine gene expression domains, nuclear-localized...”
- Constructing Networks of Organelle Functional Modules in Arabidopsis
Penga, Current genomics 2016 - “...AT5G59220 AT5G44070 AT5G61810 AT4G17230 AT1G27200 AT3G14050 AT5G43150 AT3G50260 AT3G28340 AT2G26530 AT2G35710 AT5G26920 AT3G50760 AT1G66090 AT1G21790 AT3G46110 AT1G29330 AT1G72520 AT1G50740 AT1G77450 AT5G67210 AT5G54300 AT5G06320 AT1G73805 AT2G23810 AT5G63790 AT5G10695 AT5G63790 AT5G06320 AT3G48090 AT3G06500 AT2G17040 AT4G19120 AT5G56980 AT4G01950 AT2G22080 AT5G47910 AT4G23810 AT1G02390 AT1G76650 AT1G43910 AT1G27770 AT4G36500 AT2G46510 AT3G25600 AT1G61890...”
- Detection of allele-specific methylation through a generalized heterogeneous epigenome model
Peng, Bioinformatics (Oxford, England) 2012 - “...3 16266681 16266822 21 + AT3TE65915 < AT3G44718 3 16934173 16934369 20 AT3TE68630 + > AT3G46110 + 4 4097347 4097458 20 + > AT4TE17760 4 4547945 4548048 39 AT4TE19110 < AT4G07747 5 13812896 13813035 21 + AT5TE49235 5 15205421 15205719 23 + AT5TE55020 5 15268332 15268498...”
- Divergent functions of VTI12 and VTI11 in trafficking to storage and lytic vacuoles in Arabidopsis
Sanmartín, Proceedings of the National Academy of Sciences of the United States of America 2007 - “...insertion of VAC2 in the intergenic region between At3g46110 and At3g46120. This line expresses amounts of VAC2 that are close to the empirically determined...”
SOK2_ARATH / Q9LX14 Protein SOSEKI 2; AtSOK2; Protein UPSTREAM OF FLC from Arabidopsis thaliana (Mouse-ear cress) (see 5 papers)
AT5G10150 hypothetical protein from Arabidopsis thaliana
Aligns to 46:134 / 414 (21.5%), covers 98.9% of PF06136, 156.0 bits
- function: Part of a three-gene cluster containing FLC, UFC and DFC, which is coordinately regulated in response to vernalization (PubMed:15186749, PubMed:18156133). Also regulated by FLX (PubMed:15186749). SOSEKI proteins (SOK1-5) locally interpret global polarity cues and can influence cell division orientation to coordinate cell polarization relative to body axes, probably by guiding ANGUSTIFOLIA (AN) polarized localization (PubMed:30737509, PubMed:32004461).
subunit: Homodimer (PubMed:30737509). Forms long polymer filaments with other SOKs proteins polymers (e.g. SOK1, SOK2, SOK3 and SOK4) crucial for polar localization and biological activity (PubMed:32004461). Binds to ANGUSTIFOLIA (AN) (PubMed:32004461). - An actin remodeling role for Arabidopsis processing bodies revealed by their proximity interactome
Liu, The EMBO journal 2023 - “..., and one site downstream of the stop codon, along with equivalent sgRNAs for SOK2 (AT5G10150). Following the published protocol, we cloned all sgRNAs into a single pRU292 destination vector. This vector allows for zCas9i expression under the UBi4.2 promoter, and expression of the sgRNAs and...”
- A SOSEKI-based coordinate system interprets global polarity cues in Arabidopsis
Yoshida, Nature plants 2019 - “...SOSEKI1 (explained below; SOK1 ; At1g05577). SOK1 has 4 paralogues in the Arabidopsis genome: SOK2 (At5g10150), SOK3 (At2g28150), SOK4 (At3g46110) and SOK5 (At5g59790) ( Fig. 1a ; Extended Fig. 1 ) of which SOK5 was also 2.4-fold down-regulated in embryos with reduced MP function. To determine...”
- Spring flowering habit in field pennycress (Thlaspi arvense) has arisen multiple independent times
Dorn, Plant direct 2018 - “...upstream gene (gene model Ta000918), a homolog of the Arabidopsis gene UPSTREAM OF FLC (UFC, AT5G10150). In Arabidopsis, UFC and FLC are coregulated, however, UFC is not believed to influence the vernalization response (Andersson etal., 2008 ; Finnegan, Sheldon, Jardinaud, Peacock, & Dennis, 2004 ). A...”
- Transcriptome analysis in tissue sectors with contrasting crocins accumulation provides novel insights into apocarotenoid biosynthesis and regulation during chromoplast biogenesis
Ahrazem, Scientific reports 2018 - “...4,376977 TAIR|locus:2055007 - symbol: AT2G44940 DREB subfamily AP2-EREBP c70036_g1_i1 3,595363 1,03479 4,563596 TAIR|locus:2184133 - symbol: AT5G10150 FLC c81876_g1_i1 3,529221 1,388653 3,913438 TAIR|locus:2152642 - symbol:ARF8 AT5G37020 ARF c61931_g1_i1 3,2107 1,050902 6,123365 TAIR|locus:2016344 - symbol:OFP14 AT1G79960 OFP c78185_g1_i2 3,077502 1,988864 3,866639 TAIR|locus:2041105 - symbol:SGR5 AT2G01940 C2H2 c77057_g3_i1 3,033889...”
- Divergence of annual and perennial species in the Brassicaceae and the contribution of cis-acting variation at FLC orthologues
Kiefer, Molecular ecology 2017 - “...overlapping fragments. The first fragment spanned a region from the adjacent upstream gene (orthologue of At5g10150 ) and ended at the beginning of the first intron (amplification of intergenic region between orthologue of At5g10150 and FLC orthologue), and the second covered the region containing a part...”
- “...a partial sequence of the next upstream gene or its orthologues from A. thaliana ( At5g10150 ), all intergenic sequence between At5g10150 and its orthologues and FLC and orthologues as well as all sequences orthologues/homologous to exons and introns of FLC (including indels) and approximately 500bp...”
- Comparative analysis of FLC homologues in Brassicaceae provides insight into their role in the evolution of oilseed rape
Zou, PloS one 2012 - “...comparison. Arrows at the 5 end indicate the approximate position of the neighbour gene ( At5g10150 and its homologues; unfilled) or the gene fragment (grey) upstream of FLC. Dashed lines represent upstream sequences that were not determined. (B) Alignment of 30 bp sequences that contain putative...”
- “...GF-1 and GF-2 represent two gene fragments homologous to the R block genes, At5G10200 and At5G10150 , respectively. The genomic sequences of B. rapa , A. thaliana , and A. lyrata were used to examine the microsynteny structure around the FRI locus. Surprisingly, in contrast to...”
- PEP1 of Arabis alpina is encoded by two overlapping genes that contribute to natural genetic variation in perennial flowering
Albani, PLoS genetics 2012 - “...distance between the orthologues of the genes that flank FLC in A. thaliana (At5g10130 and At5g10150) is increased [5] , and this region includes several tandemly duplicated sequences that include parts of PEP1 ( Figure 3B ). The longest duplicated segment is approximately 2 kb and...”
- Silencing by plant Polycomb-group genes requires dispersed trimethylation of histone H3 at lysine 27
Schubert, The EMBO journal 2006 - “...it did not spread to the neighbouring genes: At5g10150 was devoid of H3K27me3 and At5g10130 showed only slight enrichment of H3K27me3 after vernalisation. We...”
- “...addition, the FLC neighbouring genes at5g10130 and at5g10150 are downregulated during prolonged cold treatment, suggesting that silencing initiated at FLC might...”
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LOC110688479 protein UPSTREAM OF FLC-like from Chenopodium quinoa
Aligns to 43:131 / 464 (19.2%), covers 100.0% of PF06136, 155.8 bits
- Integrated Metabolomic and Transcriptomic Analysis of the Quinoa Seedling Response to High Relative Humidity Stress
Li, Biomolecules 2023 - “...LOC110696285 Transposition, RNA-mediated Blue LOC110738464 Transporter LOC110705966 Glycerophosphoryl diester phosphodiesterase LOC110731861 Alcohol dehydrogenase GroES-like domain LOC110688479 Protein upstream of LOC110723960 Glycerophosphoryl diester phosphodiesterase LOC110710755 Abscisic acid receptor LOC110732716 Zinc transporter LOC110686655 Polyamine oxidase LOC110723200 Belongs to the chalcone isomerase family LOC110718261 Rho GTPase-activating protein LOC110695938 Belongs...”
SOK_MARPO / A0A2R6X6S3 Protein SOSEKI; MpSOK from Marchantia polymorpha (Common liverwort) (Marchantia aquatica) (see paper)
Aligns to 17:106 / 911 (9.9%), covers 98.9% of PF06136, 118.4 bits
- function: SOSEKI proteins locally interpret global polarity cues and can influence cell division orientation to coordinate cell polarization relative to body axes.
cofactor: Zn(2+)
subunit: Homodimer (By similarity). Forms long polymer filaments with other SOKs proteins polymers crucial for polar localization and biological activity (PubMed:32004461).
SOK1_ARATH / Q9SYJ8 Protein SOSEKI 1; AtSOK1 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT1G05577 hypothetical protein from Arabidopsis thaliana
Aligns to 13:101 / 372 (23.9%), covers 100.0% of PF06136, 117.9 bits
- function: SOSEKI proteins (SOK1-5) locally interpret global polarity cues and can influence cell division orientation to coordinate cell polarization relative to body axes, probably by guiding ANGUSTIFOLIA (AN) polarized localization.
subunit: Homodimer (PubMed:30737509). Forms long polymer filaments with other SOKs proteins polymers (e.g. SOK1, SOK2, SOK3 and SOK4) crucial for polar localization and biological activity (PubMed:32004461). Binds to ANGUSTIFOLIA (AN) (PubMed:32004461). - A SOSEKI-based coordinate system interprets global polarity cues in Arabidopsis
Yoshida, Nature plants 2019 - “...containing a Domain of Unknown Function 966 (DUF966) and named SOSEKI1 (explained below; SOK1 ; At1g05577). SOK1 has 4 paralogues in the Arabidopsis genome: SOK2 (At5g10150), SOK3 (At2g28150), SOK4 (At3g46110) and SOK5 (At5g59790) ( Fig. 1a ; Extended Fig. 1 ) of which SOK5 was also...”
- Physical Mapping in a Triplicated Genome: Mapping the Downy Mildew Resistance Locus Pp523 in Brassica oleracea L
Carlier, G3 (Bethesda, Md.) 2011 - “...Map F C5 6D7 NS At1g02270 Map F C8a 11A22 At1g06680 NS PCR C8a 89C6 At1g05577 At1g05690 PCR C5 92O1 NS At1g02990 PCR C8a 38E20 At1g06490 NS PCR C8a 16F14 At1g05577 NS Map F C5 68M7 At1g03010 NS PCR C8a 84E23 At1g07110 NS PCR C8a 54F20...”
SOK3_PHYPA / A0A2K1J5A5 Protein SOSEKI 3; PpSOK3 from Physcomitrium patens (Spreading-leaved earth moss) (Physcomitrella patens) (see paper)
Aligns to 10:100 / 709 (12.8%), covers 100.0% of PF06136, 107.0 bits
- function: SOSEKI proteins locally interpret global polarity cues and can influence cell division orientation to coordinate cell polarization relative to body axes.
cofactor: Zn(2+)
subunit: Homodimer (By similarity). Forms long polymer filaments with other SOKs proteins polymers crucial for polar localization and biological activity (PubMed:32004461).
SOK1_PHYPA / A0A2K1JJ00 Protein SOSEKI 1; PpSOK1 from Physcomitrium patens (Spreading-leaved earth moss) (Physcomitrella patens) (see paper)
Aligns to 10:100 / 701 (13.0%), covers 98.9% of PF06136, 100.7 bits
- function: SOSEKI proteins locally interpret global polarity cues and can influence cell division orientation to coordinate cell polarization relative to body axes.
cofactor: Zn(2+)
subunit: Homodimer (By similarity). Forms long polymer filaments with other SOKs proteins polymers crucial for polar localization and biological activity (PubMed:32004461).
SOK4_PHYPA / A9RNY0 Protein SOSEKI 4; PpSOK4 from Physcomitrium patens (Spreading-leaved earth moss) (Physcomitrella patens) (see paper)
Aligns to 24:114 / 390 (23.3%), covers 96.6% of PF06136, 88.7 bits
- function: SOSEKI proteins locally interpret global polarity cues and can influence cell division orientation to coordinate cell polarization relative to body axes.
subunit: Homodimer (By similarity). Forms long polymer filaments with other SOKs proteins polymers crucial for polar localization and biological activity (PubMed:32004461).
SOK2_PHYPA / A0A2K1L2D9 Protein SOSEKI 2; PpSOK2 from Physcomitrium patens (Spreading-leaved earth moss) (Physcomitrella patens) (see paper)
Aligns to 11:102 / 636 (14.5%), covers 97.8% of PF06136, 84.0 bits
- function: SOSEKI proteins locally interpret global polarity cues and can influence cell division orientation to coordinate cell polarization relative to body axes.
subunit: Homodimer (By similarity). Forms long polymer filaments with other SOKs proteins polymers crucial for polar localization and biological activity (PubMed:32004461).
NP_001325459 UPSTREAM OF FLC-like protein (DUF966) from Arabidopsis thaliana
Aligns to 1:44 / 279 (15.8%), covers 49.4% of PF06136, 72.3 bits
Or search for genetic data about PF06136 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory