Family Search for PF04852 (ALOG_dom)
PaperBLAST, GapMind, SitesBLAST, and Sites on a Tree will be down for server maintenance on Friday March 29.
Running HMMer for PF04852
PF04852 hits 27 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
NP_001306073 protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 4 from Solanum lycopersicum
Aligns to 47:172 / 208 (60.6%), covers 99.2% of PF04852, 228.7 bits
LOC107943309, XP_016732548 protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 4-like from Gossypium hirsutum
Aligns to 54:179 / 216 (58.3%), covers 99.2% of PF04852, 227.1 bits
- Gossypium hirsutum gene of unknown function, Gohir.A02G039501.1, encodes a potential DNA-binding ALOG protein involved in gene regulation
Zirkel, microPublication biology 2023 - “...to gain clues to potential function. One of those uncharacterized proteins encoded by the gene LOC107943309 (Gohir.A02G039501_UTX-TM1_v2.1) in upland cotton G ossypium hirsutum genome (L. accession Texas Marker-1 (TM-1) version 2.0, annotation version 2.1) was termed light-dependent short hypocotyls 4-like (NCBI: XP_016732548, UniProt: A0A1U8MC48). Here we...”
- “...Texas Marker-1 (TM-1) version 2.0, annotation version 2.1) was termed light-dependent short hypocotyls 4-like (NCBI: XP_016732548, UniProt: A0A1U8MC48). Here we present bioinformatic evidence that this protein is a part of the ALOG ( A rabidopsis L SH1 (light-dependent short hypocotyl) and O ryza G 1) family...”
LOC21408627 protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 4 from Morus notabilis
Aligns to 39:164 / 245 (51.4%), covers 96.8% of PF04852, 226.7 bits
GRMZM2G359892 putative protein of unknown function (DUF640) domain family protein from Zea mays
Aligns to 36:161 / 247 (51.0%), covers 99.2% of PF04852, 225.8 bits
- Genetic Variation in ZmPAT7 Contributes to Tassel Branch Number in Maize
Guan, International journal of molecular sciences 2022 - “...S4_122747978 4 122,747,978 1.53 10 1 2 qTBN6 S6_153206873 6 153,206,873 2.97 10 1 2 GRMZM2G359892 ijms-23-02586-t003_Table 3 Table 3 List of eQTL for ZmPAT7 and the annotation of candidate genes. Code of eQTL Peak_SNP p _Value V4_Gene_Id Annotation eQTL-1 2:26,517,652 3.05 10 6 Zm00001d002917 RNA-binding...”
LOC18774140 protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 5 from Prunus persica
Aligns to 42:167 / 232 (54.3%), covers 98.4% of PF04852, 224.8 bits
- Identification and Analysis of Long Non-Coding RNAs Related to UV-B-Induced Anthocyanin Biosynthesis During Blood-Fleshed Peach (Prunus persica) Ripening
Zhang, Frontiers in genetics 2022 - “...the lncRNAs. Reverse-Transcription Quantitative PCR The expression trends of some genes, including COP10 (LOC18775225), HY5 (LOC18774140), UVR8 (LOC18782602), COP1 (LOC18778124), PAL (LOC18772065), F3H (LOC18777306), UFGT (LOC18782003), and LDOX (LOC18777055), were examined. These results were consistent with the trend of FPKM ( Figure 6 ). FIGURE 6...”
- “...biosynthesis-related genes UVR8 (Loc18782602) , UFGT (Loc18782003) , PAL (Loc18772065) , LDOX (Loc18777055) , HY5 (Loc18774140) , F3 H (Loc18777306) , COP10 (Loc18775225) , and COP1 (Loc18778124) in peach fruit. The error bar represents the mean + standard error of three repeated measurements (SE) using one-way...”
AT1G07090 LSH6 (LIGHT SENSITIVE HYPOCOTYLS 6) from Arabidopsis thaliana
Aligns to 19:144 / 196 (64.3%), covers 96.8% of PF04852, 223.8 bits
- Genetic Model Identification and Major QTL Mapping for Petiole Thickness in Non-Heading Chinese Cabbage
Liu, International journal of molecular sciences 2024 - “...0/4 Intracellular transport BraA09g063540.3C - - 0/0 Uncharacterized protein BraA09g063550.3C AT1G07110 FRUCTOSE-2,6-BISPHOSPHATASE 0/0 6-phosphofructo-2-kinase/Fructose-2,6-bisphosphatase BraA09g063560.3C AT1G07090 SITIVE HYPOCOTYLS-6; LSH6 0/0 Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 6 BraA09g063570.3C AT1G07080 - 0/0 Gamma-interferon-responsive lysosomal thiol protein BraA09g063580.3C AT1G06990 - 0/0 GDSL esterase/lipase AT1G06990 isoform X1 BraA09g063590.3C AT1G06980 - 0/0...”
- Genetic dissection of maize (Zea maysL.) trace element traits using genome-wide association studies
Zhu, BMC plant biology 2023 - “...to plant fertilization, which can positively regulate seed development [ 41 ]. The homologous gene AT1G07090 of Zm00001d038016 encodes the AtLSH6 protein, and its homologous protein AtLSH1 is functionally dependent on photosensitive pigments, which then mediates light regulation of seedling development [ 42 ]. AT1G18440, a...”
- Shade triggers posttranscriptional PHYTOCHROME-INTERACTING FACTOR-dependent increases in H3K4 trimethylation
Calderon, Plant physiology 2022 - “...E 1 Yes N/A AT5G02190 PCS1 2.27 1.19 57 E E 1 Ind Yes N/A AT1G07090 LSH6 1.09 1.14 13457 E E 1 Ind Yes N/A AT1G67265 DVL3 4.26 2.16 1345 E E 1 Ind Yes N/A AT1G60060 At1g60060 2.14 2.03 4 E E 1 Yes...”
- Common and unique elements of the ABA-regulated transcriptome of Arabidopsis guard cells
Wang, BMC genomics 2011 - “...(UDP-glucosyl transferase 72E1) 7 AT4G17460 * HAT1 (homeobox-leucine zipper protein 1); DNA binding/transcription factor 7 AT1G07090 LSH6 (LIGHT SENSITIVE HYPOCOTYLS 6) 6 AT1G08810*^ MYB60 (myb domain protein 60); DNA binding/transcription factor 6 AT1G29430 auxin-responsive family protein 6 AT1G51850 leucine-rich repeat protein kinase, putative 6 AT1G52190 proton-dependent...”
LSH3_ARATH / O82268 Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 3; Protein ORGAN BOUNDARY 1 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT2G31160 LSH3 (LIGHT SENSITIVE HYPOCOTYLS 3) from Arabidopsis thaliana
NP_565716 LIGHT-DEPENDENT SHORT HYPOCOTYLS-like protein (DUF640) from Arabidopsis thaliana
Aligns to 42:167 / 219 (57.5%), covers 96.8% of PF04852, 223.6 bits
- function: Probable transcription regulator that acts as a developmental regulator by promoting cell growth in response to light (By similarity). Required for the maintenance of the shoot apical meristem and for the formation of lateral organs. Promotes petal formation and growth, but may suppress organ differentiation in the boundary region.
disruption phenotype: No phenotype, probably due to redundant function of paralogs. - Genome-Wide Association Study Reveals Candidate Genes for Flowering Time in Cowpea (Vigna unguiculata [L.] Walp.)
Paudel, Frontiers in genetics 2021 - “...Vigun07g171300 Vu07 28639274 28644217 2_42453 28483321 CRY2 AT1G04400 Vigun07g171900 Vu07 28713837 28716092 2_42453 28483321 LSH3 AT2G31160 Vigun08g124100 Vu08 29426933 29428985 1_0362 29639172 UGT87A2 AT2G30140 Vigun08g127400 Vu08 29776374 29777564 1_0362 29639172 BBX32 AT3G21150 Vigun08g128600 Vu08 29870661 29873299 1_0362 29639172 Snf1 kinase AT1G80940 Vigun09g003600 Vu09 249165 253046 2_39424...”
- Identification of QTNs and their candidate genes for flowering time and plant height in soybean using multi-locus genome-wide association studies
Han, Molecular breeding : new strategies in plant improvement 2021 - “...MM85086 FT1 13 Glyma.10g037600 Glyma.03g227300 GmPHYA4 AT4G22810 AT2G31160 Gene name Homologous gene Candidate gene QTN Trait Position (bp) Comparative genomic...”
- AINTEGUMENTA and AINTEGUMENTA-LIKE6 directly regulate floral homeotic, growth, and vascular development genes in young Arabidopsis flowers
Krizek, Journal of experimental botany 2021 - “...ChIP-Seq binding peak position Log2 fold change ( ant ail6 or 35S:ANT-GR ) Boundary genes AT2G31160 LSH3/OBO1 Upstream; downstream 0.90 ( ant ail6 ) AT3G23290 LSH4 Upstream 0.85 ( ant ail6 ) AT4G32980 ATH1 Overlap start 1.12 ( ant ail6 ) 0.238 (4 h 35S:ANT-GR )...”
- Using the Yeast Three-Hybrid System to Identify Proteins that Interact with a Phloem-Mobile mRNA
Cho, Frontiers in plant science 2012 - “...protein 2E73 CV506455 50 #538 AT1G18080 ATARCA (Transducin/WD40 repeat-like superfamily protein) E118 TC197724 5 #539 AT2G31160 LSH3 | Protein of unknown function (DUF640) 1E54 CV502385 50 #542 AT2G42610 LSH10 | Protein of unknown function (DUF640) 1E64 TC202398 50 #543 AT4G28940 Phosphorylase superfamily protein E113 TC195965 5...”
- “...TC195833 5 #66 AT2G42610 LSH10 | Protein of unknown function (DUF640) 1E64 TC202398 10 #69 AT2G31160 LSH3 | Protein of unknown function (DUF640) 2E54 DR034011 5 #610 AT1G58684 Ribosomal protein S5 family protein E111 TC225313 5 #614 AT2G42610 LSH10 | Protein of unknown function (DUF640) 1E64...”
- Organ boundary1 defines a gene expressed at the junction between the shoot apical meristem and lateral organs
Cho, Proceedings of the National Academy of Sciences of the United States of America 2011 - “...and 936 bp upstream of the translational start of At2g31160. The gene interrupted by the T-DNA insert in J2341 should have the same expression pattern as seen...”
- “...driving ER-GFP. We tested the mRNA expression pattern of At2g31160, closest to the T-DNA insertion site. At2g31160 mRNA expression was not detected by in situ...”
- CUP-SHAPED COTYLEDON1 transcription factor activates the expression of LSH4 and LSH3, two members of the ALOG gene family, in shoot organ boundary cells.
Takeda, The Plant journal : for cell and molecular biology 2011 (PubMed)- GeneRIF: CUC1 directly activates transcription of the nuclear factor genes LSH4 and LSH3, which may suppress organ differentiation in the boundary region.
GRMZM2G147241 putative protein of unknown function (DUF640) domain family protein from Zea mays
Aligns to 27:152 / 200 (63.0%), covers 96.0% of PF04852, 223.2 bits
- Genome-Wide Identification and Characterization of the ALOG Domain Genes in Rice
Li, International journal of genomics 2019 - “...and Arabidopsis (see Supplementary Figure S3 ). For instance, GRMZM2G459645 , GRMZM2G095382 , GRMZM2G081515 , GRMZM2G147241 , GRMZM2G061499 , and GRMZM2G034385 are highly expressed in the stem and shoot apical meristem (SAM), resembling the highly expressed AtLSH1 , AtLSH3 , AtLSH4 , and AtLSH10 in Arabidopsis...”
XP_012089329 protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 1 from Jatropha curcas
Aligns to 35:161 / 198 (64.1%), covers 96.8% of PF04852, 222.9 bits
G1L6_ORYSJ / Q6K5X1 Protein G1-like6; OsG1L6; Protein ABNORMAL FLOWER AND DWARF 1; Protein BEAK LIKE SPIKELET 1; Protein BEAK-SHAPED GRAIN 1; Protein TRIANGULAR HULL 1 from Oryza sativa subsp. japonica (Rice) (see 6 papers)
XP_015624971 protein G1-like6 from Oryza sativa Japonica Group
Aligns to 69:193 / 248 (50.4%), covers 97.6% of PF04852, 222.4 bits
- function: Transcription factor required for lateral development of the lemma and palea (PubMed:22203474, Ref.9, PubMed:23526395, PubMed:25224972, PubMed:26486996, PubMed:29057928, PubMed:30725309). Involved in the regulation of grain hull development (PubMed:23526395). Possesses transactivation activity in yeast, and may determine grain shape and size by modifying gene expression in the grain hull (PubMed:23526395). Regulates the expression of cell proliferation and expansion related genes (PubMed:26486996). Acts as a transcriptional repressor and regulates cell expansion during the lateral development of spikelet (PubMed:29057928). May act upstream of hormone-related genes and starch and sucrose metabolism-related genes, which may be responsible for lemma and palea development, and grain filling, respectively (PubMed:30725309). Does not seem to function at stages of floral-organ initiation and patterning (Ref.9).
subunit: Homodimer.
disruption phenotype: Triangular hull with tortuous lemma and palea (PubMed:22203474, PubMed:29057928). Defects in development of lemma and palea, which have a beak-like form (Ref.9, PubMed:25224972, PubMed:30725309). Beak-shaped grains of decreased width, thickness and weight with a loosely interlocked lemma and palea that are unable to close tightly (PubMed:23526395, PubMed:26486996, PubMed:29057928). Poor grain filling (PubMed:22203474, Ref.9, PubMed:23526395, PubMed:25224972, PubMed:26486996, PubMed:29057928, PubMed:30725309). - Ectopic expression of Jatropha curcas JcTAW1 improves the vegetative growth, yield, and drought resistance of tobacco
Peng, BMC plant biology 2023 - “...this work), and in rice, the closest homologous TAW1 to JcTAW1 is G1-like 6 | XP_015624971 (Figure S 3 ). The T1 JcTAW1 transgenic tobacco lines were strictly identified with three pairs of primers (Fig. 1 A), and the JcTAW1 expression pattern in transgeniclines was further...”
- A role for TRIANGULAR HULL1 in fine-tuning spikelet morphogenesis in rice.
Sato, Genes & genetic systems 2014 (PubMed)- GeneRIF: TRIANGULAR HULL1 (TH1) is likely to be involved in the fine-tuning of lemma/palea morphogenesis.
- Beak-shaped grain 1/TRIANGULAR HULL 1, a DUF640 gene, is associated with grain shape, size and weight in rice.
Yan, Science China. Life sciences 2013 (PubMed)- GeneRIF: Studies indicate that mutations of bsg1-1, bsg1-2 and triangular hull1-1 (th1-1) occurred in the DUF640 coding sequence, and that the Os02g0811000 gene was responsible for the phenotype of bsg1/th1-1.
GRMZM2G162109 uncharacterized protein LOC100273939 from Zea mays
Aligns to 40:165 / 247 (51.0%), covers 99.2% of PF04852, 222.3 bits
- Genome-Wide Identification and Characterization of the ALOG Domain Genes in Rice
Li, International journal of genomics 2019 - “..., AtLSH3 , AtLSH4 , and AtLSH10 in Arabidopsis hypocotyl, node, and shoot apex. Furthermore, GRMZM2G162109 , GRMZM2G168371 , and GRMZM2G027302 are not only expressed in the stem and SAM but also highly expressed in the husk and seeds. Specifically, GRMZM2G168371 and GRMZM2G027302 , the maize...”
- “...OsG1L8 in rice sheath and stem (Figures 4(a) and 6 ). The high expression of GRMZM2G162109 , GRMZM2G168371 , and GRMZM2G027302 in maize husk and seeds resembles the markedly high expression of OsG1 and OsG1L6 in rice panicles ( Figure 4(a) and Figure S3 ). The...”
AT2G42610 LSH10 (LIGHT SENSITIVE HYPOCOTYLS 10) from Arabidopsis thaliana
NP_565978 LIGHT-DEPENDENT SHORT HYPOCOTYLS-like protein (DUF640) from Arabidopsis thaliana
Aligns to 13:138 / 177 (71.2%), covers 98.4% of PF04852, 222.2 bits
- Identification of new potential downstream transcriptional targets of the strigolactone pathway including glucosinolate biosynthesis
Hellens, Plant direct 2023 - “...AT2G18550, AT2G22860, AT5G16600, AT5G24420, AT5G15830, AT1G65860, AT1G01110, AT4G25100, AT1G16410, AT1G19670, AT5G23010, AT3G19710, AT3G50970, AT4G15100, AT4G12030, AT2G42610, AT5G59090, AT1G66020, AT4G33420, AT5G38710, AT1G64160, AT5G60020, AT3G22740, AT3G58990, AT1G30760, AT5G25980, AT3G03190, AT4G13770, AT5G64530, AT5G25160, AT1G47400, AT3G21420, AT4G20210, AT1G04240, AT1G04250, AT1G04550, AT1G15580, AT1G17140, AT1G19850, AT1G23080, AT1G28010, AT1G29510, AT1G34670, AT1G48660, AT1G56650, AT1G57560,...”
- Arabidopsis LSH10 transcription factor and OTLD1 histone deubiquitinase interact and transcriptionally regulate the same target genes
Vo, Communications biology 2023 - “...LSH10 is a 177-amino acid residue protein (Supplementary Fig. 2 ) encoded by the Arabidopsis At2G42610 gene. It belongs to a 10-member family of ALOG (Arabidopsis LSH1 and Oryza G1) protein family in Arabidopsis (Supplementary Fig. 3a ) as well as in numerous other dicotyledonous plant...”
- Linnemannia elongata (Mortierellaceae) stimulates Arabidopsis thaliana aerial growth and responses to auxin, ethylene, and reactive oxygen species
Vandepol, PloS one 2022 - “...AT4G33720 Development Growth promotes cell growth in response to light 0.96 0.7 1.16 0.77 LSH10 AT2G42610 xanthine dehydrogenase 2 0.82 1 0.91 0.75 XDH2 AT4G34900 Root thalianol hydroxylase cytochrome P450, family 708, subfamily A, polypeptide 2 -1.16 -1.19 THAH AT5G48000 Thalianol synthase 1 -1.93 -1.71 THAS...”
- Characterization of rhizome transcriptome and identification of a rhizomatous ER body in the clonal plant Cardamine leucantha
Araki, Scientific reports 2020 - “...to Pathogenesis-related protein 4 ( PR-4 , AT3G04720), Light-dependent Short Hypocotyls 10 ( LSH10 , AT2G42610), Peroxidase 37 ( AtPrx37 , AT4G08770), GDSL-like Lipase 23 ( GLL23 , AT1G54010), Peroxidase 39 ( AtPrx39 , AT4G11290), Methionine Sulfoxide Reductase B9 ( MSRB9 , AT4G21850) and -glucosidase 23...”
- “...4.37 AT3G04720 Pathogenesis-related protein 4 (PR-4) 1 isotig20431 0.33 0.16 1.46 7.34 7.44 4.72 5.05 AT2G42610 Light-dependent Short Hypocotyls 10 (LSH10) 1 isotig06471 1.52 0.46 0.76 0.08 7.04 7.61 8.15 3.66 AT4G08770 Peroxidase 37 (AtPrx37 /Per37) 1 isotig17255 3.59 1.28 6.61 6.74 7.68 6.75 AT1G54010 GDSL-like...”
- Two Loci, RiAF3 and RiAF4, Contribute to the Annual-Fruiting Trait in Rubus
Jibran, Frontiers in plant science 2019 - “...1.43 AT1G29390 Cold regulated thylakoid membrane Ro03_G13391 39,478,286 -0.03 AT4G18130 Phytochrome E Ro03_G05247 40,252,833 0.50 AT2G42610 Light Sensitive Hypocotyls 10 Ro03_G06544 40,834,857 -0.5 AT1G28330 Dormancy-Associated Protein-like 1 Ro03_G06488 41,189,726 -0.16 AT4G04920 Sensitive to Freezing 6 RNAseq was performed on axillary buds from three biological replicates each...”
- Genome-Wide Identification and Characterization of Warming-Related Genes in Brassica rapa ssp. pekinensis
Song, International journal of molecular sciences 2018 - “...short hypocotyl 9 (LSH9) Bra021000 83 85 77 189 112 605 2.3 5.4 0.9 3.2 AT2G42610 Light-dependent short hypocotyl 10 (LSH10) Bra016865 422 617 197 1008 1013 2079 2.4 2.1 0.3 2.1 SF AT1G65660 Pre-mRNA splicing Prp18-interacting factor (SMP1) Bra023741 141 232 1190 664 589 1712...”
- 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 - “...2.1 0.022 Solyc12g005700 A_96_P016566 BT012940 AT2G32280 unknown protein 2.4 0.011 5.4 0.004 Solyc10g007310 A_96_P084909 BW687670 AT2G42610 LSH10 (LIGHT SENSITIVE HYPOCOTYLS 10) 2.3 0.017 3.6 0.002 Solyc03g114130 A_96_P219824 AK329003 AT3G01430 unknown 1.8 0.002 1.9 0.003 Solyc01g081270 A_96_P152326 AK320517 AT3G09270 ATGSTU8 (GLUTATHIONE S-TRANSFERASE TAU 8) 1.6 0.011 1.6...”
- Using the Yeast Three-Hybrid System to Identify Proteins that Interact with a Phloem-Mobile mRNA
Cho, Frontiers in plant science 2012 - “...and unknown proteins (Table A3 in Appendix). Interestingly, LSH10, a close sequence match to AtLSH10 (AT2G42610), was identified from 10 clones along with another LSH member, LSH3, which was isolated twice. Twenty-seven clones (23.3%) were categorized as undefined clones, i.e., unknown or no hit from the...”
- “...function, and RNA metabolism (Wachter et al., 2012 ). B5RBP3 is alight-dependent short hypocotyl (LSH10, AT2G42610) protein with a Domain of Unknown Function (DUF640, Figure 3 ). In Arabidopsis , there are 10 LSH genes and in potato, 15 (Figure 4 A). The function of most...”
- Arabidopsis LSH10 transcription factor and OTLD1 histone deubiquitinase interact and transcriptionally regulate the same target genes.
Vo, Communications biology 2023 - GeneRIF: Arabidopsis LSH10 transcription factor and OTLD1 histone deubiquitinase interact and transcriptionally regulate the same target genes.
LSH4_ARATH / Q9LW68 Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 4; Protein ORGAN BOUNDARY 4 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
NP_001078202 LIGHT-DEPENDENT SHORT HYPOCOTYLS-like protein (DUF640) from Arabidopsis thaliana
AT3G23290 LSH4 (LIGHT SENSITIVE HYPOCOTYLS 4) from Arabidopsis thaliana
Aligns to 33:161 / 195 (66.2%), covers 93.7% of PF04852, 222.1 bits
AT3G04510 LSH2 (LIGHT SENSITIVE HYPOCOTYLS 2) from Arabidopsis thaliana
NP_187101 LIGHT-DEPENDENT SHORT HYPOCOTYLS-like protein (DUF640) from Arabidopsis thaliana
Aligns to 21:146 / 201 (62.7%), covers 98.4% of PF04852, 221.5 bits
- Differential root and shoot magnetoresponses in Arabidopsis thaliana
Paponov, Scientific reports 2021 - “...and 7 were involved in DNA, nucleotide and protein binding ( At1g01980 , At2g33270 , At3g04510 , At3g18550 , At5g23260 , At5g60140, At5g61080) , a gene involved in seed storage ( At5g55420 ), a gene with heme binding, peroxidase activity ( At5g58400 ) and 5 genes...”
- “...3 1.54 1.25 1.02 1.08 1.08 1.05 1.02 1.01 1.05 1.29 1.31 1.19 2.23 2.89 At3g04510 LIGHT SENSITIVE HYPOCOTYLS 2. LSH2 1.24 1.07 1.28 1.24 1.08 1.04 1.35 1.07 1.42 1.16 1.02 1.83 2.48 2.21 At3g18550 TCP transcription factor, closely related to teosinte branched1, arrests axillary...”
- The Arabidopsis KH-Domain RNA-Binding Protein ESR1 Functions in Components of Jasmonate Signalling, Unlinking Growth Restraint and Resistance to Stress
Thatcher, PloS one 2015 - “...Arabidopsis defensin-like protein AT1G28370 ERF11 2.6 3.2E-02 ERF domain protein 11 AT1G63055 7.9 3.3E-02 Unknown AT3G04510 LSH2 2.9 3.4E-02 Protein of unknown function (DUF640) AT4G13410 ATCSLA15 2.3 3.6E-02 Nucleotide-diphospho-sugar transferases superfamily protein AT5G44430 PDF1.2c 12.8 3.6E-02 plant defensin 1.2C AT5G43290 WRKY49 3.5 3.9E-02 WRKY DNA-binding protein...”
- Molecular characterization of Arabidopsis thaliana LSH1 and LSH2 genes.
Lee, Genes & genomics 2020 (PubMed)- GeneRIF: Molecular characterization of Arabidopsis thaliana LSH1 and LSH2 genes.
LSH1_ARATH / Q6NNI3 Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 1; Protein ORGAN BOUNDARY 2 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
NP_198201 LIGHT-DEPENDENT SHORT HYPOCOTYLS-like protein (DUF640) from Arabidopsis thaliana
AT5G28490 LSH1 (LIGHT-DEPENDENT SHORT HYPOCOTYLS 1) from Arabidopsis thaliana
Aligns to 13:138 / 190 (66.3%), covers 99.2% of PF04852, 221.5 bits
AT5G58500 LSH5 (LIGHT SENSITIVE HYPOCOTYLS 5) from Arabidopsis thaliana
Aligns to 7:133 / 182 (69.8%), covers 97.6% of PF04852, 220.5 bits
- PP2A Phosphatases Take a Giant Leap in the Post-Genomics Era
Bheri, Current genomics 2019 - “...and PP2A-C5 (At1g69960) catalytic subunits while the C II subfamily includes PP2A-C3 (At2g42500) and PP2A-C4 (At5g58500) subunits [ 28 ]. The B subunit families include two B subunit isoforms ( and ), nine B subunit isoforms (, , , , , , , , and ),...”
8p5qA / O82268 8p5qA
Aligns to 1:116 / 129 (89.9%), covers 91.3% of PF04852, 220.5 bits
- Ligands: dna; zinc ion (8p5qA)
LOC4338491 protein G1-like9 from Oryza sativa Japonica Group
Aligns to 53:180 / 284 (45.1%), covers 96.8% of PF04852, 219.7 bits
LOC21387330 protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 10 from Morus notabilis
Aligns to 29:155 / 194 (65.5%), covers 96.0% of PF04852, 218.8 bits
LOC4341811 protein G1-like2 from Oryza sativa Japonica Group
Aligns to 14:135 / 277 (44.0%), covers 94.4% of PF04852, 217.4 bits
- Knocking Out the Transcription Factor OsNAC092 Promoted Rice Drought Tolerance
Wang, Biology 2022 - “...light stimulation response that is involved in carbon fixation and carbon metabolism in photosynthetic organisms. LOC4341811 encodes a protein G1L2 that is involved in the development of multicellular organisms (GO: 0007275) and postembryonic plant morphogenesis (GO: 0090698). LOC4331514 encodes a protein OsJ_09298 which is involved in...”
AT1G78815 LSH7 (LIGHT SENSITIVE HYPOCOTYLS 7) from Arabidopsis thaliana
Aligns to 28:153 / 195 (64.6%), covers 99.2% of PF04852, 217.3 bits
XP_004233194 protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 4-like from Solanum lycopersicum
Aligns to 28:151 / 181 (68.5%), covers 96.0% of PF04852, 215.5 bits
XP_004239743 protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 1-like from Solanum lycopersicum
Aligns to 30:154 / 211 (59.2%), covers 94.4% of PF04852, 214.1 bits
AT4G18610 LSH9 (LIGHT SENSITIVE HYPOCOTYLS 9) from Arabidopsis thaliana
Aligns to 21:151 / 191 (68.6%), covers 97.6% of PF04852, 210.2 bits
AT1G16910 LSH8 (LIGHT SENSITIVE HYPOCOTYLS 8) from Arabidopsis thaliana
Aligns to 11:136 / 164 (76.8%), covers 96.0% of PF04852, 209.3 bits
G1_ORYSJ / Q8GVZ6 Protein G1; Protein ELONGATED EMPTY GLUME from Oryza sativa subsp. japonica (Rice) (see 2 papers)
Aligns to 12:169 / 276 (57.2%), covers 92.9% of PF04852, 186.3 bits
- function: Probable transcription regulator that acts as a developmental regulator by promoting cell growth in response to light (By similarity). Transcription regulator that restrains empty glumes growth, lemmas of the sterile florets located at the lateral side of the rice spikelet, to maintain their small size, probably by repressing lemma identity via transcription regulation.
disruption phenotype: Enlarged sterile lemma in florets of the spikelet, caused by homeotic transformation of the sterile lemma into a lemma. Elongated empty glumes, which mimic the lemmas and have the epidermal morphology of lemmas with four or five vascular bundles.
RPP2A_ARATH / F4JT78 Disease resistance protein RPP2A; EC 3.2.2.6 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
NP_193685 nucleoside-triphosphatase/transmembrane receptor/nucleotide binding/ATP binding protein from Arabidopsis thaliana
AT4G19500 ATP binding / nucleoside-triphosphatase/ nucleotide binding / protein binding / transmembrane receptor from Arabidopsis thaliana
Aligns to 482:535 / 1309 (4.1%), covers 33.3% of PF04852, 43.5 bits
- function: Disease resistance protein that cooperates with RPP2B to confer resistance to Hyaloperonospora parasitica isolate Cala2.
catalytic activity: H2O + NAD(+) = ADP-D-ribose + H(+) + nicotinamide (RHEA:16301) - Show me your ID: NLR immune receptors with integrated domains in plants
Marchal, Essays in biochemistry 2022 - “...PRGDB236455 (Glyma.18G281700) G. max ULP1 protease NA - P. pachyrhizi [ 107 ] RPP2A TNL NP_193685 A. thaliana ecotype Col-0 AAA (2x) RPP2B NP_001328446 Hyaloperonospora arabidopsidis [ 108 ] RRS1B TNL NM_180802 A. thaliana ecotype Col-0 WRKY RPS4B NP_001330960 Pseudomonas syringae [ 42 ] RRS1-R TNL...”
- Predicting Cloned Disease Resistance Gene Homologs (CDRHs) in Radish, Underutilised Oilseeds, and Wild Brassicaceae Species
Cantila, Plants (Basel, Switzerland) 2022 - “...155 ] B. cinerea and H. arabidopsidis At_RPP1 (F4J339 U ) [ 156 ], At_RPP2a (F4JT78 U ) and At_RPP2b (F4JT80 U ) [ 157 ], At_RPP4 (F4JNA9 U ) [ 158 ], At_RPP5 (F4JNB7 U ) [ 159 ], At_RPP7 (Q8W3K0 U ) [ 160...”
- Mining of Cloned Disease Resistance Gene Homologs (CDRHs) in Brassica Species and Arabidopsis thaliana
Cantila, Biology 2022 - “...arabidopsidis) F4J339 U [ 63 ] At_RPP2a TNL unknown but interacts with RPP2b (H. arabidopsidis) F4JT78 U [ 64 ] At_RPP2b TNL unknown but interacts with RPP2a (H. arabidopsidis) F4JT80 U At_RPP4 TNL ATR4 (H. arabidopsidis) F4JNA9 U [ 65 ] At_RPP5 TNL ATR5 (H. arabidopsidis)...”
- Arabidopsis thaliana Accessions from the Chernobyl Exclusion Zone Show Decreased Sensitivity to Additional Acute Irradiation
Podlutskii, Plants (Basel, Switzerland) 2022 - “...were found for AT1G14250 (probable apyrase 5), AT5G35480 (hypothetical protein), AT2G29300 (NAD(P)-binding Rossmann-fold superfamily protein), AT4G19500 (disease resistance protein), and AT2G27402 (plastid transcriptionally active protein) ( Table S3 ). Among the 66 downregulated genes, the strongest responses were observed for the genes AT1G25083 (glutamine amidotransferase type...”
- Light regulates alternative splicing outcomes via the TOR kinase pathway
Riegler, Cell reports 2021 - “...regulators AS1 and AS2; APT5 (AT5G11160), an adenine phosphoribosyltransferase acting in AMP salvage; and RPP2A (AT4G19500), a TIR-NBS-LRR (TNL) receptor that is required for RPP2-mediated resistance to Peronospora parasitica isolate Cala2. We validated the DTU results by conducting the seedling treatment assay another three times, independently,...”
- Impact of DNA Demethylases on the DNA Methylation and Transcription of Arabidopsis NLR Genes
Kong, Frontiers in genetics 2020 - “...the wild-type plants ( Figure 6 and Supplementary Table S3 ). In the UPRs of AT4G19500 and AT4G19510 , three cytosine sequence contexts were highly modified by DNA methylation in the wild-type and ros1 mutant plants, and CG methylation was observed within their transcribed regions (...”
- “...plants ( Figures 6 , 7 and Supplementary Tables S3 , S4 ). In addition, AT4G19500 and AT4G19510 were the same as these two genes, but their methylation levels were considerably lower in the extent of modification ( Figures 6 , 7 and Supplementary Tables S3...”
- Variation Patterns of NLR Clusters in Arabidopsis thaliana Genomes
Lee, Plant communications 2020 - “...lines in Figure5 A). In Col-0, there were four genes with two NB-ARC domains, including AT4G19500 ( RPP2A ) in cluster RPP2 . By inspecting the genes that fell within this range, we could detect instances where two vastly different NB-ARC domains with clear separation were...”
- Identification and expression profiling analysis of NBS-LRR genes involved in Fusarium oxysporum f.sp. conglutinans resistance in cabbage
Liu, 3 Biotech 2019 - “...are orthologous or have relatively high similarity with AT4G19500, while the orthologous gene of Bo7g106620 and Bo7g106660 is AT4G19510, and both AT4G19500 and...”
- “...(https://string-db.org/cgi/input.pl) showed that the products of AT4G19500 and AT4G19510 have known interactions and are co-expressed. The NLS prediction...”
- Oomycetes Used in Arabidopsis Research
Herlihy, The arabidopsis book 2019 (secret) - Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis thaliana
Yu, BMC genomics 2014 - “...region of chromosome 4 in A. thaliana genome. Only two genes in this tandem array (AT4G19500 and AT4G19510) preserved tripled copies and other two genes (AT4G19520 and AT4G19530) have retained one copy in B. oleracea genome respectively. In B. rapa genome, we found that only AT4G19500...”
- “...B. oleracea respectively, which appeared in one phylogenetic sub tree (Figure 3 B). The genes AT4G19500 and AT4G19510 in tandem array might have important role in process of A. thaliana diseases resistance, so they retained three copies after triplication in B. oleracea genome. AT4G19520 and AT4G19530...”
- ALOG domains: provenance of plant homeotic and developmental regulators from the DNA-binding domain of a novel class of DIRS1-type retroposons
Iyer, Biology direct 2012 - “...N-terminus (e.g. gi: 297804202; Arabidopsis lyrata ) or in the middle of the protein (e.g. AT4G19500 of Arabidopsis thaliana and SORBIDRAFT_05g008160 of Sorghum bicolor ) (Figure 2 ). The ALOG domains in these Arabidopsis and Brassica proteins lack the ZnR insert, whereas the Sorghum version retains...”
- More
Or search for genetic data about PF04852 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory