Family Search for PF03479 (DUF296)
PF03479.15 hits 55 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
AHL19_ARATH / Q9SR17 AT-hook motif nuclear-localized protein 19 from Arabidopsis thaliana (Mouse-ear cress) (see 3 papers)
AT3G04570 DNA-binding protein-related (RefSeq) from Arabidopsis thaliana
NP_566232 AT-hook motif nuclear-localized protein 19 from Arabidopsis thaliana
Aligns to 108:229 / 315 (38.7%), covers 99.1% of PF03479, 105.8 bits
- function: Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs) (By similarity). Negatively regulates plant innate immunity (PTI) to pathogens through the down-regulation of the PAMP-triggered FRK1 expression (PubMed:20738724). Positively regulates defense against fungal Verticillium infection (PubMed:21864046).
disruption phenotype: Enhanced susceptibility to Verticillium wilt resulting in wilting, stunting and chlorosis. - Function annotation of an SBP-box gene in Arabidopsis based on analysis of co-expression networks and promoters
Wang, International journal of molecular sciences 2009 - “...GDSL-motif lipase/hydrolase family protein AT2G45430 DNA-binding protein-related AT4G21650 subtilase family protein UCC2__UCC2 (UCLACYANIN 2); copper AT3G04570 DNA-binding protein-related AT2G44790 ion binding AT4G32650 ARABIDOPSIS THALIANA K+ RECTIFYING CHANNEL 1 AT3G28500 60S acidic ribosomal protein P2 (RPP2C) AT3G14680 CYP72A14 AT4G12550 Auxin-Induced in Root cultures 1 AT1G20900 ESCAROLA AT4G20860...”
- The Arabidopsis thaliana DNA-binding protein AHL19 mediates verticillium wilt resistance.
Yadeta, Molecular plant-microbe interactions : MPMI 2011 (PubMed)- GeneRIF: AHL19 acts as a positive regulator of plant defense.
AHL22_ARATH / O22130 AT-hook motif nuclear-localized protein 22 from Arabidopsis thaliana (Mouse-ear cress) (see 3 papers)
NP_182067 AT-hook motif nuclear-localized protein 22 from Arabidopsis thaliana
AT2G45430 DNA-binding protein-related (RefSeq) from Arabidopsis thaliana
Aligns to 117:234 / 317 (37.2%), covers 98.1% of PF03479, 103.1 bits
AHL21_ARATH / O82166 AT-hook motif nuclear-localized protein 21; Protein GIANT KILLER from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
NP_181070 Putative AT-hook DNA-binding family protein from Arabidopsis thaliana
AT2G35270 DNA-binding protein-related (RefSeq) from Arabidopsis thaliana
Aligns to 106:219 / 285 (40.0%), covers 100.0% of PF03479, 102.9 bits
- function: Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs). Binds to the MARs present in the ETTIN (ETT) promoter leading to a negative regulation of its gene expression. Functions as a molecular node downstream of the homeotic protein AGAMOUS (AG), regulating patterning and differentiation of reproductive organs. Acts as a chromatin remodeling factor that modifies the architecture of ETTIN (ETT) chromatin by modulating H3 methylation leading to the regulation of ETT expression. Seems to be involved in the regulation of a set of reproductives genes including CRABS CLAW (CRC), JAGGED (JAG) and KNUCKLES (KNU).
disruption phenotype: Reproductive defects. - AGAMOUS controls GIANT KILLER, a multifunctional chromatin modifier in reproductive organ patterning and differentiation.
Ng, PLoS biology 2009 - GeneRIF: GIANT KILLER (AT2G35270) acts as a molecular node downstream of AGAMOUS, regulating patterning and differentiation of reproductive organs through chromatin organization
- Mediator of tolerance to abiotic stress ERF6 regulates susceptibility of Arabidopsis to Meloidogyne incognita
Warmerdam, Molecular plant pathology 2019 - “...At2G34300 8 2 14848612 G:T 150:199 4 4.28 At2G35250 At2G35215, At2G35220, At2G35230, At2G35240, At2G35250. At2G35260, At2G35270 9 2 18338888 A:G 211:138 4.6 4.56 At2G44440 At2G44400, At2G44410, At2G44420, At2G44430, At2G44440, At2G44450, At2G44460 10 3 287272 C:T 131:218 4.4 4.19 At3G01800 At3G01770, At3G01780, At3G01790, At3G01800, At3G01810, At3G01820, At3G01830....”
- Network component analysis provides quantitative insights on an Arabidopsis transcription factor-gene regulatory network
Misra, BMC systems biology 2013 - “...Arabidopsis gene model are: 1 - NAP (At1g69490), 2 - CRC (At1g69180), 3 - GIK (At2g35270), 4 - APL (At2g27330), 5 - AGL2 (At5g15800), 6 - AGL4 (At3g02310), 7 - AGL8 (At5g60910), 8 - AGL3 (At2g03710), 9 - ACS8 (At4g37770), 10 - ADR1 (At1g33560), 11 -...”
- AGAMOUS controls GIANT KILLER, a multifunctional chromatin modifier in reproductive organ patterning and differentiation
Ng, PLoS biology 2009 - “...multiple downstream targets in plants. Results GIK Is a Direct Target of AG We identified At2G35270 (isolation name, 2-ATH ; AHL21 [32] ) as a putative direct target of AG using bioinformatics screening ( Figure 1A, B ) of the Arabidopsis genome for potential AG binding...”
- “...article are as follows: AGAMOUS ( AG , At4g18960 ), GIANT KILLER ( GIK , At2g35270 ), ETTIN (ETT , At2g33860 ), CRABS CLAW ( CRC , At1g69180 ), JAGGED ( JAG , At1g68480 ), KNUCKLES ( KNU , At5g14010 ), LEUNIG ( LUG , At4g32551...”
AHL26_ARATH / Q9SZ70 AT-hook motif nuclear-localized protein 26 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT4G12050 DNA-binding protein-related (RefSeq) from Arabidopsis thaliana
Aligns to 146:260 / 339 (33.9%), covers 100.0% of PF03479, 102.4 bits
- function: Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs).
- Mediator of tolerance to abiotic stress ERF6 regulates susceptibility of Arabidopsis to Meloidogyne incognita
Warmerdam, Molecular plant pathology 2019 - “...At3G56750, At3G56760, At3G770 12 4 7211220 C:T 104:245 4.2 4.15 At4G12030 At4G12010, At4G12020, At4G12030, At4G12040, At4G12050 13 4 9765013 C:T 133:216 4 3.83 At4G17505 At4G17490, At4G17500, At4G17505, At4G17510, At4G17520, At4G17530 14 4 9843096 C:T 96:253 4.1 4.30 At4G17680 At4G17660, At4G17670, At4G17670, At4G17680, At4G17690, At4G17695 15 4...”
AHL24_ARATH / O49662 AT-hook motif nuclear-localized protein 24 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
Aligns to 133:249 / 324 (36.1%), covers 100.0% of PF03479, 102.2 bits
- function: Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs).
G7KG44 AT-hook motif nuclear-localized protein from Medicago truncatula
Aligns to 128:241 / 325 (35.1%), covers 100.0% of PF03479, 101.8 bits
AHL20_ARATH / Q8GWQ2 AT-hook motif nuclear-localized protein 20 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT4G14465 DNA-binding protein-related (RefSeq) from Arabidopsis thaliana
Aligns to 95:208 / 281 (40.6%), covers 100.0% of PF03479, 100.5 bits
XP_015641725 AT-hook motif nuclear-localized protein 18 from Oryza sativa Japonica Group
Aligns to 139:253 / 328 (35.1%), covers 99.1% of PF03479, 100.2 bits
AHL23_ARATH / O23620 AT-hook motif nuclear-localized protein 23 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT4G17800 DNA-binding protein-related (RefSeq) from Arabidopsis thaliana
Aligns to 110:223 / 292 (39.0%), covers 100.0% of PF03479, 100.1 bits
- function: Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs).
- Use of transcriptomics and co-expression networks to analyze the interconnections between nitrogen assimilation and photorespiratory metabolism
Pérez-Delgado, Journal of experimental botany 2016 - “...Number of connections Gene (Kazusa 3.0 ) Ortholog gene in Arabidopsis Ljwgs_121486.1_at Unknown 31 Lj2g3v1984810.1 At4g17800 Ljwgs_035337.1_at* Trihelix 31 Lj0g3v0261399.1 At5g63420 Ljwgs_142668.1_at* mTERF 30 Lj2g3v2197630.1 At4g02990 chr2.CM0132.46_at bHLH 23 Lj2g3v1984450.1 At4g37850 Ljwgs_149102.1_s_at Unknown 17 Lj4g3v3015070.1 At4g12750 chr5.CM0048.61_at bHLH 17 Lj5g3v1533330.1 At1g09530 Ljwgs_015129.1_at* bHLH 16 Lj3g3v0028580.1 At2g22770...”
- Conserved microstructure of the Brassica B Genome of Brassica nigra in relation to homologous regions of Arabidopsis thaliana, B. rapa and B. oleracea
Navabi, BMC genomics 2013 - “...10 3 3.3 At4g17730 DL 4900 67 1 67 At4g17760 DL 4915 19 2 9.5 At4g17800 DL 4935 85 3 28.3 Contigs of overlapping BAC clones were assembled based on common digestion patterns observed for two or more genes. In addition, all 483 BAC clones were...”
- “...the presence or absence of eight genes (At4g17260, At4g17300, At4g17380, At4g17440, At4g17650, At4g17750, At4g17760, and At4g17800) that are present in the chromosome 4 region, but not in the chromosome 5 region [ 29 , 44 ]. At this macro-level the only apparent major difference between the...”
- 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 - “...TA54084_4081 AT3G23240 ERF1 (ETHYLENE RESPONSE FACTOR 1) 4.9 0.014 2.3 0.019 Solyc01g080960 a A_96_P017531 AK330067 AT4G17800 DNA-binding protein-related | Predicted AT-hook DNA-binding family protein 4.7 0.014 4.1 0.009 Solyc08g076010 A_96_P172039 BE431711 AT5G45580 transcription factor | Homeodomain-like superfamily protein 3.6 0.017 3.1 0.011 Solyc02g085500 a A_96_P013166 OVATE...”
- Expression Cassettes For Root-Preferential Expression In Plants
KEETMAN, 2010 - AGAMOUS controls GIANT KILLER, a multifunctional chromatin modifier in reproductive organ patterning and differentiation
Ng, PLoS biology 2009 - “...[32] , [33] , we produced an RNAi silencing construct for the highly similar gene At4g17800 (67% amino acid identity) and created the transgenic plants on the gik mutant background. However, we did not observe any obvious enhanced effects in the transgenic plants (unpublished data). The...”
- “...showed reproductive defects. To generate the 35S::GIK2-RNAi construct, an N-terminal fragment of the GIK2 ( AT4g17800 ; 39260 bp) coding region was amplified using UltraPfu-High-Fidelity DNA polymerase to produce BamHI-GIK2-Nter-ClaI and XhoI-GIK2-Nter-KpnI fragments. These fragments were cloned into the pKANNIBAL vector and later into the pMLBART...”
AHL18_ARATH / Q9LZX7 AT-hook motif nuclear-localized protein 18 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
NP_191646 AT-hook motif nuclear-localized protein 18 from Arabidopsis thaliana
AT3G60870 DNA-binding protein-related (RefSeq) from Arabidopsis thaliana
Aligns to 87:198 / 265 (42.3%), covers 99.1% of PF03479, 99.7 bits
- function: Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs) (By similarity). Acts redundantly with AHL22, AHL27 and AHL29 in the regulation of flowering and regulation of the hypocotyl elongation (PubMed:19517252).
- At-Hook Motif Nuclear Localised Protein 18 as a Novel Modulator of Root System Architecture.
Širl, International journal of molecular sciences 2020 - GeneRIF: At-Hook Motif Nuclear Localised Protein 18 as a Novel Modulator of Root System Architecture.
- At-Hook Motif Nuclear Localised Protein 18 as a Novel Modulator of Root System Architecture
Širl, International journal of molecular sciences 2020 - “...activity. They modulate gene expression and affect various developmental processes in plants. We identify AHL18 (At3G60870) as a developmental modulator of root system architecture and growth. AHL18 is involved in regulation of the length of the proliferation domain and number of dividing cells in the root...”
- “...these correspond well with expression pattern of AHL18 . AT-hook motif nuclear protein 18 AHL18 At3G60870 Arabidopsis Lateral root development Root apical meristem Cell proliferation 1. Introduction The root system is essential for plant anchorage, water and nutrition acquisition, and mediating interactions with the soil environment...”
AHL7_ARATH / Q4V3E0 AT-hook motif nuclear-localized protein 7 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
Aligns to 124:240 / 318 (36.8%), covers 98.1% of PF03479, 99.7 bits
- function: Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs).
GRMZM2G119168 DNA-binding protein from Zea mays
Aligns to 82:197 / 273 (42.5%), covers 99.1% of PF03479, 99.4 bits
- Transcriptional analyses of natural leaf senescence in maize
Zhang, PloS one 2014 - “...[83] GRMZM2G088212 AT1G20620 Catalase 3(CAT3), SENESCENCE 2 Induced by age and senescence [84] , [85] GRMZM2G119168 AT1G20900 AHL27, AT-HOOK MOTIF NUCLEAR-LOCALIZED PROTEIN 27 Delayed leaf senescence [86] GRMZM2G047404 AT1G61800 GLUCOSE-6-PHOSPHATE/PHOSPHATE TRANSLOCATOR 2 (GPT2) Senescence associated gene [41] , [87] AC207347.3_FG005 AT1G73220 ORGANIC CATION/CARNITINE TRANSPORTER1 (OCT1) Strong...”
AHL1_ARATH / Q8VYJ2 AT-hook motif nuclear-localized protein 1 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT4G12080 DNA-binding family protein (RefSeq) from Arabidopsis thaliana
Aligns to 171:287 / 356 (32.9%), covers 98.1% of PF03479, 99.4 bits
- function: Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs). May play a function in the positioning of chromatin fibers within the nucleus.
- De novo computational identification of stress-related sequence motifs and microRNA target sites in untranslated regions of a plant translatome
Munusamy, Scientific reports 2017 - “...determines the activity of the miRNA in either cleaving or inhibiting the mRNA expression. Genes AT4G12080, AT1G53160 and AT2G03750 had target sites for the miR156/miR157 in their 3 UTRs. The AT1G53160 encodes the transcription factor SPL (SQUAMOSA promoter binding protein-like), which is involved in the regulation...”
- Unravelling Protein-Protein Interaction Networks Linked to Aliphatic and Indole Glucosinolate Biosynthetic Pathways in Arabidopsis
Nintemann, Frontiers in plant science 2017 - “...0 0 11 At3G62200 Putative endonuclease or glycosyl hydrolase 74.2 Nucleus 13 1 0 14 At4G12080 AT-hook motif nuclear-localized protein 1 (AHL1) 37.3 Nucleus, nucleoplasm 5 0 0 5 At4G14990 Topoisomerase II-associated protein (PAT1H2) 86.5 Nucleus 14 5 1 20 At4G16830 Hyaluronan/mRNA binding family 37.5 Cytoplasm,...”
- Transcript profiling of crown rootless1 mutant stem base reveals new elements associated with crown root development in rice
Coudert, BMC genomics 2011 - “...PROTEIN FROM PLANTS 9) [ 54 ] Os08g02490 8,64 AT hook motif domain containing protein At4g12080 DNA-binding family protein O Os02g24740 8,14 OsSAUR9 - Auxin-responsive SAUR gene family member At4g34760 auxin-responsive family protein [ 55 , 56 ] Os03g51580 6,89 helix-loop-helix DNA-binding domain containing protein At2g22750...”
- The maize root stem cell niche: a partnership between two sister cell populations
Jiang, Planta 2010 - “...lines are the gifts from Mendel Biotechnology Inc., Hayward, CA. Briefly, for the 35S::AHL1 construct, At4g12080 cDNA was cloned into the Sal I/Not I site of pMEN65 downstream from the CaMV35S promoter. For construction of the 35S::RHC1a, At2g40830 genomic DNA was introduced into pMEN65 downstream from...”
- “...plants were used for 35S::AHL1 lines. T-DNA insertion lines for At2g45050 (Salk_008743, Salk_008794 and Salk_008845), At4g12080 (Salk_024324, Salk_026823, Salk_052728 and Salk_086713, Salk_092100) and At2g40830 (Salk_127503, Salk_143110, Salk_137684, Salk_037121) were obtained from the ABRC. Lines showing the short root phenotype were genotyped by PCR using the primers...”
- UV-B responsive microRNA genes in Arabidopsis thaliana
Zhou, Molecular systems biology 2007 - “...At1g69170 (SPL4) Binding protein-like At2g33810 (SPL3), At5g43270 (SPL2) Transcription factor At3g15270 (SPL5) At2g35320, At2g45990, At3g28690 At4g12080, At4g28660, At4g36860 At5g18590, At5g08620, At5g38610 miR159/319 At3g11440, At4g18390, At5g06100 MYB factors At3g06450, At3g61740, At3g15030 At4g37770, At5g09410, At4g26930 At5g17580, At5g56790, At5g55020 At2g26950, At5g67090, At2g32460 At1g30210, At1g53230, At2g26960 At2g31070 miR160 At2g28350(ARF10), At4g30080(ARF16)...”
B4FRV0 AT-hook motif nuclear-localized protein from Zea mays
Aligns to 180:296 / 391 (29.9%), covers 98.1% of PF03479, 99.3 bits
- Phosphoproteomic analysis of the response of maize leaves to drought, heat and their combination stress.
Hu, Frontiers in plant science 2015 - “...27 37040 574595 5.17 H 1 xxxxxxx R xx S xxxxxxxxxx BF4F7Z5; BF4F976; B4FI93; B4FRF2; B4FRV0; B4FUV7; B6SRZ6; B6SXN6; B6T1H0; B6T2A6; B6TDN3; B6TQS9; B6TWH2; B6U787; B8A0K2; C0HIM6; C0P3W9; C0P4D8; C0P9L7; C0PCR0; C0PDN0; C0PD30; K7TRK2; K7U573; K7V0H0; K7VBI0; K7VBA5; K7W2Z7; K7WC16; Q41729; Q9ATN2 11.33 31 132 55507...”
- “...C0P3W9; C0PD66 13.09 7 36 2559 574595 43.66 4 xxxxxxxxx RT xxxxxxxxxx B4FB20; B4FGQ4; B4FQU2; B4FRV0; BF4F7W7; B6SRZ6; C0HE61; C0PLM8; C0PLZ2; K7V4D9; K7VD18 7.28 11 29 27693 572036 7.84 DH 1 xxxxxxx R xx S xxxxxxxxx A3KLI0; BF4F976; B4FI93; B4FRF2; B4FUV7; B4FXQ9; B6SJ15; B6SRZ6; B6SXN6; B6T1H0;...”
B6TI42 AT-hook motif nuclear-localized protein from Zea mays
Aligns to 180:296 / 377 (31.0%), covers 98.1% of PF03479, 99.1 bits
AHL13_ARATH / Q940I0 AT-hook motif nuclear-localized protein 13; AT-hook protein 2 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT4G17950 DNA-binding family protein (RefSeq) from Arabidopsis thaliana
Aligns to 222:340 / 439 (27.1%), covers 99.1% of PF03479, 98.3 bits
G3PDP5 PPC domain-containing protein from Gasterosteus aculeatus
Aligns to 11:123 / 148 (76.4%), covers 97.2% of PF03479, 97.2 bits
- Dietary Creatine Supplementation in Gilthead Seabream (Sparus aurata): Comparative Proteomics Analysis on Fish Allergens, Muscle Quality, and Liver
Schrama, Frontiers in physiology 2018 - “...A OS Danio rerio 2,170 26,836/26,776 4.72/4.7 6 25 0.002 0.0023 2.03 CR2>CR5> CR8>CTRL 1,214 G3PDP5 Uncharacterized protein OS Gasterosteus aculeatus [after blast on 28-04-2017 bifunctional protein GlmU-like ( Salmo salar )] 1,661 15,732/13,637 5.34/5.0 1 9 0.016 0.0462 1.73 CR8>CR2> CR5>CTRL Mw, molecular weight; pI,...”
AHL4_ARATH / Q9FHM5 AT-hook motif nuclear-localized protein 4 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT5G51590 DNA-binding protein-related (RefSeq) from Arabidopsis thaliana
NP_199972 AT hook motif DNA-binding family protein from Arabidopsis thaliana
Aligns to 179:295 / 419 (27.9%), covers 98.1% of PF03479, 96.0 bits
- function: Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs) (By similarity). Acts redundantly with AHL3 to regulate the formation of tissue boundary between the xylem and procambium in the root meristem. Cell-to-cell movement of AHL4 from the procambium to the xylem is critical for its function in root vascular patterning (PubMed:23335615).
subunit: Homodimer. Interacts with AHL3.
disruption phenotype: Misspecification of tissue boundaries between the xylem and procambium. - Vascular Cambium Development
Nieminen, The arabidopsis book 2015 - “...TIF NUCLEAR LOCALIZED PROTEIN3 (AHL3; At4g25320) and AHL4 (At5g51590), which also move to the xylem axis from the surrounding tissues, regulate the boundary...”
- Cell-to-cell movement of two interacting AT-hook factors in Arabidopsis root vascular tissue patterning.
Zhou, The Plant cell 2013 - GeneRIF: The cell-to-cell communication mediated by mobile AHL3 and AHL4 is critical for establishing the boundary between the procambium and xylem.
AHL2_ARATH / O49658 AT-hook motif nuclear-localized protein 2 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT4G22770 DNA-binding family protein (RefSeq) from Arabidopsis thaliana
Aligns to 151:267 / 334 (35.0%), covers 98.1% of PF03479, 95.2 bits
- function: Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs).
- NOVOMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-Genome
Teune, Journal of nucleic acids 2010 - “...but no explicit annotation. One novoMIR hit is located on chromosome 4 between At4G22760 and At4G22770 close to the 3 terminus of the latter, but on the opposite strand; for further details, see Figure 3 and Figure S9. The next hit (see Figure 3 and Figure...”
AHL10_ARATH / O22812 AT-hook motif nuclear-localized protein 10; AT-hook protein 1 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT2G33620 DNA-binding family protein / AT-hook protein 1 (AHP1) (RefSeq) from Arabidopsis thaliana
Aligns to 164:280 / 351 (33.3%), covers 98.1% of PF03479, 94.1 bits
- function: Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs).
- AtDRO1 is nuclear localized in root tips under native conditions and impacts auxin localization
Waite, Plant molecular biology 2020 - “...domain 5.79 5.66E03 AT2G31810 AT2G31810 ACT domain-containing small subunit of acetolactate synthase protein 5.53 4.03E02 AT2G33620 AT2G33620 AT hook motif DNA-binding family protein 5.07 4.23E02 AT3G59430 AT3G59430 Unknown protein 4.85 2.25E03 AT3G42725 AT3G42725 Putative membrane lipoprotein 4.73 4.18E03 AT5G12330 LRP1 Encodes LRP1 (LATERAL ROOT PRIMORDIUM 1)...”
- Greenbug (Schizaphis graminum) herbivory significantly impacts protein and phosphorylation abundance in switchgrass (Panicum virgatum)
Zogli, Scientific reports 2020 - “...DEGs-up DPs-up Pavir.1NG430900 AT4G13940 S-adenosyl- l -homocysteine hydrolase 1 L T KSQADYISVPIEGPYKPAHYR DEGs-up DPs-up Pavir.2KG411435 AT2G33620 AT hook motif DNA-binding family protein VAPAAPS S PPSR DEGs-up DPs-up Pavir.2KG484600 AT4G05150 Octicosapeptide/Phox/Bem1p family protein SDAAE T PRQHGDEDEASVPAR DEGs-up DPs-down Pavir.2KG572300 AT1G53050 Protein kinase superfamily protein IADFGLASFFDPNHKQPM T SR...”
- Epigenetic signatures associated with imprinted paternally expressed genes in the Arabidopsis endosperm
Moreno-Romero, Genome biology 2019 - “...of seven genes belonging to the highest score category but predicted to be maternally ( AT2G33620 , AT1G43580 , AT1G47530 , AT1G64660 , AT2G30590 , AT4G15390 ) or biallelically expressed ( AT5G53160 ). We detected a GFP signal in the endosperm only for construct AT1G64660 (Fig....”
- “...we used the ClonExpress MultiS One Step Cloning kit. Promoters (2kb) and genic sequences of AT2G33620 , AT1G43580 , AT1G47530 , AT1G64660 , AT2G30590 , AT4G15390 , and AT5G53160 were amplified from WT Col-0 genomic DNA using primers specified in Additionalfile 1 : Table S6 and...”
- cDNA-AFLP analysis reveals differential gene expression in incompatible interaction between infected non-heading Chinese cabbage and Hyaloperonospora parasitica
Xiao, Horticulture research 2016 - “...x 72 AB474716 126 AT5G42220 AT5G42220 Bra027974 AT5G42220 _A09 ST x x 73 AB474644 121 AT2G33620 AHL10 Bra021865 BcAHL10 _A04 ST x x x 74 AB474713 129 AT3G15290 AT3G15290 Bra027263 AT3G15290 _A05 EM X X x 75 AB474703 127 AT3G48990 AAE3 Bra018019 BcAAE3 _A06 EM x...”
- Proteome distribution between nucleoplasm and nucleolus and its relation to ribosome biogenesis in Arabidopsis thaliana
Palm, RNA biology 2016 - “...RPP1 RPP1 RPP2A RPP2A At1g59870 At2g03150 At2g33620 At3g08530 At3g44750 At3g52930 At4g23040 At4g25340 At4g31880 At4g38680 At5g11670 At5g19770 At5g42080...”
AHL27_ARATH / Q9S7C9 AT-hook motif nuclear-localized protein 27; DNA-binding protein ESCAROLA; Protein ORESARA 7 from Arabidopsis thaliana (Mouse-ear cress) (see 6 papers)
AT1G20900 ESC (ESCAROLA); double-stranded DNA binding (RefSeq) from Arabidopsis thaliana
NP_173514 Putative AT-hook DNA-binding family protein from Arabidopsis thaliana
Aligns to 114:236 / 311 (39.5%), covers 100.0% of PF03479, 94.0 bits
- function: Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs) (PubMed:17971039, PubMed:19517252). Negatively regulates plant innate immunity (PTI) to pathogens through the down-regulation of the PAMP- triggered FRK1 expression (PubMed:20738724). Acts redundantly with AHL18, AHL22 and AHL29 in the regulation of flowering and regulation of the hypocotyl elongation (PubMed:19517252). Acts as a chromatin remodeling factor that negatively regulates the leaf senescence (PubMed:17971039). Acts redundantly with AHL29/SOB3 to modulate hypocotyl growth inhibition in response to light (PubMed:18088311).
subunit: Homodimer. Interacts with AHL12, AHL25, AHL29, TCP4, TCP13, EF114, ATAF2/NAC081, histone H2B.1, histone H3.3 and histone H4.
disruption phenotype: AHL27 and AHL29 double mutant exhibit a long hypocotyl phenotype in the light. - Transcriptional analyses of natural leaf senescence in maize
Zhang, PloS one 2014 - “...GRMZM2G088212 AT1G20620 Catalase 3(CAT3), SENESCENCE 2 Induced by age and senescence [84] , [85] GRMZM2G119168 AT1G20900 AHL27, AT-HOOK MOTIF NUCLEAR-LOCALIZED PROTEIN 27 Delayed leaf senescence [86] GRMZM2G047404 AT1G61800 GLUCOSE-6-PHOSPHATE/PHOSPHATE TRANSLOCATOR 2 (GPT2) Senescence associated gene [41] , [87] AC207347.3_FG005 AT1G73220 ORGANIC CATION/CARNITINE TRANSPORTER1 (OCT1) Strong senescence...”
- Function annotation of an SBP-box gene in Arabidopsis based on analysis of co-expression networks and promoters
Wang, International journal of molecular sciences 2009 - “...AT3G28500 60S acidic ribosomal protein P2 (RPP2C) AT3G14680 CYP72A14 AT4G12550 Auxin-Induced in Root cultures 1 AT1G20900 ESCAROLA AT4G20860 FAD-binding domain-containing protein AT1G60680 ARF-GAP DOMAIN 2 AT4G28680 tyrosine decarboxylase, putative AT3G53130 LUTEIN DEFICIENT 1 AT5G63600 flavonol synthase, putative AT3G51895 SULFATE TRANSPORTER 1 AT2G01760 ARABIDOPSIS RESPONSE REGULATOR 14...”
- Coordination of matrix attachment and ATP-dependent chromatin remodeling regulate auxin biosynthesis and Arabidopsis hypocotyl elongation.
Lee, PloS one 2017 - GeneRIF: Data show that the light-inducible AHL proteins ESCAROLA (ESC)/AHL27 and SUPPRESSOR OF PHYTOCHROME B-4 #3 (SOB3)/AHL29 bind directly to an scaffold/matrix attachment regions (S/MARs) region of the YUCCA 9 (YUC9) promoter and suppress its expression to inhibit hypocotyl growth in light-grown seedlings.
- The AT-hook-containing proteins SOB3/AHL29 and ESC/AHL27 are negative modulators of hypocotyl growth in Arabidopsis.
Street, The Plant journal : for cell and molecular biology 2008 (PubMed)- GeneRIF: These data indicate that SOB3 and ESC act redundantly to modulate hypocotyl growth inhibition in response to light.
- Transcriptome Analysis of Calcium- and Hormone-Related Gene Expressions during Different Stages of Peanut Pod Development
Li, Frontiers in plant science 2017 - “...protein 2 Arabidopsis 0 comp45947 Q298L5 Mitochondrial Rho GTPase Sophophora 5.00 e - 87 comp42934 Q9S7C9 Putative DNA-binding protein ESCAROLA Arabidopsis 5.00 e - 6 Hormone Related Unigenes and Their Functional Categories Genes related to hormone response were screened out by GO analysis. There were 40...”
AHL3_ARATH / Q9SB31 AT-hook motif nuclear-localized protein 3 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
AT4G25320 DNA-binding protein-related (RefSeq) from Arabidopsis thaliana
NP_194262 AT hook motif DNA-binding family protein from Arabidopsis thaliana
Aligns to 167:283 / 404 (29.0%), covers 98.1% of PF03479, 93.6 bits
- function: Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs) (By similarity). Acts redundantly with AHL4 to regulate the formation of tissue boundary between the xylem and procambium in the root meristem (PubMed:23335615).
subunit: Homodimer. Interacts with AHL4.
disruption phenotype: Misspecification of tissue boundaries between the xylem and procambium. - Vascular Cambium Development
Nieminen, The arabidopsis book 2015 - “...2010). AT-HOOK MO- TIF NUCLEAR LOCALIZED PROTEIN3 (AHL3; At4g25320) and AHL4 (At5g51590), which also move to the xylem axis from the surrounding tissues,...”
- Cell-to-cell movement of two interacting AT-hook factors in Arabidopsis root vascular tissue patterning.
Zhou, The Plant cell 2013 - GeneRIF: The cell-to-cell communication mediated by mobile AHL3 and AHL4 is critical for establishing the boundary between the procambium and xylem.
AHL16_ARATH / Q9SJG4 AT-hook motif nuclear-localized protein 16; Protein TRANSPOSABLE ELEMENT SILENCING VIA AT-HOOK; Protein TEK from Arabidopsis thaliana (Mouse-ear cress) (see 6 papers)
AT2G42940 DNA-binding family protein (RefSeq) from Arabidopsis thaliana
NP_181822 Putative AT-hook DNA-binding family protein from Arabidopsis thaliana
Aligns to 81:194 / 257 (44.4%), covers 96.3% of PF03479, 93.2 bits
- function: Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs) (PubMed:25336567). Encodes a nuclear matrix protein that acts in the maintenance of genomic integrity by silencing TEs and repeat-containing genes through epigenetic machinery. Acts as a chromatin remodeling factor that modifies the architecture of FLC and FWA chromatin by modulating both H3 acetylation and methylation leading to the regulation of FLC and FWA expression (PubMed:23394836, PubMed:23836195). Negatively regulates floral repressors including MAF4 and MAF5 (PubMed:23733063). Plays a transcription activation role in anther development. Regulates the expression of arabinogalactan proteins (AGPs) involved in the formation of the nexine layer of the pollen wall (PubMed:25336567, PubMed:24804694). Binds AGP6, AGP11, AGP23 and AGP40 promoters (PubMed:25336567).
subunit: Interacts with FVE/MSI4 and MSI5 which are components of HDAC corepressor complexes.
disruption phenotype: Abnormal pollen wall with the absence of the nexine and intine layers causing microspore abortion and male sterility. - Comparative transcriptome profiling of the fertile and sterile flower buds of a dominant genic male sterile line in sesame (Sesamum indicum L.)
Liu, BMC plant biology 2016 - “...stilbene synthase 1.00 4.242.36 SIN_1001388 AT4G21330 2E-36 129 DYT1, bHLH transcription factor 2.07 0.480.15 SIN_1003502 AT2G42940 1E-90 272 AT-hook DNA-binding protein 3.82 7.001.23 SIN_1007695 AT2G19070 0 540 SHT 7.68 13.911.03 SIN_1013713 AT3G27730 0 1274 ROCK-N-ROLLERS/AtMER3 1.57 0.740.15 SIN_1020712 AT4G29250 2E-141 416 acyl-transferase family protein 4.40 3.454.02...”
- Identification of tapetum-specific genes by comparing global gene expression of four different male sterile lines in Brassica oleracea
Ma, Plant molecular biology 2015 - “...0.969 A AT2G38240 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein 3.035 1.621 1.630 0.377 A AT2G42940 Predicted AT-hook DNA-binding family protein 36.341 0.336 0.086 2.476 A AT2G45630 d -isomer specific 2-hydroxyacid dehydrogenase family protein 3.502 1.118 1.133 1.450 A AT3G05780 LON3 lon protease 3 3.075 0.311...”
- The tapetal AHL family protein TEK determines nexine formation in the pollen wall
Lou, Nature communications 2014 - “...was isolated in a collection of T-DNA-tagged lines 30 . The T-DNA is inserted in At2g42940 (see below), which was previously designated as TRANSPOSABLE ELEMENT SILENCING VIA AT-HOOK ( TEK ). Knockdown of TEK led to late flowering 31 . Here we focus on the mechanism...”
- “...of the TAILPCR product showed that the T-DNA was inserted in the only exon of At2g42940, which completely abolished the expression of At2g42940 ( Fig. 3b ). For genetic complementation, we cloned the 2,277-bp genomic region, including the promoter and 3-untranslated region of At2g42940 from wild...”
- Prediction of components of the sporopollenin synthesis pathway in peach by genomic and expression analyses
Ríos, BMC genomics 2013 - “...BURP domain protein 4 PpB89 Glycine-rich protein 3 PpB88 3 PpB71 DNA-binding protein (AT-hook) 3 At2g42940 [ 28 ] ppa025857m Protease inhibitor/seed storage/LTP 3 PpB79 Cupin 3 ppa014645m Carboxyl-terminal peptidase 3 ppa009110m Chlorophyll A-B binding protein 3 ppa008777m Cinnamoyl-CoA reductase 3 TKPR2/CCRL6 [ 11 ] ppa005633m...”
- “...late tapetum development and pollen wall biosynthesis [ 15 , 16 , 18 ]. Interestingly, At2g42940 gene, coding for an AT-hook DNA-binding protein highly similar to peach PpB71, was found specifically expressed in the wild-type tapetum after meiosis, and unexpectedly up-regulated in the ms1 mutant [...”
- The bZIP Transcription Factor PERIANTHIA: A Multifunctional Hub for Meristem Control
Maier, Frontiers in plant science 2011 - “...[ Vitis vinifera ] (GB:CAO70018.1); contains InterPro domain Plant Basic Secretory Protein (InterPro:IPR007541) 265263_at 0.56 AT2G42940 DNA-binding family protein 266814_at 0.38 AT2G44910 Homeobox-leucine zipper protein 4 (HB-4)/HD-ZIP protein 4 258704_at 0.47 AT3G09780 Protein kinase family protein 256283_at 0.52 AT3G12540 Similar to unknown protein [ Arabidopsis thaliana...”
- Mitochondrially-targeted expression of a cytoplasmic male sterility-associated orf220 gene causes male sterility in Brassica juncea
Yang, BMC plant biology 2010 - “...an alcohol dehydrogenase (At3g42960) were also down-regulated in transgenic stem mustard, as were some genes (At2g42940, At1g76470, At3g07450, At1g20370, At4g30470 and At4g34850) that have been reported to be associated with pollen development. All of the down-regulated genes detected in transgenic plants are listed in supplementary data...”
- “...expressed genes in transgenic stem mustard observed in this study Gene ID Gene Description Fold At2g42940 DNA-binding family protein 2.5 At2g42840 protodermal factor 1 (PDF1) 4.6 At1g75940 glycosyl hydrolase family 1 protein/anther-specific protein ATA27 2.09 At1g01280 cytochrome P450 family protein 3.59 At1g76470 cinnamoyl-CoA reductase family 3.41...”
- The ASH1 HOMOLOG 2 (ASHH2) histone H3 methyltransferase is required for ovule and anther development in Arabidopsis
Grini, PloS one 2009 - “...PLoS 2 (7): e117 (2006) buds 0.72 1.65 At2g42660 MYB TF - pollen 1.11 2.15 At2g42940 AHL16 Fujimoto et al., Plant Mol Biol 56: 225239 (2004) flower 1.23 2.35 At2g46020 BRM Hurtado et al., Plant Mol Biol 62: 291304 (2006) n.t. 0.99 1.98 At2g46770 NST1 Mitsuda...”
- A spatial dissection of the Arabidopsis floral transcriptome by MPSS
Peiffer, BMC plant biology 2008 - “...the expression set [Figure 3fg (anti-sense), 3h (sense)]. Using relaxed parameters, a putative stamen-enriched gene, At2g42940, was found expressed in both carpel and stamen primordium [Figure 3n (anti-sense), 3o (sense)]. Therefore, some genes enriched for the stamen or gynoecium may be expressed within both reproductive organs;...”
- “...the septum. Predicted to be localized within the stamen and the carpel by MPSS. (N) At2g42940 (anti-sense probe) (O) (sense control probe) weak signal on stamen and carpel primordial. Identified as a putative stamen-enriched transcript by MPSS. (P) AP3 (anti-sense control probe). Within the more stringent...”
- The temporal regulation of TEK contributes to pollen wall exine patterning.
Xiong, PLoS genetics 2020 - GeneRIF: Results showed that the correct regulation of timing of TEK expression is required for pollen wall exine patterning and is coordinated with other pollen developmental events for the processes of pollen wall formation and pollen grain maturation.
- The AT-hook/PPC domain protein TEK negatively regulates floral repressors including MAF4 and MAF5.
Xu, Plant signaling & behavior 2013 - GeneRIF: MADS AFFECTING FLOWERING 4 (MAF4) and MAF5 are upregulated in TEK knockdown plants. TEK negatively regulates floral repressors including MAF4 and MAF5. [TEK]
NP_001159201 uncharacterized protein LOC100304287 from Zea mays
Aligns to 138:251 / 341 (33.4%), covers 98.1% of PF03479, 92.3 bits
LOC108209748 AT-hook motif nuclear-localized protein 5-like from Daucus carota subsp. sativus
Aligns to 161:276 / 345 (33.6%), covers 99.1% of PF03479, 91.8 bits
VCA0587 conserved hypothetical protein (NCBI ptt file) from Vibrio cholerae O1 biovar eltor str. N16961
Aligns to 3:111 / 130 (83.8%), covers 95.3% of PF03479, 91.7 bits
- The transcriptional regulator VqmA increases expression of the quorum-sensing activator HapR in Vibrio cholerae
Liu, Journal of bacteriology 2006 - “...VC0491, VC0669, VC0770, VC1492, VC2155, VCA0324, VCA0367, VCA0483, VCA0587, VCA0887 VC0669, VC1492, VC2155, VCA1097 2 2 ZLV102 and ZLV104 were grown in AKI...”
HMPREF0357_11250 DNA-binding protein from Erysipelothrix rhusiopathiae ATCC 19414
Aligns to 2:110 / 138 (79.0%), covers 98.1% of PF03479, 91.5 bits
AHL17_ARATH / Q9LTA2 AT-hook motif nuclear-localized protein 17 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT5G49700 DNA-binding protein-related (RefSeq) from Arabidopsis thaliana
Aligns to 84:204 / 276 (43.8%), covers 99.1% of PF03479, 91.5 bits
AHL29_ARATH / Q9C9K7 AT-hook motif nuclear-localized protein 29; Protein SUPPRESSOR OF PHYB-4#3 from Arabidopsis thaliana (Mouse-ear cress) (see 3 papers)
AT1G76500 SOB3 (SUPPRESSOR OF PHYB-4#3); DNA binding (RefSeq) from Arabidopsis thaliana
NP_177776 Putative AT-hook DNA-binding family protein from Arabidopsis thaliana
Aligns to 100:222 / 302 (40.7%), covers 100.0% of PF03479, 91.4 bits
- function: Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs) (By similarity). Acts redundantly with AHL18, AHL22 and AHL27 in the regulation of flowering and regulation of the hypocotyl elongation (PubMed:19517252). Acts redundantly with AHL27/ESC to modulate hypocotyl growth inhibition in response to light (PubMed:18088311).
subunit: Homodimer. Interacts with AHL5, AHL12, AHL25, AHL27, TCP4, TCP13 and EF114.
disruption phenotype: AHL27 and AHL29 double mutant exhibit a long hypocotyl phenotype in the light. - Genome-Wide Discriminatory Information Patterns of Cytosine DNA Methylation
Sanchez, International journal of molecular sciences 2016 - “...K08819 cyclin-dependent kinase 12/13 (EC:2.7.11.22 2.7.11.23) 0.81 AT1G69940 PPME1; pectinesterase PPME1; K01051 pectinesterase (EC:3.1.1.11) 0.55 AT1G76500 SOB3; AT-hook motif nuclear localized protein 29 0.42 AT2G05990 MOD1; K00208 enoyl-[acyl-carrier protein] reductase I (EC:1.3.1.9 1.3.1.10) 0.77 AT2G11000 MAK10; MAK10-like protein 1.07 AT2G28660 chloroplast-targeted copper chaperone protein 1.43 AT2G30750...”
- Brassinosteroid signaling converges with SUPPRESSOR OF PHYTOCHROME B4-#3 to influence the expression of SMALL AUXIN UP RNA genes and hypocotyl growth.
Favero, The Plant journal : for cell and molecular biology 2017 - GeneRIF: The results indicate that SOB3 and BR signaling converge to influence the transcription of hypocotyl growth-promoting SAUR19 subfamily members.
- Coordination of matrix attachment and ATP-dependent chromatin remodeling regulate auxin biosynthesis and Arabidopsis hypocotyl elongation.
Lee, PloS one 2017 - GeneRIF: Data show that the light-inducible AHL proteins ESCAROLA (ESC)/AHL27 and SUPPRESSOR OF PHYTOCHROME B-4 #3 (SOB3)/AHL29 bind directly to an scaffold/matrix attachment regions (S/MARs) region of the YUCCA 9 (YUC9) promoter and suppress its expression to inhibit hypocotyl growth in light-grown seedlings.
- SUPPRESSOR OF PHYTOCHROME B4-#3 Represses Genes Associated with Auxin Signaling to Modulate Hypocotyl Growth.
Favero, Plant physiology 2016 - GeneRIF: SOB3 modulates hypocotyl elongation in young seedlings by directly repressing the transcription of genes associated with auxin signaling.
- The AT-hook-containing proteins SOB3/AHL29 and ESC/AHL27 are negative modulators of hypocotyl growth in Arabidopsis.
Street, The Plant journal : for cell and molecular biology 2008 (PubMed)- GeneRIF: These data indicate that SOB3 and ESC act redundantly to modulate hypocotyl growth inhibition in response to light.[SOB3]
AT3G04590 DNA-binding family protein (RefSeq) from Arabidopsis thaliana
Aligns to 172:284 / 309 (36.6%), covers 99.1% of PF03479, 90.7 bits
AHL15_ARATH / Q9M2S3 AT-hook motif nuclear-localized protein 15; AT-hook protein of GA feedback 2 from Arabidopsis thaliana (Mouse-ear cress) (see 3 papers)
AT3G55560 AGF2 (AT-hook protein of GA feedback 2) (RefSeq) from Arabidopsis thaliana
Aligns to 116:230 / 310 (37.1%), covers 97.2% of PF03479, 90.5 bits
- function: Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs) (By similarity). Binds the DNA sequence GNFEI (GA-negative feedback element I) in the GA3OX1 promoter (PubMed:17277098). Negatively regulates plant innate immunity (PTI) to pathogens through the down-regulation of the PAMP-triggered FRK1 expression (PubMed:20738724).
- Transcriptional programs regulated by both LEAFY and APETALA1 at the time of flower formation
Winter, Physiologia plantarum 2015 - “...using gene annotations downloaded from TAIR on August 28, 2014. The genes AT5G24910, AT4G23060 and AT3G55560 were manually added to the GO term response to GA stimulus. P -values were adjusted for multiple testing using the BenjaminiHochberg method ( Benjamini and Hochberg 1995 ) implemented in...”
- Transcriptomic characterization of a synergistic genetic interaction during carpel margin meristem development in Arabidopsis thaliana
Wynn, PloS one 2011 - “...in the CMM or in CMM-derived tissues (e.g. ovules). These include AT1G02800 ( ATCEL2 ), AT3G55560 ( AGF2 ), AT5g57720 ( REM15 ) AT2g46870 ( NGA1 ), AT1G68640 ( PAN ), AT2G34710 ( PHB ), AT4G37750 ( ANT ), AT1G70560 ( TAA1 ), AT5G18000 ( VDD...”
- “...9.49 9.21 8.95 8.24 2.90 At3g13960 AtGRF5, transcriptional regulator + 9.21 9.30 8.25 7.84 1.61 At3g55560 AGF2, DNA-binding protein + 8.47 8.00 8.22 7.26 2.18 At4g00180 YABBY3 , transcription factor + 9.27 8.38 8.64 7.05 2.50 At4g37750 AINTEGUMENTA, DNA binding + 10.80 9.65 10.69 8.91 2.18...”
- Expression-based discovery of candidate ovule development regulators through transcriptional profiling of ovule mutants
Skinner, BMC plant biology 2009 - “...-4.78 -1.26 -2.59 (8) At1g68640 PAN bZIP family (floral organ nmber) -2.16 -1.17 1.31 (2) At3g55560 AGF2 DNA-binding At-hook family -2.69 -1.16 -1.54 (10) At4g24150 ATGRF8 growth-regulating factor family -2.70 -1.10 -1.13 (9) At1g76110 --- HMG1/2, ARID/BRIGHT DNA-binding domain -3.01 -1.20 -1.14 (4) At1g04880 --- HMG1/2,...”
- “...groups and provides important information for understanding gene function. In situ hybridizations were performed for At3g55560 ( AT-HOOK PROTEIN OF GA FEEDBACK 2 , AGF2 ), that encodes an At-hook DNA binding protein [ 102 ]. This gene showed a 2.7 fold decrease in ant relative...”
LOC108210904 AT-hook motif nuclear-localized protein 28-like from Daucus carota subsp. sativus
Aligns to 97:207 / 271 (41.0%), covers 98.1% of PF03479, 90.4 bits
AHL9_ARATH / O80834 AT-hook motif nuclear-localized protein 9 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT2G45850 DNA-binding family protein (RefSeq) from Arabidopsis thaliana
Aligns to 163:278 / 348 (33.3%), covers 98.1% of PF03479, 90.3 bits
- function: Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs).
- Intrusive Growth of Phloem Fibers in Flax Stem: Integrated Analysis of miRNA and mRNA Expression Profiles
Gorshkov, Plants (Basel, Switzerland) 2019 - “...inflorescence meristem receptor-like kinase 2 3.04 3.50 10 12 2.87 8.73 10 11 a,c,d,e,f,g,h,i,j,k Lus10030381 AT2G45850 AT hook motif DNA-binding family protein 2.87 4.96 10 33 2.56 4.37 10 26 a,b,c,d,e,f,g,h,i,j,k Lus10027060 AT3G59680 2.67 4.26 10 4 3.39 4.96 10 6 a,b,c,d,e,f,g,h,i,j,k Lus10023357 AT2G34710 HB14,PHB Homeobox-leucine...”
AHL8_ARATH / Q9FIR1 AT-hook motif nuclear-localized protein 8 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
Aligns to 181:297 / 386 (30.3%), covers 99.1% of PF03479, 90.3 bits
- function: Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs).
AHL6_ARATH / Q9LVB0 AT-hook motif nuclear-localized protein 6 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT5G62260 DNA binding (RefSeq) from Arabidopsis thaliana
Aligns to 161:276 / 404 (28.7%), covers 97.2% of PF03479, 90.2 bits
AHL25_ARATH / Q6DBQ1 AT-hook motif nuclear-localized protein 25; AT-hook protein of GA feedback 1 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
NP_195265 AT-hook protein of GA feedback 1 from Arabidopsis thaliana
AT4G35390 AGF1 (AT-hook protein of GA feedback 1); transcription factor (RefSeq) from Arabidopsis thaliana
Aligns to 91:206 / 299 (38.8%), covers 99.1% of PF03479, 89.9 bits
- function: Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs) (By similarity). Binds the DNA sequence GNFEI (GA-negative feedback element I) in the GA3OX1 promoter. Binding to GNFEI sequence is required for GA-negative feedback regulation of GA3OX1.
subunit: Homodimer. Interacts with AHL27 and AHL29. - AGF1, an AT-hook protein, is necessary for the negative feedback of AtGA3ox1 encoding GA 3-oxidase.
Matsushita, Plant physiology 2007 - GeneRIF: AGF1 plays a role in the homeostasis of gibberellins through binding to the cis-acting sequence of the GA-negative feedback of AtGA3ox1. [AGF1]
- Polycomb repressive complex 2 controls the embryo-to-seedling phase transition
Bouyer, PLoS genetics 2011 - “...AT1G03790), SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 8 (SPL8, AT1G02065), AT-hook protein of GA feedback 1 (AGF1, AT4G35390), GIBBERELLIC ACID METHYLTRANSFERASE 2 (GAMT2, AT5G56300). The up-regulation of many important seed regulatory genes raised the hypothesis that fie seedlings, albeit macroscopically resembling wild type seedlings, display seed phase characteristics....”
AHL14_ARATH / A1L4X7 AT-hook motif nuclear-localized protein 14 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
Aligns to 172:284 / 411 (27.5%), covers 99.1% of PF03479, 89.8 bits
- function: Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs).
ECs3799 hypothetical protein (NCBI ptt file) from Escherichia coli O157:H7 str. Sakai
Z4267 orf; hypothetical protein (NCBI ptt file) from Escherichia coli O157:H7 EDL933
Aligns to 13:121 / 143 (76.2%), covers 99.1% of PF03479, 87.9 bits
- Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
Bergholz, BMC microbiology 2007 - “...2.10 6 ECs3586 hypE plays structural role in maturation of all 3 hydrogenases 2.10 6 ECs3799 O157 orf; hypothetical protein 2.92 6 ECs3800 O157 orf; hypothetical protein 2.33 6 ECs3802 O157 putative ATP-binding protein of ABC transport system 2.40 6 ECs3833 ansB periplasmic L-asparaginase II 3.41...”
- “...ygeW 2.08 2 ECs4759 metE -2.76 1 ECs3749 yqeC 2.45 2 ECs4791 glnL -2.80 1 ECs3799 O157 -2.69 6 ECs4870 metF -3.65 1 ECs3800 O157 -2.43 6 ECs4885 ppc -3.62 1 ECs3802 O157 -2.43 6 ECs4887 argC -3.99 1 ECs3811 yggG 2.28 2 ECs4888 argB -3.62...”
- Magnesium Sensing Regulates Intestinal Colonization of Enterohemorrhagic Escherichia coli O157:H7
Liu, mBio 2020 - “...PhoQ/PhoP two-component regulatory system senses low magnesium levels and signals to the O island 119-encoded Z4267 (LmiA; low magnesium-induced regulator A), directly activating loci of enterocyte effacement genes to promote EHEC O157:H7 adherence in the large intestine. Disruption of this pathway significantly decreased EHEC O157:H7 adherence...”
- “...that can prevent enteric infections. KEYWORDS bacterial adherence magnesium locus of enterocyte effacement (LEE) virulence Z4267 gene regulation Natural Science Foundation of Tianjin City (Tianjin Natural Science Foundation) https://doi.org/10.13039/501100006606 20JCQNJC11700 17JCQNJC09300 Yang Bin National Natural Science Foundation of China (NSFC) https://doi.org/10.13039/501100001809 31800125 31530083 Yang Bin cover-date...”
- Disruption of rcsB by a duplicated sequence in a curli-producing Escherichia coli O157:H7 results in differential gene expression in relation to biofilm formation, stress responses and metabolism
Sharma, BMC microbiology 2017 - “...Unknown 4.58 9.0E-09 Z3965 Unknown 2.33 1.5E-03 Z4126 Unknown 4.31 3.0E-04 Z4151 Unknown 3.84 7.4E-07 Z4267 Unknown +5.52 2.3E-03 Z4268 Unknown +4.92 4.3E-06 yggG Z4280 Unknown 1.71 0.02 Z4318 Unknown +1.30 0.04 ygjT Z4441 Unknown 2.25 5.0E-03 yhaM Z4462 Unknown +2.34 0.03 yiaB Z4988 Unknown 4.71...”
- The interacting Cra and KdpE regulators are involved in the expression of multiple virulence factors in enterohemorrhagic Escherichia coli
Njoroge, Journal of bacteriology 2013 - “...from E. coli K-12), such as Z0639, Z0640, Z3388, Z4267, and espFu (encoding an effector necessary for formation of attaching and effacing lesions on epithelial...”
- “...Z0640* Z1163*** Z1602*** Z2077 Z3388 Z3934 Z4267 espG** Z5890 Consensus TGAAGCGGTTC TGAAGCGGTTC TGAATCGATC TGAATCGATC TGAATGGATTA TGAATCGCTTAT TGAATGGTTTAT...”
- Lateral gene transfer (LGT) between Archaea and Escherichia coli is a contributor to the emergence of novel infectious disease
Faguy, BMC infectious diseases 2003 - “...O157:H7 designation Location (O island) Best BLAST hit to ORF from: Best guess at function Z4267 119 Methanobacterium thermoautotrophicum ABC transporter : cations? Z4271 119 Methanobacterium thermoautotrophicum ABC transporter : cations? Z5331 155 Helicobacter pylori ? Z0509 25 Yersinia pestis ? Z5989 172 Halobacterium sp. NRC-1...”
AHL5_ARATH / Q8GXB3 AT-hook motif nuclear-localized protein 5 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT1G63470 DNA-binding family protein (RefSeq) from Arabidopsis thaliana
Aligns to 178:293 / 378 (30.7%), covers 98.1% of PF03479, 87.7 bits
PF0619 hypothetical protein (NCBI ptt file) from Pyrococcus furiosus DSM 3638
Aligns to 6:119 / 134 (85.1%), covers 99.1% of PF03479, 86.9 bits
XP_027189914 AT-hook motif nuclear-localized protein 14 from Cicer arietinum
Aligns to 103:216 / 322 (35.4%), covers 97.2% of PF03479, 86.7 bits
XP_003590926 AT-hook motif nuclear-localized protein 14 from Medicago truncatula
Aligns to 110:223 / 329 (34.7%), covers 97.2% of PF03479, 85.9 bits
AHL28_ARATH / Q9M9R4 AT-hook motif nuclear-localized protein 28 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
Aligns to 31:151 / 206 (58.7%), covers 99.1% of PF03479, 83.9 bits
- function: Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs).
AHL11_ARATH / Q8L7L5 AT-hook motif nuclear-localized protein 11 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT3G61310 DNA-binding family protein (RefSeq) from Arabidopsis thaliana
Aligns to 165:280 / 354 (32.8%), covers 98.1% of PF03479, 83.7 bits
- function: Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs).
- Transcriptional regulatory framework for vascular cambium development in Arabidopsis roots
Zhang, Nature plants 2019 - “...AT3G50650; AGL14 , AT4G11880; ATHB53 , AT5G66700; ATHB5 , AT5G65310; WRI3 , AT1G16060; AHL11 , AT3G61310; MYB47 , AT1G18710; MYB95 , AT1G74430; MYB87 , AT4G37780; STY2 , AT4G36260; RAS1 , AT1G09950; AtERF019 , AT1G22810; AtERF021 , AT1G71450; AtERF029 , AT4G25490; AtERF032 , AT1G63030; AtERF043 , AT4G32800;...”
- The hunt for hypoxia responsive natural antisense short interfering RNAs
Moldovan, Plant signaling & behavior 2010 - “...natsiRNA. The three associated hypoxia upregulated genes AT3g61310 (DNA binding protein), At2g38470 (WRKY33) and At5g42270 (VAR1; ATP-dependent peptidase) are...”
- “...0.37 0.53 AT3G56940 1.53 1.87 AT3G56950 0.38 0.44 AT3G61310 1.73 2.08 AT3G61300 0.45 0.22 AT4G03080 1.73 1.69 AT4G03070 0.46 0.31 0.68 AT4G05460 1.50 1.37...”
- UV-B responsive microRNA genes in Arabidopsis thaliana
Zhou, Molecular systems biology 2007 - “...transcription factor CAATNATTG At4g32880 (ATHB-8), At5g60690 (REV) At1g30490 miR167 At5g37020, At5g19950 ARF transcription factor At1g02800, At3g61310 miR169 At1g17590, At1g54160, At1g72830 CBF HAP2-like factors CCAAT At3g20910, At5g12840 At1g70700, At1g80770 miR170/171 At4g00150, At5g61480 Scarecrow-like transcription factor At2g45160, At3g60630 miR172 At2g28550 (TOE1), At4g36920 (AP2) APETALA2-like factor At5g60120 (TOE2), At5g67180...”
AHL12_ARATH / Q8LPN5 AT-hook motif nuclear-localized protein 12 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT1G63480 DNA-binding family protein (RefSeq) from Arabidopsis thaliana
Aligns to 161:276 / 361 (32.1%), covers 98.1% of PF03479, 81.0 bits
- function: Transcription factor that specifically binds AT-rich DNA sequences related to the nuclear matrix attachment regions (MARs).
subunit: Homodimer. Interacts with AHL27, AHL29 and ATAF2/NAC081. - Cytokinin-overinduced transcription factors and thalianol cluster genes in CARBOXYL-TERMINAL DOMAIN PHOSPHATASE-LIKE 4-silenced Arabidopsis roots during de novo shoot organogenesis
Fukudome, Plant signaling & behavior 2018 - “...cluster, and two are each from independent clusters (AT1G63480 and AT3G16430). Therefore, the thalianol cluster is the sole operon-like cluster over-induced in...”
- Electromagnetic Field Seems to Not Influence Transcription via CTCT Motif in Three Plant Promoters
Sztafrowski, Frontiers in plant science 2017 - “...transposase family 24 3.5 0.0035 1.0000 AT3G13140 Hydroxyproline-rich glycoprotein family protein 23 5.6 0.0005 1.0000 AT1G63480 DNA-binding family protein 23 5.0 0.0009 1.0000 AT5G58550 Paralog of ETO1, a negative regulator of ACS5 involved in ethylene biosynthesis pathway 23 4.2 0.0019 1.0000 AT1G36403 Transposable element gene; mutator-like...”
- Comparative analysis of plant immune receptor architectures uncovers host proteins likely targeted by pathogens
Sarris, BMC biology 2016 - “...OEC115 AT3G21490 HMA Heavy metal-associated domain OEC115 AT3G10480 NAM No apical meristem (NAM) protein OEC45 AT1G63480 DUF296 Domain of unknown function (DUF296) OEC45 AT4G00120 HLH Helix-loop-helix DNA-binding domain OEC45 AT1G12520 HMA Heavy metal-associated domain OEC45 AT3G22420 Pkinase Protein kinase domain OEC59 AT4G08320 TPR_11 TPR repeat OEC67...”
- The peroxiredoxin and glutathione peroxidase families in Chlamydomonas reinhardtii
Dayer, Genetics 2008 - “...At2g48150; GPX5, At3g63080; GPX6, At4g11600; GPX7, At4g31870; GPX8, At1g63480; Cr, Chlamydomonas reinhardtii as in Table 2; Hs, Homo sapiens GPX1, P07203; GPX2,...”
CTC_01209 DNA-binding protein from Clostridium tetani E88
Aligns to 8:121 / 139 (82.0%), covers 94.4% of PF03479, 80.3 bits
- More than a Toxin: Protein Inventory of Clostridium tetani Toxoid Vaccines
Möller, Proteomes 2019 - “...CTC_01332 Transketolase U Q895G9 CTC_01305 Uncharacterized protein U Q895P6 CTC_01225 Serine/threonine protein kinase M Q895R2 CTC_01209 Uncharacterized protein U Q895T9 CTC_01178 NADH oxidase M, C Q896G9 CTC_01036 Uncharacterized protein U Q896I3 CTC_01021 Electron transport complex subunit G M Q896J5 CTC_01009 Conserved protein, putative N-acetylmuramoyl-L-alanine amidase M...”
Q895R2 PPC domain-containing protein from Clostridium tetani (strain Massachusetts / E88)
Aligns to 21:134 / 152 (75.0%), covers 94.4% of PF03479, 79.9 bits
- More than a Toxin: Protein Inventory of Clostridium tetani Toxoid Vaccines
Möller, Proteomes 2019 - “...Q895E4 CTC_01332 Transketolase U Q895G9 CTC_01305 Uncharacterized protein U Q895P6 CTC_01225 Serine/threonine protein kinase M Q895R2 CTC_01209 Uncharacterized protein U Q895T9 CTC_01178 NADH oxidase M, C Q896G9 CTC_01036 Uncharacterized protein U Q896I3 CTC_01021 Electron transport complex subunit G M Q896J5 CTC_01009 Conserved protein, putative N-acetylmuramoyl-L-alanine amidase...”
SA0649 hypothetical protein (NCBI) from Staphylococcus aureus subsp. aureus N315
Aligns to 8:121 / 140 (81.4%), covers 95.3% of PF03479, 76.1 bits
- Novel Nucleoside Diphosphatase Contributes to Staphylococcus aureus Virulence
Imae, The Journal of biological chemistry 2016 - “...values. The LD50 values of the gene-deletion mutants of SA0649, SA0873, SA0949, and SA1292 were more than 2-fold that of the parent strain (Fig. 1B). The LD50...”
- “...the parent strain (Fig. 1B). These findings suggest that SA0649, SA0873, SA0949, and SA1292 contribute to S. aureus virulence and that SA1684 plays a critical...”
- Genome-wide analysis of ruminant Staphylococcus aureus reveals diversification of the core genome
Ben, Journal of bacteriology 2008 - “...2017 by University of California, Berkeley SA0584 SA0648 SA0649 Classification by functionb Description 6314 BEN ZAKOUR ET AL. J. BACTERIOL. and transposon and...”
- Effect of promoter region mutations and mgrA overexpression on transcription of norA, which encodes a Staphylococcus aureus multidrug efflux transporter
Kaatz, Antimicrobial agents and chemotherapy 2005 - “...Bmr, Blt, and QacA/B. There is an open reading frame (SA0649 in the S. aureus N315 genome) on the opposite strand and immediately upstream of norA that encodes...”
- “...a number of DNA-binding proteins. The putative promoter of SA0649 overlaps with that of norA, suggesting that the two genes may be coordinately regulated. No...”
CPM_0795 DUF296 domain-containing protein from Cuniculiplasma divulgatum
Aligns to 8:119 / 138 (81.2%), covers 95.3% of PF03479, 75.6 bits
AT2G36560 DNA-binding protein-related (RefSeq) from Arabidopsis thaliana
Aligns to 106:224 / 574 (20.7%), covers 97.2% of PF03479, 74.3 bits
- Paternally expressed imprinted genes establish postzygotic hybridization barriers in Arabidopsis thaliana
Wolff, eLife 2015 - “...in reciprocal crosses between Col and Bur-0 accessions ( Wolff et al., 2011 ). While At2g36560 (PEG5), At4g05470 (PEG8), At1g67830 (FXG1), At1g17770 (SUVH7), At1g57800 (VIM5) and AT1g48910 (YUC10) were also identified to be imprinted in Col and L er accessions, At1g11810 (PEG1), At1g49290 (PEG2), At1g60400 (PEG3),...”
- Perturbation of parentally biased gene expression during interspecific hybridization
Burkart-Waco, PloS one 2015 - “...8 173 11.47 3.7 AT2G32370 HDG3 1 13740 63.05 0.0 0 431 e NA NA AT2G36560 DNA-binding 3 51959 85.27 0.1 2 113 6.63 0.5 AT2G40520 Nucleotidyltransferase 3 2961 70.89 1.6 6 123 47.67 18.9 AT4G11940 ADM 4 42576 78.70 0.1 0 468 e NA NA...”
- Regulation of imprinted gene expression in Arabidopsis endosperm
Hsieh, Proceedings of the National Academy of Sciences of the United States of America 2011 - “...al. Number AT1G17770 AT1G31640 AT1G48910 AT1G57800 AT1G60410 AT2G21930 AT2G36560 AT4G11940 AT5G63740 Annotation CxL M/P #/F/D/M F/M F/D/M F/D F/M F/M F/D/M F/D...”
- “...genes (SUVH7, AGL92, At1g60410 F-box, At2g21930 F-box, YUC10, At2g36560, and HDG3) is reduced in endosperm fertilized with met1 pollen, indicating that DNA...”
- Transcriptional profiles underlying parent-of-origin effects in seeds of Arabidopsis thaliana
Tiwari, BMC plant biology 2010 - “...ligase activity) At2g26050 zinc ion binding unknown At2g30810 gibberellin-regulated family protein response to gibberellin stimulus At2g36560 DNA-binding protein-related unknown At2g39640 glycosyl hydrolase family 17 protein carbohydrate metabolic processes At2g43670 glycosyl hydrolase family 17 protein unknown At2g45110 ATEXPB4 beta-expansin cellulose and pectin-containing cell wall loosening At3g02670 proline-rich...”
SYNW0765 conserved hypothetical protein (VIMSS) from Synechococcus sp. WH 8102
Aligns to 2:109 / 202 (53.5%), covers 98.1% of PF03479, 69.5 bits
- Computational prediction of the osmoregulation network in Synechococcus sp. WH8102
Mao, BMC genomics 2010 - “...candidates for GgtB (b0529) of E. coli , and probably involved in glucosylglycerol synthesis. SYNW0754, SYNW0765, SYNW1250, SYNW2099 and SYNW2471 are added since they have very similar phylogenetic profiles with those of GpgSP (SYNW2436, 2434), and they are probably involved in glucosylglycerate synthesis. Figure 2 Genes...”
LS25_1541 DNA-binding protein from Lactobacillus sakei subsp. sakei LS25
Aligns to 8:121 / 140 (81.4%), covers 94.4% of PF03479, 61.6 bits
LSA1467 Hypothetical protein (NCBI) from Lactobacillus sakei subsp. sakei 23K
Aligns to 8:121 / 140 (81.4%), covers 94.4% of PF03479, 61.5 bits
- Global transcriptome response in Lactobacillus sakei during growth on ribose
McLeod, BMC microbiology 2011 - “...protein -0.9 -0.5 LSA1446 lsa1446 Hypothetical protein -0.6 -0.6 -0.7 LSA1466 lsa1466 Hypothetical protein 0.6 LSA1467 lsa1467 Hypothetical protein -0.6 -1.1 LSA1524 lsa1524 Hypothetical protein 0.7 LSA1540 lsa1540 Hypothetical extracellular protein precursor 0.7 LSA1563 lsa1563 Hypothetical integral membrane protein -0.6 -0.6 LSA1610 lsa1610 Hypothetical integral membrane...”
SMc00259 hypothetical protein (RefSeq) from Sinorhizobium meliloti 1021
Aligns to 178:285 / 285 (37.9%), covers 96.3% of PF03479, 47.8 bits
- Members of the Sinorhizobium meliloti ChvI regulon identified by a DNA binding screen
Bélanger, BMC microbiology 2013 - “...3 A). These results suggest that ChvI acts by repressing the transcription of the SMc00264 SMc00259 operon. Figure 3 Transcriptional fusion assays and the SMc00261 operon. ( A ) GusA activities were measured for fusions in genes SMc00262 and SMc00261 in wild-type (Rm1021) and chvI261 mutant...”
- “...ligase. These genes are also followed by SMc00260 coding for a putative short-chain dehydrogenase and SMc00259 coding for a hypothetical protein. Upstream of these genes lay genes for a transcriptional regulator of the IclR family (SMc00263) and another short-chain dehydrogenase (SMc00264). Our earlier studies failed to...”
msl6857 hypothetical protein (NCBI) from Mesorhizobium loti MAFF303099
Aligns to 2:75 / 94 (78.7%), covers 52.3% of PF03479, 34.2 bits
Or search for genetic data about PF03479 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory