Family Search for PF07039 (DUF1325)
PF07039.11 hits 19 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
SGF29_HUMAN / Q96ES7 SAGA-associated factor 29; Coiled-coil domain-containing protein 101; SAGA complex-associated factor 29 from Homo sapiens (Human) (see 6 papers)
Aligns to 158:288 / 293 (44.7%), covers 99.2% of PF07039, 137.5 bits
- function: Chromatin reader component of some histone acetyltransferase (HAT) SAGA-type complexes like the TFTC-HAT, ATAC or STAGA complexes (PubMed:19103755, PubMed:20850016, PubMed:26421618, PubMed:21685874, PubMed:26578293). SGF29 specifically recognizes and binds methylated 'Lys-4' of histone H3 (H3K4me), with a preference for trimethylated form (H3K4me3) (PubMed:20850016, PubMed:26421618, PubMed:21685874, PubMed:26578293). In the SAGA-type complexes, SGF29 is required to recruit complexes to H3K4me (PubMed:20850016). Involved in the response to endoplasmic reticulum (ER) stress by recruiting the SAGA complex to H3K4me, thereby promoting histone H3 acetylation and cell survival (PubMed:23894581).
subunit: Interacts with dimethylated and trimethylated 'Lys-4' of histone H3 (H3K4me2 and H3K4me3), with a preference for the trimethylated form (H3K4me3) (PubMed:21685874, PubMed:26578293). Component of some SAGA-type complexes (PubMed:20850016). Component of the ADA2A-containing complex (ATAC), composed of KAT14, KAT2A, TADA2L, TADA3L, ZZ3, MBIP, WDR5, YEATS2, CCDC101 and DR1 (PubMed:19103755). Interacts with TADA3L, GCN5L2, SUPT3H and MYC (By similarity). - A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity.
Zhou, Genomics 2009 - “...YCL010C SGF29 SaGa associated Factor 29kDa; Probable 29kKDa Subunit of SAGA histone acetyltransferase complex 0.527 Q96ES7 SAGA-associated factor 29 homolog YNR031C SSK2 Map kinase kinase kinase (MAPKKK) of the high- osmolarity signal transduction pathway 0.552 BAA13204 Mitogen-activated protein kinase kinase kinase 4 YDR028C REG1 Regulatory subunit...”
SGF29_RAT / P0C606 SAGA-associated factor 29; rSGF29; Coiled-coil domain-containing protein 101; SAGA complex-associated factor 29 from Rattus norvegicus (Rat) (see paper)
XP_006230294 SAGA-associated factor 29 isoform X1 from Rattus norvegicus
Aligns to 158:288 / 293 (44.7%), covers 99.2% of PF07039, 137.4 bits
- function: Chromatin reader component of some histone acetyltransferase (HAT) SAGA-type complexes like the TFTC-HAT, ATAC or STAGA complexes (PubMed:17334388). SGF29 specifically recognizes and binds methylated 'Lys-4' of histone H3 (H3K4me), with a preference for trimethylated form (H3K4me3) (By similarity). In the SAGA-type complexes, SGF29 is required to recruit complexes to H3K4me (By similarity). Involved in the response to endoplasmic reticulum (ER) stress by recruiting the SAGA complex to H3K4me, thereby promoting histone H3 acetylation and cell survival (By similarity). May be involved in MYC-mediated oncogenic transformation (PubMed:17334388).
subunit: Interacts with dimethylated and trimethylated 'Lys-4' of histone H3 (H3K4me2 and H3K4me3), with a preference for the trimethylated form (H3K4me3). Component of some SAGA-type complexes. Component of the ADA2A-containing complex (ATAC), composed of KAT14, KAT2A, TADA2L, TADA3L, ZZ3, MBIP, WDR5, YEATS2, CCDC101 and DR1 (By similarity). Interacts with TADA3L, GCN5L2, SUPT3H and MYC (PubMed:17334388). - The male-specific factor Sry harbors an oncogenic function.
Murakami, Oncogene 2014 (PubMed)- GeneRIF: Data show that Sry is involved in male-specific malignant conversion of rodent hepatocellular carcinoma via Sgf29 upregulation.
Q9W2I4 FI01566p from Drosophila melanogaster
Aligns to 143:273 / 289 (45.3%), covers 98.5% of PF07039, 127.1 bits
SGF29_YEAST / P25554 SAGA-associated factor 29; 29 kDa SAGA-associated factor; SAGA histone acetyltransferase complex 29 kDa subunit from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 6 papers)
NP_009917 Sgf29p from Saccharomyces cerevisiae S288C
YCL010C SaGa associated Factor 29kDa; Probable 29kKDa Subunit of SAGA histone acetyltransferase complex (RefSeq) from Saccharomyces cerevisiae
Aligns to 127:250 / 259 (47.9%), covers 98.5% of PF07039, 122.2 bits
- function: Chromatin reader component of the transcription regulatory histone acetylation (HAT) complexes SAGA and SLIK (PubMed:10026213, PubMed:15647753, PubMed:21685874, PubMed:24307402). In the SAGA complex, SGF29 specifically recognizes and binds methylated 'Lys-4' of histone H3 (H3K4me), with a preference for trimethylated form (H3K4me3) (PubMed:21685874). SGF29 is also required for heterochromatin boundary formation function (PubMed:24307402). SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes At the promoters, SAGA is required for recruitment of the basal transcription machinery (PubMed:10026213). It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8) (PubMed:10026213). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs) (PubMed:10026213). SLIK is proposed to have partly overlapping functions with SAGA (PubMed:15647753). It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus (PubMed:15647753).
subunit: Component of the 1.8 MDa SAGA complex, which consists of at least of TRA1, CHD1, SPT7, TAF5, ADA3, SGF73, SPT20/ADA5, SPT8, TAF12, TAF6, HFI1/ADA1, UBP8, GCN5, ADA2, SPT3, SGF29, TAF10, TAF9, SGF11 and SUS1. TAF5, TAF6, TAF9, TAF19, TAF12 and ADA1 seem to be present in 2 copies. SAGA is built of 5 distinct domains with specialized functions. Domain I (containing TRA1) probably represents the activator interaction surface. Domain II (containing TAF5 and TAF6, and probably TAF9 and TAF10), domain III (containing GCN5, TAF10, SPT7, TAF5 and ADA1, and probably ADA2, ADA3 and TAF12), and domain IV (containing HFI1/ADA1 and TAF6, and probably TAF9) are believed to play primarily an architectural role. Domain III also harbors the HAT activity. Domain V (containing SPT3 and SPT20, and probably SPT8) represents the TBP- interacting module, which may be associated transiently with SAGA. Interacts with dimethylated and trimethylated 'Lys-4' of histone H3 (H3K4me2 and H3K4me3), with a preference for the trimethylated form (H3K4me3). Component of the SLIK complex, which consists of at least TRA1, CHD1, SPT7, TAF5, ADA3, SPT20, RTG2, TAF12, TAF6, HFI1, UBP8, GCN5, ADA2, SPT3, SGF29, TAF10 and TAF9. - Cloning, purification, crystallization and preliminary crystallographic analysis of the tandem tudor domain of Sgf29 from Saccharomyces cerevisiae.
Li, Acta crystallographica. Section F, Structural biology and crystallization communications 2010 - GeneRIF: tandem tudor domain at the C-terminus of Sgf29 was crystallized using the hanging-drop vapour-diffusion method and the crystals diffracted to 1.92 A resolution
- iOPTICS-GSO for identifying protein complexes from dynamic PPI networks
Lei, BMC medical genomics 2017 - “...( GO:0001075 ) 0.47 4 YCR042C YML114C YMR005W YML015C YPL011C YMR236W YGR274C YBR198C YGL112C YLR055C YCL010C YDR448W YPL254W 1.67E-21 transcription factor activity ( GO:0001075 ) 0.41 5 YLR129W YLR409C YDR449C YCR057C YPL266W YPR112C YDR299W YGR128C YPL126W YJR002W YDR324C YNL132W YPL217C YBL004W YDL148C YER082C YHR196W YGR090W YCL059C...”
- Mining Temporal Protein Complex Based on the Dynamic PIN Weighted with Connected Affinity and Gene Co-Expression
Shen, PloS one 2016 - “...YOR116C YKL144C YOR207C YNR003C YBR245C DNA-directed RNA polymerase activity | AmiGO 0.51 6 7.24e-11 YHR099W YCL010C YBR198C YDR448W YGL066W YOR244W YNL189W YHR090C YGR002C YFL024C YEL018W YDR392W YDR359C YDR146C histone acetyltransferase activity | AmiGO 0.16 7 7.17e-08 YGR252W YOL148C YDL140C YPR187W YOR224C YOR151C YOL145C YLR418C YJR017C YGR136W...”
- HKC: an algorithm to predict protein complexes in protein-protein interaction networks
Wang, Journal of biomedicine & biotechnology 2011 - “...(catalog 510.190.10.20.10 in the complexcat benchmark), and their overlap ratio is 0.93. The two proteins YCL010c and YGL066w that are not recovered by cluster 12 have only one interaction with the cluster and do not exhibit good graph theoretic property. Actually, based on the available information...”
- “...with the SAGA complex (size 16), and their overlap ratio is 0.93. The two proteins YCL010c and YGL066w that are not contained in the predicted cluster are isolated nodes with only one edge connecting with the cluster. (c) An example of a well-matched cluster, involving 7...”
- A core-attachment based method to detect protein complexes in PPI networks
Wu, BMC bioinformatics 2009 - “...YNL232W YOL021C YOL142W YOR001W YOR076C exosome (RNase complex) 0.805 13 4 5.00e-24 YBR081C YBR198C YBR253W YCL010C YDR167W YDR176W YDR216W YDR448W YGL112C YGR252W YHR099W YMR236W YPL254W SAGA complex 0.452 11 5 9.90e-23 YBR081C YBR198C YDR167W YDR176W YDR392W YDR448W YEL009C YER148W YGL112C YGR274C YHR099W YMR236W YOL148C YPL254W YPR086W...”
- A genome-wide screen in Saccharomyces cerevisiae reveals pathways affected by arsenic toxicity
Zhou, Genomics 2009 - “...0.5181 Q9NQY0 Bridging integrator 3 YGL012W ERG4 Sterol C-24 (28) reductase 0.5262 Q14739 Lamin-B receptor YCL010C SGF29 SaGa associated Factor 29kDa; Probable 29kKDa Subunit of SAGA histone acetyltransferase complex 0.527 Q96ES7 SAGA-associated factor 29 homolog YNR031C SSK2 Map kinase kinase kinase (MAPKKK) of the high- osmolarity...”
- Genome-wide mapping of the coactivator Ada2p yields insight into the functional roles of SAGA/ADA complex in Candida albicans
Sellam, Molecular biology of the cell 2009 - “...orf19.3035 0 Rtg2 Other Sgf29 Tra1 YGL252C -- -- YCL010C YHR099W orf19.7074 orf19.139 8.8e-58 0 S. cerevisiae protein HAT Gcn5 (Ada4) Ada Ada1 Ada2 Ada3 Spt...”
- Comparative functional genomic analysis identifies distinct and overlapping sets of genes required for resistance to monomethylarsonous acid (MMAIII) and arsenite (AsIII) in yeast
Jo, Toxicological sciences : an official journal of the Society of Toxicology 2009 - “...YNL025C YCR081W YLR006C YJL128C YOL081W YCR068W YGR133W YGR057C YCL010C YML041C YNL329C YDL082W 50% IC20 Standard name 75lM 150lM PFD1 SAS4 SAS5 SAS2 CIN2 ARR1...”
- Chemogenetic fingerprinting by analysis of cellular growth dynamics
Warringer, BMC chemical biology 2008 - “...assumption). Genes included in the screen were: FLO1, PIM1, TAT1, YBR074w, PHO3, YBR099c, APE3, APM3, YCL010C, YCL047C, CVT17, YCR073W, SRB8, YCR101C, YCR106W, YCR195C, YDL109c, YDL124w, DLD1, YDL175c, UGA4, GDH2, RRI1, SHS1, YDR026c, YDR101c, YDR132c, SWM1, GLO2, SUM1, YDR384c, HAT2, PRB1, CAN1, VTC1, DOT6, FTR1, YGL010w, ATE1,...”
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XP_003547705 SAGA-associated factor 29 homolog B isoform X3 from Glycine max
Aligns to 130:264 / 269 (50.2%), covers 100.0% of PF07039, 121.0 bits
XP_003547704 SAGA-associated factor 29 homolog B isoform X1 from Glycine max
Aligns to 132:266 / 271 (49.8%), covers 100.0% of PF07039, 120.9 bits
SGF29_SCHPO / Q9USW9 SAGA-associated factor 29 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see 4 papers)
NP_596000 SAGA complex subunit Sgf29 from Schizosaccharomyces pombe
SPBC1921.07c SAGA complex subunit Sgf29 (predicted) (RefSeq) from Schizosaccharomyces pombe
Aligns to 115:243 / 244 (52.9%), covers 98.5% of PF07039, 117.0 bits
- function: Chromatin reader component of the transcription regulatory histone acetylation (HAT) complex SAGA (PubMed:21642955, PubMed:26401015). Sgf29 specifically recognizes and binds methylated 'Lys-4' of histone H3 (H3K4me), with a preference for trimethylated form (H3K4me3) (PubMed:26401015). In the SAGA complex, sgf29 is required to facilitate crosstalk between gcn5 acetyltransferase activity and H3K4me3 recognition (PubMed:26401015). At the promoters, SAGA is required for recruitment of the basal transcription machinery (PubMed:19056896). It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction and promoter selectivity, interaction with transcription activators, and chromatin modification through histone acetylation and deubiquitination (PubMed:19056896). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac) (PubMed:19056896).
subunit: Component of the SAGA complex. - Nucleosome competition reveals processive acetylation by the SAGA HAT module.
Ringel, Proceedings of the National Academy of Sciences of the United States of America 2015 - GeneRIF: Data indicate that Spt-Ada-Gcn5 acetyltransferase (SAGA) coactivator complex contains a separable subcomplex known as the histone acetyltransferase (HAT) module that contains the HAT, Gcn5, bound to Sgf29.
- A genome-wide screen of genes involved in cadmium tolerance in Schizosaccharomyces pombe
Kennedy, Toxicological sciences : an official journal of the Society of Toxicology 2008 - “...sin3 SPAC29A4.20 ELP3/YPL086C kap1 gcn5 SPBC1921.07c SPBC28F2.10c SPAC1952.05 SGF29/YCL010C NGG1/YDR176W GCN5/YGR252W SPAC6B12.05c IES2/YNL215W SPCC18.06c...”
XP_003633806 uncharacterized protein LOC100250716 isoform X2 from Vitis vinifera
Aligns to 131:265 / 270 (50.0%), covers 100.0% of PF07039, 115.2 bits
XP_003633807 uncharacterized protein LOC100250716 isoform X1 from Vitis vinifera
Aligns to 142:276 / 281 (48.0%), covers 100.0% of PF07039, 115.0 bits
XP_001417743 predicted protein from Ostreococcus lucimarinus CCE9901
Aligns to 179:313 / 314 (43.0%), covers 99.2% of PF07039, 112.5 bits
SG29B_ARATH / Q500Z7 SAGA-associated factor 29 homolog B; AtSGF29b; 29 kDa SAGA-associated factor homolog B from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT5G40550 hypothetical protein (RefSeq) from Arabidopsis thaliana
Aligns to 134:268 / 273 (49.5%), covers 100.0% of PF07039, 112.4 bits
- function: Chromatin reader component of the transcription regulatory histone acetylation (HAT) complexe SAGA.
- Spt-Ada-Gcn5-Acetyltransferase (SAGA) Complex in Plants: Genome Wide Identification, Evolutionary Conservation and Functional Determination
Srivastava, PloS one 2015 - “...AtSGF29a At3g27460 OsSGF29 Os12g19350 Flowering initiation, Auxiliary role in salt stress [ 61 ] AtSGF29b At5g40550 - Tra1 TRRAP AtTRA1a At2g17930 OsTRA1 Os07g45064 - AtTRA1b At4g36080 - ND: Not detected. Alignment and phylogenetic analysis Clustal-X version 1.83 software program was used for multiple sequence alignment of...”
- “...( Table 1 and S2 Table ). Further, we also identified two proteins, At3g27460 and At5g40550 in Arabidopsis encoding SGF29, as reported recently [ 61 ] and one protein in O . sativa (Os12g19350) ( Table 1 and S2 Table ). TRA1 is a representative of...”
- Composition of the SAGA complex in plants and its role in controlling gene expression in response to abiotic stresses
Moraga, Frontiers in plant science 2015 - “...ADA3 XP_001782560 ADA3 (At4g29790) Os05g28300 XP_002265763 SGF29 SGF29/STAF36 XP_001755688 SGF29a (At3g27460) Os12g19350 XP_003633806 XP_001785583 SGF29b (At5g40550) XP_003633807 SPT SPT8 ND ND ND ND ND SPT20/ADA5 SPT20/FAM48A XP_001762074 SPT20 (At1g72390) Os01g02860 XP_002272317 SPT7 STAF65/STAF65 XP_001767625 HAF1 (At1g32750) Os06g43790 XP_010656962 XP_001779301 HAF2 (At3g19040) SPT3 SPT3 XP_001759999 TAF13 (At1g02680)...”
SG29A_ARATH / Q8RXY6 SAGA-associated factor 29 homolog A; AtSGF29a; 29 kDa SAGA-associated factor homolog A from Arabidopsis thaliana (Mouse-ear cress) (see paper)
AT3G27460 hypothetical protein (RefSeq) from Arabidopsis thaliana
Aligns to 131:265 / 270 (50.0%), covers 100.0% of PF07039, 112.3 bits
- function: Chromatin reader component of the transcription regulatory histone acetylation (HAT) complexe SAGA (By similarity). Involved in salt stress tolerance. Enhances the effect of ADA2B in the positive regulation of salt-induced gene expression (PubMed:21193996).
disruption phenotype: Delayed flowering. Increased tolerance to salt stress. - Composition of the SAGA complex in plants and its role in controlling gene expression in response to abiotic stresses
Moraga, Frontiers in plant science 2015 - “...Os03g53960 XP_002262737 XP_001784968 XP_002268970 ADA3 ADA3 XP_001782560 ADA3 (At4g29790) Os05g28300 XP_002265763 SGF29 SGF29/STAF36 XP_001755688 SGF29a (At3g27460) Os12g19350 XP_003633806 XP_001785583 SGF29b (At5g40550) XP_003633807 SPT SPT8 ND ND ND ND ND SPT20/ADA5 SPT20/FAM48A XP_001762074 SPT20 (At1g72390) Os01g02860 XP_002272317 SPT7 STAF65/STAF65 XP_001767625 HAF1 (At1g32750) Os06g43790 XP_010656962 XP_001779301 HAF2 (At3g19040)...”
- AIP1 is a novel Agenet/Tudor domain protein from Arabidopsis that interacts with regulators of DNA replication, transcription and chromatin remodeling
Brasil, BMC plant biology 2015 - “...microarray experiments available in Genevestigator ( https://genevestigator.com ) [ 40 ]. The genes AT5G07350 and AT3G27460 from Class IV are out of analysis since there are no probes in the available microarray data Interestingly, the Arabidopsis Agenet/Tudor genes were highly expressed in reproductive tissues and evolutionary...”
- Spt-Ada-Gcn5-Acetyltransferase (SAGA) Complex in Plants: Genome Wide Identification, Evolutionary Conservation and Functional Determination
Srivastava, PloS one 2015 - “...ND AtCHR5 At2g13370 OsCHD1 OsJ_25446 Embryo development; Seed maturation [ 106 ] Sgf29 STAF36 AtSGF29a At3g27460 OsSGF29 Os12g19350 Flowering initiation, Auxiliary role in salt stress [ 61 ] AtSGF29b At5g40550 - Tra1 TRRAP AtTRA1a At2g17930 OsTRA1 Os07g45064 - AtTRA1b At4g36080 - ND: Not detected. Alignment and...”
- “...human CHD2 ( Table 1 and S2 Table ). Further, we also identified two proteins, At3g27460 and At5g40550 in Arabidopsis encoding SGF29, as reported recently [ 61 ] and one protein in O . sativa (Os12g19350) ( Table 1 and S2 Table ). TRA1 is a...”
- Genetic screens for floral mutants in Arabidopsis thaliana: enhancers and suppressors
Dinh, Methods in molecular biology (Clifton, N.J.) 2014 - “...T3D7-F GGTATCGATTGAGCAAATAA T3D7-R ACATGCGTCTGCTTGGAG AT2G47160 CHR3 F24P17 ACTGCACATTGCACGAACA F24P17 GGATGGCAACTTAGGCTGAA AT3G06400 K1G2-F ATGAGCTTTAGGAGTGTGTA K1G2-R AATTTTGTCCCAAAAGAATA AT3G27460 CIW4-F GTTCATTAAACTTGCGTGTGT CIW4-R TACGGTCAGATTGAGTGATTC AT3G50820 T20O10-F AAATGCCAGGGGAATAGA T20O10-R CAAACCATGCAATGATGC AT3G62988 CHR4 CIW5-F GGTTAAAAATTAGGGTTACGA CIW5-R AGATTTACGTGGAAGCAAT AT4G01710 CIW6-F CTCGTAGTGCACTTTCATCA CIW6-R CACATGGTTAGGGAAACAATA AT4G13575 4CER450255F CACAAGACAACACCAAAAAC 4CER450255R AGAAGGAATGGCTTCATCTA AT4G20095 AP22-F ATTATGTTAGGAAAATGAGAT AP22-R GCGTTGTAAGAATTAAGAA...”
XP_002968194 SAGA-associated factor 29 homolog A isoform X2 from Selaginella moellendorffii
Aligns to 137:271 / 276 (48.9%), covers 99.2% of PF07039, 112.0 bits
XP_016878383 SAGA-associated factor 29 isoform X1 from Homo sapiens
Aligns to 158:258 / 258 (39.1%), covers 77.3% of PF07039, 111.5 bits
CNAG_06392 SAGA-associated factor 29 from Cryptococcus neoformans var. grubii H99
Aligns to 155:317 / 318 (51.3%), covers 99.2% of PF07039, 111.4 bits
XP_003576694 SAGA-associated factor 29 homolog A from Brachypodium distachyon
Aligns to 145:279 / 284 (47.5%), covers 100.0% of PF07039, 108.4 bits
PPTG_04971 hypothetical protein from Phytophthora parasitica INRA-310
Aligns to 170:304 / 309 (43.7%), covers 98.5% of PF07039, 100.8 bits
NP_001326215 SGF29 tudor-like domain-containing protein from Arabidopsis thaliana
Aligns to 131:245 / 251 (45.8%), covers 77.3% of PF07039, 86.5 bits
NP_001330202 SGF29 tudor-like domain-containing protein from Arabidopsis thaliana
Aligns to 134:252 / 301 (39.5%), covers 77.3% of PF07039, 85.8 bits
Or search for genetic data about PF07039 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory