Family Search for PF11935 (SYMPK_PTA1_N)
April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.
PF11935 hits 17 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
PTA1_YEAST / Q01329 Pre-tRNA-processing protein PTA1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 2 papers)
NP_009356 RNA-processing protein PTA1 from Saccharomyces cerevisiae S288C
NP_009356, YAL043C Pta1p from Saccharomyces cerevisiae
Aligns to 91:333 / 785 (31.0%), covers 100.0% of PF11935, 216.5 bits
- function: Essential in pre-tRNA processing. Component of the cleavage and polyadenylation factor (CPF) complex, which plays a key role in polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factors including the CFIA complex and NAB4/CFIB. Component of the APT complex, which may be involved in polyadenylation-independent transcript 3'-end formation
subunit: Component of the cleavage and polyadenylation factor (CPF) complex, which is composed of PTI1, SYC1, SSU72, GLC7, MPE1, REF2, PFS2, PTA1, YSH1/BRR5, SWD2, CFT2/YDH1, YTH1, CFT1/YHH1, FIP1 and PAP1. Component of the APT complex, which is a subcomplex of CPF, and is composed of PTI1, SYC1, SSU72, GLC7, REF2, PTA1 and SWD2. - Molecular details of the CPSF73-CPSF100 C-terminal heterodimer and interaction with Symplekin
Thore, Open biology 2023 - “...(Q9UKF6, 460-684), hsCPSF100 (Q9P2I0, 651-782), hsSympk (Q92797, 539-1100); scYsh1 (Q06224, 474-779), scCft2 (Q12102, 718-859), scPta1 (Q01329, 559-785), scSyc1 (Q08553, 1-188); spYsh1 (O13794, 464-757), spCft2 (O74740, 637-797), spPta1 (Q10222, 445-670); tcCPSF73 (Q6BCB3, 482-762), tcCPSF100 (Q6BCB1, 626-802), tcSympk (A0A7J6XPR2, 573-928); ceCPSF73(Q95PY8, 458-707), ceCPSF100 (O17403, 633-843), ceSympk (O16929, 525-1143);...”
- A direct interaction between CPF and RNA Pol II links RNA 3' end processing to transcription
Carminati, Molecular cell 2023 - “...of vectors carrying APT complexes For APT, E.coli codon - optimized genes encoding Pta1 (Uniprot Q01329 ), Ref2-StrepII-tag (SII) (Uniprot P42073 ), Pti1 (Uniprot O49339 ), Swd2 (Uniprot P36104 ), Glc7 (Uniprot P32598 ), Ssu72 (Uniprot P53538 ), and Syc1 (Q08553) (Gene Art, Thermo Fisher) were...”
- The nucleotide sequence of chromosome I from Saccharomyces cerevisiae
Bussey, Proceedings of the National Academy of Sciences of the United States of America 1995 - “...sp P27825 sp Q01574 sp P25611 sp P15298 sp P23884 sp Q01329 sp P11433 sp P13365 sp P06182 sp P00549 sp P32234 sp P17889 sp P28005 gp X64536 sp P31109 sp P32492...”
- The essential N terminus of the Pta1 scaffold protein is required for snoRNA transcription termination and Ssu72 function but is dispensable for pre-mRNA 3'-end processing.
Ghazy, Molecular and cellular biology 2009 - GeneRIF: the amino terminus of Pta1 has an inhibitory effect and this effect can be neutralized through the interaction with Ssu72.
- Involvement of Pta1, Pcf11 and a KlCYC1 AU-rich element in alternative RNA 3'-end processing selection in yeast.
Seoane, FEBS letters 2009 (PubMed)- GeneRIF: Data report the involvement of yeast RNA processing factors Pta1 and Pcf11 in alternative 3'-end RNA processing.
- Protein functional module identification method combining topological features and gene expression data
Zhao, BMC genomics 2021 - “...YGL173C, YJL124C, YJR022W, tri-snRNP processing YKL173W, YLR147C,YLR275W, YMR268C, complex YNL118C, YPR178W, YOL149W, YNL147W, YLR438C-A 2.77e-27 YAL043C, YDR195W, YDR228C, YDR301W, mRNA cleavage mRNA YER133W, YGR156W, YJL033W, YJR093C, factor complex polyadenylation YKL018W, YKL059C, YKR002W, YLR115W, YLR277C, YMR061W, YNL317W, YPR107C 5.92e-18 YBR081C, YBR198C, YDR145W, YDR167W, transcription factor RNA polymerase...”
- Developmentally regulated internal transcription initiation during meiosis in budding yeast
Zhou, PloS one 2017 - “...Name Gene Name Start Location a MSE b Lardenois et al. c Gene Description d YAL043c PTA1 +1116145 Yes Yes Essential subunit of holo-CPF YAR050w FLO1 +78920 No Yes Lectin-like cell wall protein (flocculin) YBL063w e KIP1 +497212 No No Kinesin-related motor protein YBR069c TAT1 +5854...”
- A multi-network clustering method for detecting protein complexes from multiple heterogeneous networks
Ou-Yang, BMC bioinformatics 2017 - “...YNL189W, YNL232W snoRNA 3-end processing genes, 85.7% YOR001W, YOR076C, YGR158C, YGR195W YOL021C, YOL142W 5 8.98e-31 YAL043C, YDR195W, YDR228C, YDR301W mRNA polyadenylation 13 out of 17 YJL033W, YJR093C, YKL018W, YKL059C genes, 76.5% YLR277C, YMR061W, YNL317W, YOR179C YKR002W, YLR115W, YER133W, YGR156W YPR107C 7 5.85e-32 YBR146W, YBR251W, YDR036C, YDR041W...”
- Construction of ontology augmented networks for protein complex prediction
Zhang, PloS one 2013 - “...GO:0004842 (ubiquitin-protein ligase activity) 4.38e-05 GO:0030015 (CCR4-NOT core complex) 1.46e-28 5 YER133W YKL059C YLR115W YGR156W YAL043C YKR002W YJR093C YNL317W YDR301W YDR195W YLR277C YPR107C YNL222W 0.87 GO:0006378 (mRNA polyadenylation) 1.29e-26 GO:0003723 (RNA binding) 1.58e-07 GO:0005847 (CFII complex) 1.20e-37 6 YPL178W YGR013W YIL061C YHR086W YML046W YLR275W YFL017W-A YBR119W...”
- A comparison of the functional modules identified from time course and static PPI network data
Tang, BMC bioinformatics 2011 - “...YPL150W DNA-directed RNA polymerase III complex 0.54 16 2 5.58e-29 YOR179C YJR093C YLR115W YKL018W YNL222W YAL043C YDR228C YNL317W YKL059C YDR195W YER133W YDR301W YPR107C YGR156W YLR277C YDR412W YMR260C YHR100C YJL033W YOR250C YKR002W YML030W YGL256W YOR227W mRNA cleavage and polyadenylation specificity factor complex 0.63 15 3 4.64e-24 YGL004C...”
- Toward a comprehensive temperature-sensitive mutant repository of the essential genes of Saccharomyces cerevisiae
Ben-Aroya, Molecular cell 2008 - “...Gene Name(s) Description rRNA Defect Percent Reduction YAL043C PTA1, FUN39 Subunit of holo-CPF, mRNA, snoRNA pre-tRNA processing; binds phospho-CTD of RNAPII...”
- “...2003 ), but we observed no such defects. The YAL043C ( PTA1 ) gene encodes a subunit of the holo-CPF complex involved in mRNA 3 end formation/polyadenylation...”
- Pre-messenger RNA processing factors in the Drosophila genome
Mount, The Journal of cell biology 2000 - “...(CG2261) AAF57183 CstF-50 kD 100E1-2 NP_001315, E-129 unknown CG2097 AAF51962 Symplekin 83C1 NP_004810, E-173 Pta1, NP_009356, 5E-04 Cleavage factors I & II CG3689 AAF50278 25-kD subunit 67A6 NP_008937, E-102 unknown CG7185 AAF50445 68-kD subunit 66C5 NP_008938, 3E-34 unknown CG10228 AAF46699 Factor IA 51D2-4 KIAA0824, 7E-41 Pcf11,...”
- Depolarization of the actin cytoskeleton is a specific phenotype in Saccharomyces cerevisiae
Karpova, Journal of cell science 1998 - “...YAL051W, YAL049C, YAL048C, YAL046C, YAL045C, YAL044C, YAL042W, YAL043C, YAL040C, YAL039C, YAL037W, YAL036C, J Cell Sci. Author manuscript; available in PMC 2008...”
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AO090103000067 No description from Aspergillus oryzae RIB40
Aligns to 91:358 / 793 (33.8%), covers 100.0% of PF11935, 210.8 bits
6v4xJ / Q92797 Cryo-em structure of an active human histone pre-mRNA 3'-end processing machinery at 3.2 angstrom resolution (see paper)
Aligns to 93:310 / 311 (70.1%), covers 95.6% of PF11935, 197.8 bits
SYMPK_HUMAN / Q92797 Symplekin from Homo sapiens (Human) (see 7 papers)
NP_004810 symplekin from Homo sapiens
Aligns to 122:348 / 1274 (17.8%), covers 98.7% of PF11935, 196.8 bits
- function: Scaffold protein that functions as a component of a multimolecular complex involved in histone mRNA 3'-end processing. Specific component of the tight junction (TJ) plaque, but might not be an exclusively junctional component. May have a house-keeping rule. Is involved in pre-mRNA polyadenylation. Enhances SSU72 phosphatase activity.
subunit: Found in a heat-sensitive complex at least composed of several cleavage and polyadenylation specific and cleavage stimulation factors (PubMed:16230528). Interacts with CPSF2, CPSF3 and CSTF2 (PubMed:10669729, PubMed:18688255). Interacts (via N-terminus) with HSF1; this interaction is direct and occurs upon heat shock (PubMed:14707147). Interacts with SSU72 (PubMed:20861839, PubMed:23070812). - Shifting the balance: soluble ADAM10 as a potential treatment for Alzheimer's disease
Hershkovits, Frontiers in aging neuroscience 2023 - “...Membrane 1 60 Proto-oncogene tyrosine-protein kinase Src SRC P12931 C-terminal Membrane 1 61 Symplekin SYMPK Q92797 C-terminal Membrane 1 62 Talin-1 TLN1 Q9Y490 C and N- terminal Membrane 4 63 Neurosecretory protein VGF VGF O15240 C and N- terminal Secreted 20 64 Wiskott-Aldrich syndrome protein family...”
- Molecular details of the CPSF73-CPSF100 C-terminal heterodimer and interaction with Symplekin.
Thore, Open biology 2023 - “...prediction (including Uniprot ID, amino acid range) are: hsCPSF73 (Q9UKF6, 460-684), hsCPSF100 (Q9P2I0, 651-782), hsSympk (Q92797, 539-1100); scYsh1 (Q06224, 474-779), scCft2 (Q12102, 718-859), scPta1 (Q01329, 559-785), scSyc1 (Q08553, 1-188); spYsh1 (O13794, 464-757), spCft2 (O74740, 637-797), spPta1 (Q10222, 445-670); tcCPSF73 (Q6BCB3, 482-762), tcCPSF100 (Q6BCB1, 626-802), tcSympk (A0A7J6XPR2,...”
- Quantitative plasma proteomics of survivor and non-survivor COVID-19 patients admitted to hospital unravels potential prognostic biomarkers and therapeutic targets
Flora, 2021 - Three-Dimensional Graph Matching to Identify Secondary Structure Correspondence of Medium-Resolution Cryo-EM Density Maps.
Behkamal, Biomolecules 2021 - “...13 Flagellar motor switch protein FliG 3HJL O66891 A 329 20 20 14 Symplekin 3ODS Q92797 A 415 21 16 15 Albumin 2XVV P02768 A 585 33 19 a the name of the protein; b the PDB ID of the protein used in the test. -containing...”
- Proteomic Analysis of Renal Biomarkers of Kidney Allograft Fibrosis-A Study in Renal Transplant Patients.
Mortensen, International journal of molecular sciences 2020 - “...structure maintainance 0.205 Splicing factor U2AF 65 kDa subunit P26368 Positive mRNA processing 0.199 Symplekin Q92797 Positive Cell adhesion/mRNA processing 0.156 Threonine synthase-like 1 Q8IYQ7 Negative Unknown 0.131 AP-2 complex subunit sigma P53680 Positive Protein transport 0.118 Actin-related protein 2/3 complex subunit 2 O15144 Positive Actin...”
- Quantitative Phosphoproteome Analysis of Clostridioides difficile Toxin B Treated Human Epithelial Cells.
Junemann, Frontiers in microbiology 2018 - “...Connector enhancer of kinase suppressor of ras 1 SPSLSLAPL S PR 1.62 1.26E-02 S-49 118.2 Q92797 SYMPK Symplekin SPQTLAPVGE DAMKTP S PAAEDAREPEAK 1.62 2.73E-03 S-1259 111.09 A0A096LNZ0 AAK1 Uncharacterized protein FLJ45252 LGGAVPFAPPEV S PEQAK 1.58 5.82E-04 S-217 130.37 Phosphosites with MAP kinase motifs were differently regulated...”
- Life and Death of mRNA Molecules in Entamoeba histolytica.
Valdés-Flores, Frontiers in cellular and infection microbiology 2018 - “...C4M1H2 PABP1 P11940 EHI_198750 PABP1 C4LWS1 EHI_033250 PABP2 C4M6Y2 RRBP6 Q7Z6E9 EHI_014000 RRBP6 C4LXP1 Symplekin Q92797 a UniProtKB; b AmoebaDB. Data about parasite proteins were obtained from (Lpez-Camarillo et al., 2005 , 2014 ) . The presence of these proteins in E. histolytica suggests that 3...”
- Estrone-3-Sulfate Stimulates the Proliferation of T47D Breast Cancer Cells Stably Transfected With the Sodium-Dependent Organic Anion Transporter SOAT (SLC10A6).
Karakus, Frontiers in pharmacology 2018 - “...arrays were directly used for expression analysis of SOAT by real-time PCR. Symplekin (SYMPK, Uniprot Q92797) that showed particularly low expression variability in breast cancer tissue and cell lines ( Tilli et al., 2016 ) was used as endogenous control. RNA was isolated from T47D-SOAT and...”
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- UbiA prenyltransferase domain-containing protein-1 modulates HMG-CoA reductase degradation to coordinate synthesis of sterol and nonsterol isoprenoids.
Schumacher, The Journal of biological chemistry 2018 - GeneRIF: Results indicated that reductase becomes destabilized in the absence of UBIAD1, resulting in reduced cholesterol synthesis and intracellular accumulation. Findings further establish UBIAD1 as a central player in the reductase ERAD pathway and regulation of isoprenoid synthesis.
- Rab11 Functions as an Oncoprotein via Nuclear Factor kappa B (NF-κB) Signaling Pathway in Human Bladder Carcinoma.
Gong, Medical science monitor : international medical journal of experimental and clinical research 2018 - GeneRIF: Research proved that high Rab11 expression enhances cellular multiplication and invasiveness of bladder cancer, possibly by regulating the NF-kappaB signaling pathway.
- Novel colon cancer susceptibility variants identified from a genome-wide association study in African Americans.
Wang, International journal of cancer 2017 - GeneRIF: Data indicate rs56848936 in the gene symplekin protein (SYMPK) at 19q13.3, associated with colon cancer risk.
- Nuclear accumulation of symplekin promotes cellular proliferation and dedifferentiation in an ERK1/2-dependent manner.
Zhang, Scientific reports 2017 - GeneRIF: The significance of nuclear symplekin in tumorigenesis is also highlighted, and ERK-dependent phosphorylation represents a mechanism for its subcellular sorting.
- Global Promotion of Alternative Internal Exon Usage by mRNA 3' End Formation Factors.
Misra, Molecular cell 2015 - GeneRIF: CPSF2 and SYMPK, are RBFOX2 cofactors for both inclusion and exclusion of internal exons.
- Symplekin, a polyadenylation factor, prevents MOZ and MLL activity on HOXA9 in hematopoietic cells.
Largeot, Biochimica et biophysica acta 2013 (PubMed)- GeneRIF: Symplekin interacts and co-localizes with both MOZ and MLL in immature hematopoietic cells. Its inhibition leads to a decrease of the HOXA9 protein level but not of Hoxa9 mRNA.
- Expression and distribution of symplekin regulates the assembly and function of the epithelial tight junction.
Chang, Histochemistry and cell biology 2012 (PubMed)- GeneRIF: Symplekin expression regulates the assembly of tight junctions, thus helps to maintain the integrity of the epithelial monolayer and cellular polarity.
- Symplekin promotes tumorigenicity by up-regulating claudin-2 expression.
Buchert, Proceedings of the National Academy of Sciences of the United States of America 2010 - GeneRIF: Data show that claudin-2 expression was reduced following symplekin down-regulation, and siRNA-mediated claudin-2 down-regulation increased the transepithelial resistance and decreased cyclin D1 expression and ZONAB nuclear localization.
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F1LSH0 Symplekin from Rattus norvegicus
Aligns to 122:349 / 1280 (17.8%), covers 97.8% of PF11935, 196.3 bits
NP_080881 symplekin isoform 1 from Mus musculus
Q80X82 Symplekin from Mus musculus
Aligns to 122:349 / 1288 (17.7%), covers 97.8% of PF11935, 194.4 bits
SYMPK_DROME / Q8MSU4 Symplekin from Drosophila melanogaster (Fruit fly) (see 4 papers)
NP_649580 symplekin from Drosophila melanogaster
Aligns to 116:343 / 1165 (19.6%), covers 96.9% of PF11935, 193.7 bits
- function: Component of a protein complex required for cotranscriptional processing of 3'-ends of polyadenylated and histone pre-mRNA.
subunit: Interacts with Cpsf73 and Cpsf100 forming a core cleavage factor required for both polyadenylated and histone mRNA processing. Interacts with Slbp and Lsm11. - Molecular details of the CPSF73-CPSF100 C-terminal heterodimer and interaction with Symplekin
Thore, Open biology 2023 - “...(Q9C952, 465-693), atCPSF100 (Q9LKF9, 602-739), atSympk (Q9SFZ8, 474-1092); dmCPSF73 (Q9VE51, 464-684), dmCPSF100 (Q9V3D6, 608-756), dmSympk (Q8MSU4, 516-1101); ecCPSF73 (Q8SUE4, 452-643 and 568-643), ecCPSF100 (Q8SRZ4, 525-639), ecSympk (Q8SVB3, 161-385). Full prediction details, along with all structural models, are accessible at: https://www.nmrbordeaux.org/Data/Thore_et_al_AlphaFold_models.zip . 2.10 . Electrophoretic mobility shift...”
- In vivo characterization of the Drosophila mRNA 3' end processing core cleavage complex.
Michalski, RNA (New York, N.Y.) 2015 - GeneRIF: Authors propose a model in which the core cleavage complex formation is mediated by CPSF73, CPSF100, and Symplekin C-termini, and the N-terminal region of Symplekin facilitates cotranscriptional 3' end processing of histone mRNAs.
- Drosophila Symplekin localizes dynamically to the histone locus body and tricellular junctions.
Tatomer, Nucleus (Austin, Tex.) 2014 - GeneRIF: This localization depends on the RNA binding protein ypsilon schachtel. CPSF-73 and a number of mRNAs are localized at this same site, suggesting that Symplekin participates in cytoplasmic polyadenylation at tricellular junctions.
- Crystal structure of the HEAT domain from the Pre-mRNA processing factor Symplekin.
Kennedy, Journal of molecular biology 2009 - GeneRIF: Together, these data support the conclusion that the Symplekin HEAT domain serves as a scaffold for protein-protein interactions essential to the mRNA maturation process.
SYMPK_XENLA / Q7ZYV9 Symplekin from Xenopus laevis (African clawed frog) (see 2 papers)
XP_018087329 symplekin isoform X1 from Xenopus laevis
Aligns to 112:340 / 1202 (19.1%), covers 99.1% of PF11935, 191.8 bits
- function: Involved in histone mRNA 3'-end processing (By similarity). Involved in the cytoplasmic polyadenylation element (CPE)-mediated polyadenylation of maternal mRNAs in maturing oocytes. Serves as a scaffold upon which cytoplasmic polyadenylation regulatory factors are assembled.
subunit: Identification in a complex with cpsf2, cpsf73, cpsf160 and sympk. Interacts with cpeb1, cpsf2 and papd4. - Symplekin and xGLD-2 are required for CPEB-mediated cytoplasmic polyadenylation.
Barnard, Cell 2004 (PubMed)- GeneRIF: Here, we identify a new factor essential for polyadenylation, namely, symplekin, a CPEB and CPSF binding protein that serves as a scaffold upon which regulatory factors are assembled
orf19.7041 putative uncharacterized protein CaJ7.0091 from Candida albicans (see paper)
Aligns to 96:346 / 764 (32.9%), covers 98.3% of PF11935, 191.3 bits
- CharProtDB CGD description: Putative protein of unknown function; heterozygous null mutant exhibits hypersensitivity to parnafungin and cordycepin in the C. albicans fitness test; predicted ORF in Assemblies 19, 20 and 21
O16929 DUF3453 domain-containing protein from Caenorhabditis elegans
Aligns to 112:347 / 1143 (20.6%), covers 96.1% of PF11935, 160.7 bits
- Molecular details of the CPSF73-CPSF100 C-terminal heterodimer and interaction with Symplekin
Thore, Open biology 2023 - “...tcCPSF73 (Q6BCB3, 482-762), tcCPSF100 (Q6BCB1, 626-802), tcSympk (A0A7J6XPR2, 573-928); ceCPSF73(Q95PY8, 458-707), ceCPSF100 (O17403, 633-843), ceSympk (O16929, 525-1143); atCPSF73 (Q9C952, 465-693), atCPSF100 (Q9LKF9, 602-739), atSympk (Q9SFZ8, 474-1092); dmCPSF73 (Q9VE51, 464-684), dmCPSF100 (Q9V3D6, 608-756), dmSympk (Q8MSU4, 516-1101); ecCPSF73 (Q8SUE4, 452-643 and 568-643), ecCPSF100 (Q8SRZ4, 525-639), ecSympk (Q8SVB3, 161-385)....”
PTA1_SCHPO / Q10222 mRNA cleavage and polyadenylation specificity factor complex subunit pta1 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see 2 papers)
pta1 / RF|NP_594351.2 mRNA cleavage and polyadenylation specificity factor complex subunit Pta1 from Schizosaccharomyces pombe (see 2 papers)
SPAC1071.01c mRNA cleavage and polyadenylation specificity factor complex subunit Pta1 from Schizosaccharomyces pombe
Aligns to 86:309 / 670 (33.4%), covers 91.3% of PF11935, 160.2 bits
- function: Component of the cleavage and polyadenylation factor (CPF) complex, which plays a key role in polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factors including the CFIA complex and NAB4/CFIB
subunit: Component of the cleavage and polyadenylation factor (CPF) complex, which is composed of cft1, cft2, ysh1, pta1, swd2, pfs2, dis2, yth1, ssu72, and fip1. - CharProtDB Source (per GeneDB): GeneDB_Spombe
- Bulk Segregant Analysis Reveals the Genetic Basis of a Natural Trait Variation in Fission Yeast
Hu, Genome biology and evolution 2015 - “...at 3-end SPAC3A11.06 mvp1 I 3460318 T TC One boundary of an intron is moved SPAC1071.01c pta1 I 3855790 GT G CDS is extended at 3-end SPAC29E6.03c uso1 I 4407494 T TG An intron becomes part of an exon SPAC29E6.04 b , c nnf1 I 4410191...”
- Molecular details of the CPSF73-CPSF100 C-terminal heterodimer and interaction with Symplekin
Thore, Open biology 2023 - “...(Q12102, 718-859), scPta1 (Q01329, 559-785), scSyc1 (Q08553, 1-188); spYsh1 (O13794, 464-757), spCft2 (O74740, 637-797), spPta1 (Q10222, 445-670); tcCPSF73 (Q6BCB3, 482-762), tcCPSF100 (Q6BCB1, 626-802), tcSympk (A0A7J6XPR2, 573-928); ceCPSF73(Q95PY8, 458-707), ceCPSF100 (O17403, 633-843), ceSympk (O16929, 525-1143); atCPSF73 (Q9C952, 465-693), atCPSF100 (Q9LKF9, 602-739), atSympk (Q9SFZ8, 474-1092); dmCPSF73 (Q9VE51, 464-684),...”
NP_001319093 symplekin from Arabidopsis thaliana
Aligns to 100:327 / 1325 (17.2%), covers 97.8% of PF11935, 149.3 bits
AT5G01400 ESP4 (ENHANCED SILENCING PHENOTYPE 4); binding from Arabidopsis thaliana
Aligns to 96:311 / 1467 (14.7%), covers 86.0% of PF11935, 135.8 bits
- RNA Quality Control as a Key to Suppressing RNA Silencing of Endogenous Genes in Plants
Liu, Molecular plant 2016 - “...3 AT1g32490 RNA splicing ( Herr et al., 2006 ) ESP4 ENHANCED SILENCING PHENOTYPE 4 AT5g01400 3 end processing ( Herr et al., 2006 ) ESP5 ENHANCED SILENCING PHENOTYPE 5 AT5g23880 3 end processing ( Herr et al., 2006 ) SMD1B SM DOMAIN- CONTAINING PROTEIN 1B...”
- Genome-Wide Association Analysis of Adaptation Using Environmentally Predicted Traits
van, PLoS genetics 2015 - “...EMB2770 208 343 694 143 837 213 AT4G15880 ESD4 - - 1028 - - - AT5G01400 ESP4 - - - - - 974 AT1G04400 FHA - 518 888 - - 485 AT2G21070 FIO1 - - - - 868 - AT5G10140 FLC - - - - 671...”
- Plant polyadenylation factors: conservation and variety in the polyadenylation complex in plants
Hunt, BMC genomics 2012 - “...lineage. The coding legend and representation are as described for Figure 1 . Assignment as At5g01400- or At5g27595- like were based on the alignment shown in Additional file 2 : Figure S7. Figure 7 Complement of genes encoding poly(A) polymerases in the plant lineage. The coding...”
- “...both possess single symplekin genes whose protein products resemble the protein encoded by the Arabidopsis AT5g01400 gene (Figure 6 , Additional file 1 : Table S1, Additional file 2 : Figure S7). In flowering plants, there is a second class of symplekin gene, typified by the...”
- In silico analysis of 3'-end-processing signals in Aspergillus oryzae using expressed sequence tags and genomic sequencing data
Tanaka, DNA research : an international journal for rapid publication of reports on genes and genomes 2011 - “...AT5G13480 (AtFY) hPfs2 (WDR33) 1e82 3e89 1e90 AO090103000067 Pta1 AT1G27595 (AtSYM2) Symplekin 3e21 0.085 7e05 AT5G01400 (AtSYM5) None None AT2G01730 (AtCPSF73-II) CPSF73L AO090005001504 Ssu72 AT1G73820 (Ssu72-like) hSsu72 4e48 1e38 3e41 AO090701000351 Glc7 AT2G39840 (AtPP1) PP1 e157 e141 1e154 PP1 1e151 None Ref2 None None AO090001000739 Mpe1...”
- Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling
Hunt, BMC genomics 2008 - “...2e-25 At5g65260 (PABN1) Score = 120 bits (302), Expect = 4e-26 Symplekin/Pta1 Part of CPSF At5g01400 (ESP4, SYM5) Score = 261 bits (666), Expect = 3e-67 At1g27590 (SYM1) Score = 54.3 bits (129), Expect = 3e-05 At1g27595 (SYM2) Score = 241 bits (616), Expect = 1e-61...”
- Defective RNA processing enhances RNA silencing and influences flowering of Arabidopsis
Herr, Proceedings of the National Academy of Sciences of the United States of America 2006 - “...All seven esp4 alleles mapped to a SymplekinPta1 homologue (At5g01400; Fig. 9 A and B, which is published as supporting information on the PNAS web site) that,...”
AT1G27590 hypothetical protein from Arabidopsis thaliana
Aligns to 100:248 / 264 (56.4%), covers 58.5% of PF11935, 90.1 bits
- Natural variation in the plant polyadenylation complex
Zhou, Frontiers in plant science 2023 - “...Specifically, PCFS2 was formed by merging the AT2G36485 and AT2G36480 annotations, and SYM by merging AT1G27590 and AT1G27595. Arabidopsis orthologs of the human RBBP6 were identified using BLASTP with the human RBBP6 as a query; this yielded two possible orthologs (denoted Mpe1 and PQT3 in Table1...”
- Meta-analysis of Arabidopsis thaliana microarray data in relation to heat stress response
Chaddad, Frontiers in plant science 2023 - “...to heat stress. 5.9 Genes of unknown function Several genes, including At4g23493 , At3g17110 , At1g27590 , and At4g17130 , were found to be significantly differentially expressed in this study. However, their specific functions remain unknown, emphasizing the need for further research to elucidate their roles...”
- MLPA-Based Analysis of Copy Number Variation in Plant Populations
Samelak-Czajka, Frontiers in plant science 2017 - “...one mismatch in the right TSS, distant from the ligation site) in the nearby gene AT1G27590 , not copy number variable. As a result, the signal from the mlpaD1 probe was elevated by the background signal from the alternative target site. This background signal was stable...”
- “...results. Probes mlpaD1 and mlpaD2 target the AT1G27570 gene. Additionally, probe mlpaD1 targets also the AT1G27590 gene. (A) 2D intensity plot of relative signal from probes mlpaD1 and mlpaD2; (B) 2D intensity plot of relative signal from probe mlpaD1 corrected for the presence of non-specific hybridization...”
- Arabidopsis mRNA polyadenylation machinery: comprehensive analysis of protein-protein interactions and gene expression profiling
Hunt, BMC genomics 2008 - “...Symplekin/Pta1 Part of CPSF At5g01400 (ESP4, SYM5) Score = 261 bits (666), Expect = 3e-67 At1g27590 (SYM1) Score = 54.3 bits (129), Expect = 3e-05 At1g27595 (SYM2) Score = 241 bits (616), Expect = 1e-61 No obvious homolog CFIm68/59 Unknown none -/Hrp1 Part of cleavage factor...”
- Defective RNA processing enhances RNA silencing and influences flowering of Arabidopsis
Herr, Proceedings of the National Academy of Sciences of the United States of America 2006 - “...At2g35340 At4g16680 ESP1 ESP4 x x x x 5 At1g27590 At1g27595 Actin ESP1 rRNA D AtCstF64 RRM ESP1 hinge PC4/sub1/res1 hinge PC4/sub1/res1 E CstF64 Ce CstF64 Ce...”
- “...+ + + + + + + + + 311 G ESP4 At1g27590 At1g27590 At1g27595 At1g27595 Symplekin Symplekin ESP4 rRNA H Os7g49320 At1g27590 ESP4 At 81 Pta1 Sp 92 94 71 49 40 SPK...”
AT1G27570 phosphatidylinositol 3- and 4-kinase family protein from Arabidopsis thaliana
Aligns to 100:287 / 649 (29.0%), covers 67.2% of PF11935, 77.6 bits
- A Non-redundant Function of MNS5: A Class I α-1, 2 Mannosidase, in the Regulation of Endoplasmic Reticulum-Associated Degradation of Misfolded Glycoproteins
Sun, Frontiers in plant science 2022 - “...Col-0 and Ws-2. An SNP at position chr1-9,576,968 was located in a coding region of AT1G27570 (CDS: G499A, Protein: V167I). But according to the sequence alignment, it was not predicted to be the mutant position because it is not conservative. Another SNP (G343E) was at position...”
- Network Analysis of Gene Transcriptions of Arabidopsis thaliana in Spaceflight Microgravity
Manian, Genes 2021 - “...0.993113 11.98728 0.00689 AT1G03430 AT1G26470 0.98765 8.914699 0.01235 AT1G03430 AT1G27130 AT1G27140 0.998482 25.63509 0.00152 AT1G03430 AT1G27570 0.95498 4.552277 0.04502 AT1G03430 AT1G30360 0.9732 5.985038 0.0268 AT1G03430 AT1G32460 0.4588 0.730233 0.5412 AT1G03430 AT1G34180 0.99271 11.64964 0.00729 AT1G03430 AT1G34844 0.947816 4.204318 0.05218 genes-12-00337-t002_Table 2 Table 2 Hub genes from...”
- MLPA-Based Analysis of Copy Number Variation in Plant Populations
Samelak-Czajka, Frontiers in plant science 2017 - “...and present duplications ( AT4G27080, AT5G09590 , and AT5G61700 ) or duplications and deletions ( AT1G27570, AT1G52950, AT3G21960, AT4G27080 , and AT5G54710 ). Additionally, gene AT5G09590 overlaps CNV only partially, whereas AT1G52950, AT5G54710 , and AT1G27570 are members of multigene families and are localized in the...”
- “...mlpaC 93 nt Chr1:11651708..11651754 AT1G32300 Biallelic b mlpaD1; mlpaD2 105 nt 114 nt Chr1:9575624..9575678 Chr1:9577003..9577055 AT1G27570 Multiallelic b; c mlpaE1; mlpaE2 136 nt 196 nt Chr1:19726669..19726721 Chr1:19727385..19727439 AT1G52950 Multiallelic b; c mlpaF1; mlpaF2 99 nt 120 nt Chr3:7737420..7737467 Chr3:7737872..7737929 AT3G21960 Multiallelic b; c mlpaG1; mlpaG2 128...”
Tsp_00135 hypothetical protein from Trichinella spiralis
Aligns to 109:322 / 1050 (20.4%), covers 96.1% of PF11935, 55.9 bits
Q9SFZ8 T22C5.3 from Arabidopsis thaliana
Aligns to 20:120 / 1092 (9.2%), covers 39.3% of PF11935, 40.5 bits
- Molecular details of the CPSF73-CPSF100 C-terminal heterodimer and interaction with Symplekin
Thore, Open biology 2023 - “...ceCPSF73(Q95PY8, 458-707), ceCPSF100 (O17403, 633-843), ceSympk (O16929, 525-1143); atCPSF73 (Q9C952, 465-693), atCPSF100 (Q9LKF9, 602-739), atSympk (Q9SFZ8, 474-1092); dmCPSF73 (Q9VE51, 464-684), dmCPSF100 (Q9V3D6, 608-756), dmSympk (Q8MSU4, 516-1101); ecCPSF73 (Q8SUE4, 452-643 and 568-643), ecCPSF100 (Q8SRZ4, 525-639), ecSympk (Q8SVB3, 161-385). Full prediction details, along with all structural models, are...”
Or search for genetic data about PF11935 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory