PaperBLAST
PaperBLAST Hits for 62 a.a. (TTNADRRKAA...)
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>62 a.a. (TTNADRRKAA...)
TTNADRRKAATMRERRRLSKVNEAFETLKRSTSSNPNQRLPKVEILRNAIRYIEGLQALL
RD
Running BLASTp...
Found 76 similar proteins in the literature:
1mdyA / P10085 Crystal structure of myod bhlh domain bound to dna: perspectives on DNA recognition and implications for transcriptional activation (see paper)
100% identity, 91% coverage
P21572 Myoblast determination protein 1 homolog from Coturnix japonica
94% identity, 21% coverage
P16075 Myoblast determination protein 1 homolog from Gallus gallus
94% identity, 21% coverage
NP_989545 myoblast determination protein 1 homolog from Gallus gallus
94% identity, 21% coverage
NP_788268 myoblast determination protein 1 from Rattus norvegicus
98% identity, 19% coverage
- Long non-coding RNA MALAT1 promotes cardiac remodeling in hypertensive rats by inhibiting the transcription of MyoD.
Li, Aging 2019 - GeneRIF: Long non-coding RNA MALAT1 promotes cardiac remodeling in hypertensive rats by inhibiting the transcription of MyoD.
- Comparative effects of low-level laser therapy pre- and post-injury on mRNA expression of MyoD, myogenin, and IL-6 during the skeletal muscle repair.
Alves, Lasers in medical science 2016 (PubMed)- GeneRIF: low-level laser therapy (LLLT) administered following muscle injury modulates the mRNA expression of MyoD and myogenin. Moreover, the both forms of LLLT administration were able to modulate the mRNA expression of IL-6 during the muscle repair process.
- Modulation of satellite cells activity and MyoD in rat thyroarytenoid muscle after reinnervation.
Kodama, The Laryngoscope 2015 (PubMed)- GeneRIF: NMJ formation following reinnervation might prompt recovery of M-cadherin and MyoD mRNA expression to the quiescent level of SCs
- The role of primary myogenic regulatory factors in the developing diaphragmatic muscle in the nitrofen-induced diaphragmatic hernia.
Dingemann, Pediatric surgery international 2011 (PubMed)- GeneRIF: MyoD expression is selectively decreased in the diaphragm muscle in the nitrofen model of CDH.
- Acute exhaustive exercise regulates IL-2, IL-4 and MyoD in skeletal muscle but not adipose tissue in rats.
Rosa, Lipids in health and disease 2011 - GeneRIF: The purpose of this study was to evaluate the effect of exhaustive exercise on proteins associated with muscle damage and regeneration, including IL-2, IL-4 and MyoD in muscle and adipose tissue.
- Magnesium deficiency up-regulates Myod expression in rat skeletal muscle and C2C12 myogenic cells.
Furutani, Cell biochemistry and function 2011 (PubMed)- GeneRIF: Expression of Myod and myogenin is increased in skeletal muscle of rats fed magnesium-deficient diet.
- S100B protein in myoblasts modulates myogenic differentiation via NF-kappaB-dependent inhibition of MyoD expression.
Tubaro, Journal of cellular physiology 2010 (PubMed)- GeneRIF: Intracellular S100B might modulate myoblast differentiation by interfering with MyoD expression in an NF-kappaB-dependent manner.
- Transcriptional regulation of selenoprotein W by MyoD during early skeletal muscle differentiation.
Noh, The Journal of biological chemistry 2010 - GeneRIF: SelW gene was activated by the binding of MyoD to a specific E-box during early skeletal muscle differentiation.
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MYOD1_MOUSE / P10085 Myoblast determination protein 1 from Mus musculus (Mouse) (see 10 papers)
NP_034996 myoblast determination protein 1 from Mus musculus
98% identity, 19% coverage
- function: Acts as a transcriptional activator that promotes transcription of muscle-specific target genes and plays a role in muscle differentiation (PubMed:16901893). Together with MYF5 and MYOG, co-occupies muscle-specific gene promoter core region during myogenesis. Induces fibroblasts to differentiate into myoblasts. Interacts with and is inhibited by the twist protein. This interaction probably involves the basic domains of both proteins (PubMed:21798092, PubMed:3175662).
subunit: Interacts with SUV39H1 (By similarity). Efficient DNA binding requires dimerization with another bHLH protein. Seems to form active heterodimers with ITF-2. Interacts with DDX5. Interacts with CHD2. Interacts with TSC22D3 isoform 1 and isoform 4. Interacts with SETD3 (PubMed:21832073). Interacts with P-TEFB complex; promotes the transcriptional activity of MYOD1 through its CDK9-mediated phosphorylation (PubMed:12037670). Interacts with CSRP3 (By similarity). Interacts with NUPR1 (PubMed:19723804). - MyoD-Induced Trans-Differentiation: A Paradigm for Dissecting the Molecular Mechanisms of Cell Commitment, Differentiation and Reprogramming.
Battistelli, Cells 2022 - “...in the regulatory regions of target genes [ 36 ]. The MyoD protein (UniProt codes P10085 and P15172 for mouse and human proteins, respectively) contains a basic domain, involved in DNA binding, which is a HLH domain involved in dimerization with other HLH proteins, and two...”
- Differentiated evolutionary relationships among chordates from comparative alignments of multiple sequences of MyoD and MyoG myogenic regulatory factors
Oliani, Genetics and molecular research : GMR 2015 (PubMed)- “...relationships among chordates. Protein sequences from Mus musculus (P10085 and P12979), human Homo sapiens (P15172 and P15173), bovine Bos taurus (Q7YS82 and...”
- “...were selected from nine specimens: mouse Mus musculus (P10085 and P12979), human Homo sapiens (P15172 and P15173), bovine Bos taurus (Q7YS82 and Q7YS81), wild...”
- Reprogramming cells with synthetic proteins.
Yang, Asian journal of andrology 2015 - “...DNA binding and C-terminal region. The alignment was performed using sequences derived from Uniprot: MyoD P10085; E12:P15806; Sox2:P48432; Sox17:Q61473. Oct4: octamer binding protein 4. Turning Sox17 into a pluripotency inducer Our laboratory has made efforts to scrutinize the mechanism how proteins of the 20-member Sox family...”
- Cardiolipin metabolism regulates expression of muscle transcription factor MyoD1 and muscle development.
Vo, The Journal of biological chemistry 2023 - GeneRIF: Cardiolipin metabolism regulates expression of muscle transcription factor MyoD1 and muscle development.
- Palmitic Acid Inhibits Myogenic Activity and Expression of Myosin Heavy Chain MHC IIb in Muscle Cells through Phosphorylation-Dependent MyoD Inactivation.
Matsuba, International journal of molecular sciences 2023 - GeneRIF: Palmitic Acid Inhibits Myogenic Activity and Expression of Myosin Heavy Chain MHC IIb in Muscle Cells through Phosphorylation-Dependent MyoD Inactivation.
- IL-4 Signaling Promotes Myoblast Differentiation and Fusion by Enhancing the Expression of MyoD, Myogenin, and Myomerger.
Kurosaka, Cells 2023 - GeneRIF: IL-4 Signaling Promotes Myoblast Differentiation and Fusion by Enhancing the Expression of MyoD, Myogenin, and Myomerger.
- Foxo3 Knockdown Mediates Decline of Myod1 and Myog Reducing Myoblast Conversion to Myotubes.
Gellhaus, Cells 2023 - GeneRIF: Foxo3 Knockdown Mediates Decline of Myod1 and Myog Reducing Myoblast Conversion to Myotubes.
- Nonsense-mediated mRNA decay suppresses injury-induced muscle regeneration via inhibiting MyoD transcriptional activity.
Tan, Journal of cellular physiology 2023 (PubMed)- GeneRIF: Nonsense-mediated mRNA decay suppresses injury-induced muscle regeneration via inhibiting MyoD transcriptional activity.
- MyoD is a 3D genome structure organizer for muscle cell identity.
Wang, Nature communications 2022 - GeneRIF: MyoD is a 3D genome structure organizer for muscle cell identity.
- Enhanced growth and myogenic differentiation of spheroid-derived C2C12 cells.
Jin, Bioscience, biotechnology, and biochemistry 2021 (PubMed)- GeneRIF: Enhanced growth and myogenic differentiation of spheroid-derived C2C12 cells.
- Myod1 and GR coordinate myofiber-specific transcriptional enhancers.
Rovito, Nucleic acids research 2021 - GeneRIF: Myod1 and GR coordinate myofiber-specific transcriptional enhancers.
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MYOD1_RAT / Q02346 Myoblast determination protein 1 from Rattus norvegicus (Rat) (see paper)
98% identity, 19% coverage
- function: Acts as a transcriptional activator that promotes transcription of muscle-specific target genes and plays a role in muscle differentiation. Together with MYF5 and MYOG, co-occupies muscle-specific gene promoter core region during myogenesis. Induces fibroblasts to differentiate into myoblasts. Interacts with and is inhibited by the twist protein. This interaction probably involves the basic domains of both proteins (By similarity).
subunit: Efficient DNA binding requires dimerization with another bHLH protein. Seems to form active heterodimers with ITF-2. Interacts with SUV39H1. Interacts with DDX5. Interacts with CHD2. Interacts with TSC22D3 (By similarity). Interacts with SETD3 (By similarity). Interacts with P-TEFB complex; promotes the transcriptional activity of MYOD1 through its CDK9-mediated phosphorylation (By similarity). Interacts with CSRP3 (PubMed:9234731). Interacts with NUPR1 (By similarity). - Differentiated evolutionary relationships among chordates from comparative alignments of multiple sequences of MyoD and MyoG myogenic regulatory factors
Oliani, Genetics and molecular research : GMR 2015 (PubMed)- “...Gallus gallus (P16075 and P17920), rat Rattus norvegicus (Q02346 and P20428), domestic water buffalo Bubalus bubalis (D2SP11 and A7L034), and sheep Ovis aries...”
NP_001002824 myoblast determination protein 1 from Sus scrofa
P49811 Myoblast determination protein 1 from Sus scrofa
98% identity, 19% coverage
- MYOD induced lnc-MEG3 promotes porcine satellite cell differentiation via interacting with DLST.
Liu, Epigenetics 2023 - GeneRIF: MYOD induced lnc-MEG3 promotes porcine satellite cell differentiation via interacting with DLST.
- Tributyrin, a Butyrate Pro-Drug, Primes Satellite Cells for Differentiation by Altering the Epigenetic Landscape.
Murray, Cells 2021 - GeneRIF: Tributyrin, a Butyrate Pro-Drug, Primes Satellite Cells for Differentiation by Altering the Epigenetic Landscape.
- Long Non-Coding RNA H19 Promotes Porcine Satellite Cell Differentiation by Interacting with TDP43.
Li, Genes 2020 - GeneRIF: Long Non-Coding RNA H19 Promotes Porcine Satellite Cell Differentiation by Interacting with TDP43.
- MyoD promotes porcine PPARγ gene expression through an E-box and a MyoD-binding site in the PPARγ promoter region.
Deng, Cell and tissue research 2016 (PubMed)- GeneRIF: an Enhancer box and a binding site for a cooperative co-activator of MyoD are present in the promoter region of porcine PPARgamma.
- PPARγ and MyoD are differentially regulated by myostatin in adipose-derived stem cells and muscle satellite cells.
Zhang, Biochemical and biophysical research communications 2015 (PubMed)- GeneRIF: Therefore, this study demonstrated that the different regulatory adipogenic roles of MSTN in ADSCs and MSCs act by differentially regulating PPARgamma and MyoD expression.
- Expression and variation of Myf5 and MyoD1 genes in different tissues of Wuzhishan pigs.
Hou, Genetics and molecular research : GMR 2015 (PubMed)- GeneRIF: Of the eight adult pig tissue types that were tested, the expression of Myf5 and MyoD1 was highest in the muscle tissue.
- Promoter polymorphisms in genes involved in porcine myogenesis influence their transcriptional activity.
Bongiorni, BMC genetics 2014 - GeneRIF: Single nucleotide polymorphisms in the MYOD1 and GDF8 genes are associated with genetic transcription during myogenesis in pigs.
- Effects of variation in porcine MYOD1 gene on muscle fiber characteristics, lean meat production, and meat quality traits.
Lee, Meat science 2012 (PubMed)- GeneRIF: Therefore, the g.489C>T and g.1264C>A SNPs in MYOD1 may be meaningful DNA markers that can be used for improving important porcine economic traits.
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- Differentiated evolutionary relationships among chordates from comparative alignments of multiple sequences of MyoD and MyoG myogenic regulatory factors
Oliani, Genetics and molecular research : GMR 2015 (PubMed)- “...taurus (Q7YS82 and Q7YS81), wild pig Sus scrofa (P49811 and P49812), quail Coturnix coturnix (P21572 and P34060), chicken Gallus gallus (P16075 and P17920), rat...”
- “...taurus (Q7YS82 and Q7YS81), wild pig Sus scrofa (P49811 and P49812), japanese quail Coturnix coturnix (P21572 and P34060), chicken Gallus gallus (P16075 and...”
NP_001079366 myoblast determination protein 1 homolog A from Xenopus laevis
92% identity, 21% coverage
Q7YS82 Myoblast determination protein 1 from Bos taurus
98% identity, 19% coverage
MYOD1_HUMAN / P15172 Myoblast determination protein 1; Class C basic helix-loop-helix protein 1; bHLHc1; Myogenic factor 3; Myf-3 from Homo sapiens (Human) (see 8 papers)
NP_002469 myoblast determination protein 1 from Homo sapiens
98% identity, 19% coverage
- function: Acts as a transcriptional activator that promotes transcription of muscle-specific target genes and plays a role in muscle differentiation. Together with MYF5 and MYOG, co-occupies muscle-specific gene promoter core region during myogenesis. Induces fibroblasts to differentiate into myoblasts. Interacts with and is inhibited by the twist protein. This interaction probably involves the basic domains of both proteins (By similarity).
subunit: Efficient DNA binding requires dimerization with another bHLH protein. Seems to form active heterodimers with ITF-2. Interacts with SUV39H1. Interacts with DDX5. Interacts with CHD2. Interacts with TSC22D3 (By similarity). Interacts with SETD3 (By similarity). Interacts with P-TEFB complex; promotes the transcriptional activity of MYOD1 through its CDK9-mediated phosphorylation (By similarity) (PubMed:12037670). Interacts with CSRP3. Interacts with NUPR1 (By similarity). - Automatic Text-Mining Approach to Identify Molecular Target Candidates Associated with Metabolic Processes for Myotonic Dystrophy Type 1
Kuntawala, International journal of environmental research and public health 2023 - “...regulation of DNA replication - A potential target for lung cancer. 45 [ 62 ] P15172 MYOD1 Myoblast determination protein 1 Muscle organ development, positive regulation of muscle cell differentiation, protein phosphorylation - Encodes a nuclear protein and is known to be involved in muscle regeneration...”
- MyoD-Induced Trans-Differentiation: A Paradigm for Dissecting the Molecular Mechanisms of Cell Commitment, Differentiation and Reprogramming.
Battistelli, Cells 2022 - “...regulatory regions of target genes [ 36 ]. The MyoD protein (UniProt codes P10085 and P15172 for mouse and human proteins, respectively) contains a basic domain, involved in DNA binding, which is a HLH domain involved in dimerization with other HLH proteins, and two less conserved...”
- Characterising the efficacy and bioavailability of bioactive peptides identified for attenuating muscle atrophy within a Vicia faba-derived functional ingredient.
Corrochano, Current research in food science 2021 - “...mTOR Human P62753 RS6 40S ribosomal protein S6 Human P31749 AKT1 RAC-alpha serine/threonine-protein kinase Human P15172 MYOD1 Myoblast determination protein 1 Human P13349 MYF5 Myogenic factor 5 Human P15173 MYOG Myogenin Human P23760 PAX3 Paired box protein Pax-3 Human P23759 PAX7 Paired box protein Pax-7 Human...”
- Critical review of non-histone human substrates of metal-dependent lysine deacetylases.
Toro, FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2020 - “...Substrate (Uniprot ID) Ac site KDAC (approach ) ACLY (P53396) K540 KDAC8 (i) 89 MYOD1 (P15172) n.d. KDAC1 (i) 117 ADAP1 (O75689) K272 KDAC6 (i) 88 , KDAC8 (i) 88 MAML1 (Q92585) K188 KDAC8 (c) 83 AIF1 (P55008) K11 KDAC8 (i) 90 MEF2D (Q14814) n.d. KDAC3...”
- Differentiated evolutionary relationships among chordates from comparative alignments of multiple sequences of MyoD and MyoG myogenic regulatory factors
Oliani, Genetics and molecular research : GMR 2015 (PubMed)- “...from Mus musculus (P10085 and P12979), human Homo sapiens (P15172 and P15173), bovine Bos taurus (Q7YS82 and Q7YS81), wild pig Sus scrofa (P49811 and P49812),...”
- “...mouse Mus musculus (P10085 and P12979), human Homo sapiens (P15172 and P15173), bovine Bos taurus (Q7YS82 and Q7YS81), wild pig Sus scrofa (P49811 and P49812),...”
- Interhelical loops within the bHLH domain are determinant in maintaining TWIST1-DNA complexes
Bouard, Journal of biomolecular structure & dynamics 2014 - “...(Q15672), TWIST2 (Q8WVJ9), E12 (P15923-1), HAND1 (O906004) HAND2 (P61296), NEUROD1 (Q13562), E47 (P15923-2), and MYOD1 (P15172) were downloaded from the UniProtKB/Swiss-Prot website. The mouse NEUROD1 and E47 sequences were obtained from the 2ql2 PDB files. Primary sequences, restricted to the bHLH domains, were aligned with the...”
- Structural basis for LMO2-driven recruitment of the SCL:E47bHLH heterodimer to hematopoietic-specific transcriptional targets
El, Cell reports 2013 - “...gray, dark gray, and red, respectively. UniProtKB sequence accession numbers are P17542 (SCL), Q13562 (NEUROD1), P15172 (MYOD1), P12980 (LYL1), Q16559 (TAL2), Q02575 (HEN1), Q02577 (HEN2), P15884 (E2-2), Q99081 (HEB), and P15923 (E12 and E47). PDB accession numbers are 2YPB (SCL and E47), 2QL2 (NeuroD1), and 1MDY...”
- Prioritizing disease candidate proteins in cardiomyopathy-specific protein-protein interaction networks based on "guilt by association" analysis.
Li, PloS one 2013 - “...23 6317707.232 MYBPC2 Q14324 24 4820328.071 CAV3 P56539 25 3746694.232 DCM [47] , [48] MYOD1 P15172 26 2449472.494 cardiomyopathy [78] CALM1 P62158 27 2291170.029 DCM [45] ACTB P60709 28 2039574.700 MYOG P15173 29 1304602.403 DNAH8 Q96JB1 30 1247401.222 CKM P06732 31 1139350.347 DCM [49] CAPN3 P20807...”
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- MyoD1 promotes the transcription of BIK and plays an apoptosis-promoting role in the development of gastric cancer.
Wu, Cell cycle (Georgetown, Tex.) 2024 - GeneRIF: MyoD1 promotes the transcription of BIK and plays an apoptosis-promoting role in the development of gastric cancer.
- MYOD-SKP2 axis boosts tumorigenesis in fusion negative rhabdomyosarcoma by preventing differentiation through p57Kip2 targeting.
Pomella, Nature communications 2023 - GeneRIF: MYOD-SKP2 axis boosts tumorigenesis in fusion negative rhabdomyosarcoma by preventing differentiation through p57[Kip2] targeting.
- Functional impact and targetability of PI3KCA, GNAS, and PTEN mutations in a spindle cell rhabdomyosarcoma with MYOD1 L122R mutation.
Choo, Cold Spring Harbor molecular case studies 2022 - GeneRIF: Functional impact and targetability of PI3KCA, GNAS, and PTEN mutations in a spindle cell rhabdomyosarcoma with MYOD1 L122R mutation.
- Interaction between SNAI2 and MYOD enhances oncogenesis and suppresses differentiation in Fusion Negative Rhabdomyosarcoma.
Pomella, Nature communications 2021 - GeneRIF: Interaction between SNAI2 and MYOD enhances oncogenesis and suppresses differentiation in Fusion Negative Rhabdomyosarcoma.
- The nuclear import of the transcription factor MyoD is reduced in mesenchymal stem cells grown in a 3D micro-engineered niche.
Jacchetti, Scientific reports 2021 - GeneRIF: The nuclear import of the transcription factor MyoD is reduced in mesenchymal stem cells grown in a 3D micro-engineered niche.
- MYOD1 as a prognostic indicator in rhabdomyosarcoma.
Ahmed, Pediatric blood & cancer 2021 - GeneRIF: MYOD1 as a prognostic indicator in rhabdomyosarcoma.
- MyoD1 suppresses cell migration and invasion by inhibiting FUT4 transcription in human gastric cancer cells.
Wu, Cancer gene therapy 2020 - GeneRIF: MyoD1 suppresses cell migration and invasion by inhibiting FUT4 transcription in human gastric cancer cells.
- CASZ1 induces skeletal muscle and rhabdomyosarcoma differentiation through a feed-forward loop with MYOD and MYOG.
Liu, Nature communications 2020 - GeneRIF: CASZ1 up-regulates MYOD signature genes and induces skeletal muscle differentiation in normal myoblasts and Embryonal rhabdomyosarcoma.
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D2SP11 Myogenic factor from Bubalus bubalis
98% identity, 19% coverage
NP_001035568 myoblast determination protein 1 from Bos taurus
98% identity, 19% coverage
MYOD1_DANRE / Q90477 Myoblast determination protein 1 homolog; Myogenic factor 1 from Danio rerio (Zebrafish) (Brachydanio rerio) (see 2 papers)
NP_571337 myoblast determination protein 1 homolog from Danio rerio
92% identity, 22% coverage
XP_021155627 myoblast determination protein 1 from Columba livia
94% identity, 21% coverage
NP_988972 myoblast determination protein 1 from Xenopus tropicalis
93% identity, 21% coverage
MYOD1_TAKRU / Q6Q2A8 Myoblast determination protein 1 homolog; Myogenic factor 1; TmyoD1 from Takifugu rubripes (Japanese pufferfish) (Fugu rubripes) (see paper)
89% identity, 20% coverage
- function: May act as a transcriptional activator that promotes transcription of muscle-specific target genes and plays a role in muscle differentiation.
subunit: Efficient DNA binding requires dimerization with another bHLH protein.
MYF5_MOUSE / P24699 Myogenic factor 5; Myf-5 from Mus musculus (Mouse) (see paper)
NP_032682 myogenic factor 5 from Mus musculus
82% identity, 24% coverage
- function: Acts as a transcriptional activator that promotes transcription of muscle-specific target genes and plays a role in muscle differentiation. Together with MYOG and MYOD1, co-occupies muscle-specific gene promoter core region during myogenesis. Induces fibroblasts to differentiate into myoblasts. Probable sequence specific DNA-binding protein.
subunit: Efficient DNA binding requires dimerization with another bHLH protein - A dual-color PAX7 and MYF5 in vivo reporter to investigate muscle stem cell heterogeneity in regeneration and aging.
Ancel, Stem cell reports 2024 - GeneRIF: A dual-color PAX7 and MYF5 in vivo reporter to investigate muscle stem cell heterogeneity in regeneration and aging.
- PUFA Treatment Affects C2C12 Myocyte Differentiation, Myogenesis Related Genes and Energy Metabolism.
Risha, Genes 2021 - GeneRIF: PUFA Treatment Affects C2C12 Myocyte Differentiation, Myogenesis Related Genes and Energy Metabolism.
- Dnmt3b Deficiency in Myf5+-Brown Fat Precursor Cells Promotes Obesity in Female Mice.
Wang, Biomolecules 2021 - GeneRIF: Dnmt3b Deficiency in Myf5(+)-Brown Fat Precursor Cells Promotes Obesity in Female Mice.
- MLL1 promotes myogenesis by epigenetically regulating Myf5.
Cai, Cell proliferation 2020 - GeneRIF: MLL1 facilitates proliferation of myoblasts and Pax7-positive satellite cells by epigenetically regulating Myf5.
- Loss of MyoD and Myf5 in Skeletal Muscle Stem Cells Results in Altered Myogenic Programming and Failed Regeneration.
Yamamoto, Stem cell reports 2018 - GeneRIF: An absolute requirement for either MyoD or Myf5 in muscle regeneration.
- The Dystrophin Glycoprotein Complex Regulates the Epigenetic Activation of Muscle Stem Cell Commitment.
Chang, Cell stem cell 2018 - GeneRIF: Asymmetrically dividing muscle stem cells in skeletal muscle give rise to committed cells, where the myogenic determination factor Myf5 is transcriptionally activated by Pax7.
- STAT3 suppresses Wnt/β-catenin signaling during the induction phase of primary Myf5+ brown adipogenesis.
Cantwell, Cytokine 2018 - GeneRIF: The induction phase of primary Myf5+ brown adipogenesis.
- Myf5 and Myogenin in the development of thymic myoid cells - Implications for a murine in vivo model of myasthenia gravis.
Hu, Experimental neurology 2016 (PubMed)- GeneRIF: The Myf5- and Myogenin-deficient mice showed a partial or complete, respectively, loss of TMC in an otherwise regularly structured thymus.
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NP_001100253 myogenic factor 5 from Rattus norvegicus
82% identity, 24% coverage
MYF5_HUMAN / P13349 Myogenic factor 5; Myf-5; Class C basic helix-loop-helix protein 2; bHLHc2 from Homo sapiens (Human) (see 2 papers)
NP_005584 myogenic factor 5 from Homo sapiens
82% identity, 24% coverage
- function: Transcriptional activator that promotes transcription of muscle-specific target genes and plays a role in muscle differentiation (PubMed:29887215). Together with MYOG and MYOD1, co-occupies muscle- specific gene promoter core region during myogenesis. Induces fibroblasts to differentiate into myoblasts. Probable sequence specific DNA-binding protein.
subunit: Efficient DNA binding requires dimerization with another bHLH protein. - Identification of a Novel Frameshift Variant in MYF5 Leading to External Ophthalmoplegia with Rib and Vertebral Anomalies.
Ocieczek, Genes 2024 - GeneRIF: Identification of a Novel Frameshift Variant in MYF5 Leading to External Ophthalmoplegia with Rib and Vertebral Anomalies.
- SNAIL is a key regulator of alveolar rhabdomyosarcoma tumor growth and differentiation through repression of MYF5 and MYOD function.
Skrzypek, Cell death & disease 2018 - GeneRIF: SNAIL silencing allows the re-expression of MYF5 and canonical MYOD binding, promoting alveolar rhabdomyosarcoma cell myogenic differentiation.
- Recessive MYF5 Mutations Cause External Ophthalmoplegia, Rib, and Vertebral Anomalies.
Di, American journal of human genetics 2018 - GeneRIF: The direct role of MYF5 in rib, spine, and extraocular muscle formation in humans.
- Myogenic regulatory transcription factors regulate growth in rhabdomyosarcoma.
Tenente, eLife 2017 - GeneRIF: Analysis of human rhabdomyosarcoma revealed that MYF5 and MYOD are mutually-exclusively expressed and each is required for sustained tumor growth.
- Pitx2c is reactivated in the failing myocardium and stimulates myf5 expression in cultured cardiomyocytes.
Torrado, PloS one 2014 - GeneRIF: Pitx2c expression is reactivated, while expression of Myf5 is downregulated in human systolic heart failure as determined by qRT-PCR and Western blot analyses.
- Efficient in vitro myogenic reprogramming of human primary mesenchymal stem cells and endothelial cells by Myf5.
Dimicoli-Salazar, Biology of the cell 2011 (PubMed)- GeneRIF: results are the first demonstration of a myogenic conversion of human mesenchymal and endothelial cells by Myf5
- Altered binding of MYF-5 to FOXE1 promoter in non-syndromic and CHARGE-associated cleft palate.
Venza, Journal of oral pathology & medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology 2009 (PubMed)- GeneRIF: A novel homozygous polymorphism that prevented the binding of MYF-5 to FOXE1 promoter and affected the FOXE1 expression was found in 45% nonsyndromic cleft palate.
- High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men.
Yerges, Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2009 - GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
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- Characterising the efficacy and bioavailability of bioactive peptides identified for attenuating muscle atrophy within a Vicia faba-derived functional ingredient.
Corrochano, Current research in food science 2021 - “...S6 Human P31749 AKT1 RAC-alpha serine/threonine-protein kinase Human P15172 MYOD1 Myoblast determination protein 1 Human P13349 MYF5 Myogenic factor 5 Human P15173 MYOG Myogenin Human P23760 PAX3 Paired box protein Pax-3 Human P23759 PAX7 Paired box protein Pax-7 Human Q06413 MEF2C Myocyte-specific enhancer factor 2C Human...”
- Phylogenetic analysis of the human basic helix-loop-helix proteins
Ledent, Genome biology 2002 - “...Myogenin NT_004662.3 1q31-41 P23409 Myf6 MyoD Myf6 NT_024473.2 12q21 P15172 Myf3 MyoD MyoD NT_009307.3 11p15.4 P13349 Myf5 MyoD Myf5 NT_024473.2 12q21 N011269 E2A * E12/E47 E2A NT_011269.3 19p13.3 Q99081 TF12 E12/E47 TF12 NT_010289.3 15q21 P15884 TCF4 E12/E47 TCF4 NT_011059.5 18q21.1 P15884 D TCF4b * E12/E47 TCF4...”
- “...sp|CAC37689 Myogenin MyoD P15173 sp|P12979 Myf6 MyoD P23409 ref|NP_032683.1 MyoD MyoD P15172 sp|P10085 Myf5 MyoD P13349 ref|NP_032682.1 E2A E12/E47 N011269 sp|15806 TF12 E12/E47 Q99081 ref|NP_035674.1 TCF4 E12/E47 P15884/P15884 D ref|NP_038713.1 KA1 E12/E47 ? dbj|BAA06218.1 Math1 Atonal Q92858 dbj|BAA07791.1 Math5 Atonal N024033 gb|AAC68868.1 Mist1 Mist N007757 gb|AAF17706.1...”
NP_001025534 myogenic factor 5 from Gallus gallus
82% identity, 24% coverage
P17667 Myogenic factor 5 from Bos taurus
81% identity, 24% coverage
NP_001265704 myogenic factor 5 from Sus scrofa
82% identity, 24% coverage
NP_001095249 myogenic factor 5 from Xenopus laevis
P24700 Myogenic factor 5 from Xenopus laevis
79% identity, 24% coverage
NP_988932 myogenic factor 5 from Xenopus tropicalis
77% identity, 24% coverage
NP_001163702 nautilus, isoform B from Drosophila melanogaster
84% identity, 18% coverage
7z5iA / P13349 Transcription factor myf5 bound to symmetrical site
89% identity, 85% coverage
LOC118407176 transcription factor SUM-1-like from Branchiostoma floridae
84% identity, 22% coverage
LOC109480322 transcription factor SUM-1-like from Branchiostoma belcheri
79% identity, 24% coverage
NP_571651 myogenic factor 5 from Danio rerio
75% identity, 26% coverage
- Fgf-driven Tbx protein activities directly induce myf5 and myod to initiate zebrafish myogenesis.
Osborn, Development (Cambridge, England) 2020 - GeneRIF: Fgf-driven Tbx protein activities directly induce myf5 and myod to initiate zebrafish myogenesis.
- Normal function of Myf5 during gastrulation is required for pharyngeal arch cartilage development in zebrafish embryos.
Lin, Zebrafish 2013 - GeneRIF: Loss of Myf5 function results in a cascade effect that begins with abnormal formation of the dorsal organizer during gastrulation, causing defects in myf5-knockdown embryos
- Zebrafish Dkk3a protein regulates the activity of myf5 promoter through interaction with membrane receptor integrin α6b.
Fu, The Journal of biological chemistry 2012 - GeneRIF: the secreted ligand Dkk3a binds to the membrane receptor Itgalpha6b, which increases the protein level of phosphorylated p38a and activates myf5 promoter activity of zebrafish embryos during myogenesis.
- Novel intronic microRNA represses zebrafish myf5 promoter activity through silencing dickkopf-3 gene.
Hsu, Nucleic acids research 2010 - GeneRIF: a novel intronic microRNA, miR-In300, which is derived from I300 of the first intron of zebrafish myf5, enables significant repression of myf5 promoter activity through silencing the long isoform of the Dickkopfs-3 gene.
- Multiple upstream modules regulate zebrafish myf5 expression.
Chen, BMC developmental biology 2007 - GeneRIF: cell lineage-specific expression of myf5 is delicately orchestrated by multiple modules within the distal upstream region. This study provides an insight to understand the molecular control of myf5 and myogenesis in the zebrafish.
- Foxd3 mediates zebrafish myf5 expression during early somitogenesis.
Lee, Developmental biology 2006 (PubMed)- GeneRIF: Foxd3, a well-known regulator in neural crest development, is also involved in myf5 regulation
- Myogenic regulatory factors Myf5 and Myod function distinctly during craniofacial myogenesis of zebrafish.
Lin, Developmental biology 2006 (PubMed)- GeneRIF: Myf5 and Myod function independently during cranial myogenesis.
- Novel cis-element in intron 1 represses somite expression of zebrafish myf-5.
Lin, Gene 2004 (PubMed)- GeneRIF: Functional analysis of intron 1 showed a strong, negative, cis-regulatory element located at +502/+835, and this is the first study to identify a novel, cis-acting silencer that is crucial to negatively regulating myf-5 expression.
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Smp_167400 myogenic factor, putative from Schistosoma mansoni
75% identity, 7% coverage
- A single-cell atlas of the miracidium larva of Schistosoma mansoni reveals cell types, developmental pathways, and tissue architecture
Attenborough, eLife 2024 - “...markers for muscle 2 cluster; a calcium-activated potassium channel (Smp_156150) and the transcription factor myoD (Smp_167400) show co-expression in longitudinal BWMs (arrowheads). In 100% of individuals examined, n = 30. Scale shown in B also applies to C, Di, E, and Fi. Figure 2video 1. Confocal...”
- “...situ hybridisation (WISH) of muscle cluster 2 markers calcium-activated potassium channel (Smp_156150) (cyan) and myoD (Smp_167400) (magenta), counterstained with phalloidin (green) and DAPI (white) shows expression in longitudinal body wall muscles. Scale bar = 10 m. Muscle cluster 1 (2407 cells) was distinguished from muscle cluster...”
- A single-cell atlas of the miracidium larva of the human blood flukeSchistosoma mansoni: cell types, developmental pathways and tissue architecture
Attenborough, 2023 - Single-cell deconstruction of stem-cell-driven schistosome development
Nanes, Trends in parasitology 2021 - “...(Smp_024860) klf (Smp_172480) p53 (Smp_139530) nanos-2 (Smp_051920) zfp-1 (Smp_145470) somatic stem cells cabp (Smp_340130) myoD (Smp_167400) early muscle progenitors troponin + () cabp (Smp_340130) myoD (Smp_167400) tcf15 (Smp_015670) troponin (Smp_018250) late muscle progenitors tsp2 + tsp2 (Smp_335630) tegumental progenitors cpx + 7b2 (Smp_073270) cpx (Smp_050220) neural...”
- Single-cell atlas of the first intra-mammalian developmental stage of the human parasite Schistosoma mansoni
Diaz, Nature communications 2020 - “...MIP; right: single magnified confocal sections of the dotted box. h Double FISH of myoD (Smp_167400) and troponin (Smp_018250) in adult soma, MIP. i , j Spatial distribution of actin-2 (Smp_307020) throughout the body of the parasite. i schistosomulum, MIP; j adult male, MIP. k Schematic...”
- “...Methods and Supplementary Data 7 . In a second muscle-like cluster (788 cells), an orthologue (Smp_167400) of the myoD transcription factor from S. mediterranea (dd_Smed_v6_12634_0_1) 32 was uniquely expressed (Fig. 2a ). In addition, expression of rhodopsin GPCR (Smp_153210) was enriched in this myoD + cluster...”
Q91154 Myogenic factor 5 from Notophthalmus viridescens
79% identity, 24% coverage
- Expression of myogenic regulatory factors in the muscle-derived electric organ of Sternopygus macrurus.
Kim, The Journal of experimental biology 2008 - “...(accession number AF463525_1), carp (accession number BAA33566.1), chicken (accession number S41126), red-spotted newt (accession number Q91154), Xenopus tropicalis (accession number AAL11024.1), Xenopus laevis (accession number P24700) and cow (accession number P17667). MRF4 primers corresponding to the SSGDEHVLA (sense primer) and the HWKKTCNTW (antisense primer) domains were...”
MYOD_DROME / P22816 Myogenic-determination protein; Protein nautilus; dMyd from Drosophila melanogaster (Fruit fly) (see 2 papers)
79% identity, 19% coverage
- function: May play an important role in the early development of muscle.
subunit: Efficient DNA binding requires dimerization with another bHLH protein
NP_001012406 myogenin from Sus scrofa
77% identity, 27% coverage
- Effects of MicroRNA-27a on Myogenin Expression and Akt/FoxO1 Signal Pathway during Porcine Myoblast Differentiation.
Zhang, Animal biotechnology 2018 (PubMed)- GeneRIF: Studied the effects of microRNA-27a on myogenin expression and the Akt/FoxO1 signal pathway during porcine myoblast differentiation. Overexpression of miR-27a suppressed myogenin expression during porcine myoblast differentiation, whereas inhibition of miR-27a promoted the mRNA and protein expression levels of myogenin; overexpression of miR-27a decreased the level of P-Akt/Akt and increased the protein level of FoxO1.
- The phylogeny analysis of MyoG gene in different pig breeds.
Zhu, Interdisciplinary sciences, computational life sciences 2010 (PubMed)- GeneRIF: the MyoG gene is very conservative and there are very few mutation sites between different breeds
- Uterine crowding in the sow affects litter sex ratio, placental development and embryonic myogenin expression in early gestation.
Tse, Reproduction, fertility, and development 2008 (PubMed)- GeneRIF: Relative MYOD1 expression was not different, but MYOG expression was higher in the (ligated-tube)crowded group embryos.
- Polymorphisms in coding and regulatory regions of the porcine MYF6 and MYOG genes and expression of the MYF6 gene in m. longissimus dorsi versus productive traits in pigs.
Wyszyńska-Koko, Journal of applied genetics 2006 (PubMed)- GeneRIF: mutation in exon 1 of the MYOG gene had no statistically significant association with carcass quality traits
- Effects of the MyoG gene on the partial growth traits in pigs.
Xue, Yi chuan xue bao = Acta genetica Sinica 2006 (PubMed)- GeneRIF: Significant differences were found in the birth weight and the backfat thickness among the different MyoG genotypes
LOC109480329 transcription factor SUM-1-like from Branchiostoma belcheri
76% identity, 27% coverage
LOC118407021 transcription factor SUM-1-like from Branchiostoma floridae
76% identity, 27% coverage
NP_571081 myogenin from Danio rerio
82% identity, 22% coverage
NP_001167580 myogenin from Ovis aries
D3YKV7 Myogenin from Ovis aries
77% identity, 27% coverage
- Correlation between sheep YAP1 temporal and spatial expression trends and MSTN and MyoG gene expression.
Lv, Genetics and molecular research : GMR 2015 (PubMed)- GeneRIF: Data show that Yes-associated protein 1 (YAP1) expression was significantly or and positively correlated with (MSTN) and myogenin (MyoG) at 2 days old, 2 and 6 months old.
- Cloning and expression of MyoG gene from Hu sheep and identification of its myogenic specificity.
Zhang, Molecular biology reports 2014 (PubMed)- GeneRIF: The subcellular localization and myogenic activity of MyoG were exactly detected on the basis of multiple biological analyses, which expanded our understanding of the biological function of MyoG.
- Developmental changes in IGF-I and MyoG gene expression and their association with meat traits in sheep.
Sun, Genetics and molecular research : GMR 2014 (PubMed)- GeneRIF: We conclude that the expressions of IGF-I and MyoG genes are significantly and positively correlated with early muscle traits of Hu sheep
- Differentiated evolutionary relationships among chordates from comparative alignments of multiple sequences of MyoD and MyoG myogenic regulatory factors
Oliani, Genetics and molecular research : GMR 2015 (PubMed)- “...A7L034), and sheep Ovis aries (Q90477 and D3YKV7) were searched from a non-redundant protein sequence database UniProtKB/Swiss-Prot, and subsequently analyzed...”
- “...A7L034), and sheep Ovis aries (Q90477 and D3YKV7). Next, hierarchical dendograms representing the alignments among these sequences were constructed as described...”
P49812 Myogenin from Sus scrofa
77% identity, 27% coverage
MYOG_HUMAN / P15173 Myogenin; Class C basic helix-loop-helix protein 3; bHLHc3; Myogenic factor 4; Myf-4 from Homo sapiens (Human) (see paper)
NP_002470 myogenin from Homo sapiens
77% identity, 27% coverage
- function: Acts as a transcriptional activator that promotes transcription of muscle-specific target genes and plays a role in muscle differentiation, cell cycle exit and muscle atrophy. Essential for the development of functional embryonic skeletal fiber muscle differentiation. However is dispensable for postnatal skeletal muscle growth; phosphorylation by CAMK2G inhibits its transcriptional activity in respons to muscle activity. Required for the recruitment of the FACT complex to muscle-specific promoter regions, thus promoting gene expression initiation. During terminal myoblast differentiation, plays a role as a strong activator of transcription at loci with an open chromatin structure previously initiated by MYOD1. Together with MYF5 and MYOD1, co-occupies muscle-specific gene promoter core regions during myogenesis. Also cooperates with myocyte-specific enhancer factor MEF2D and BRG1-dependent recruitment of SWI/SNF chromatin- remodeling enzymes to alter chromatin structure at myogenic late gene promoters. Facilitates cell cycle exit during terminal muscle differentiation through the up-regulation of miR-20a expression, which in turn represses genes involved in cell cycle progression. Binds to the E-box containing (E1) promoter region of the miR-20a gene. Also plays a role in preventing reversal of muscle cell differentiation. Contributes to the atrophy-related gene expression in adult denervated muscles. Induces fibroblasts to differentiate into myoblasts (By similarity).
subunit: Homodimer and heterodimer with E12; heterodimerization enhances MYOG DNA-binding and transcriptional activities. Interacts with SMARCA4/BRG1/BAF190A. Interacts (via C-terminal region) with SSRP1 and SUPT16H; the interaction is indicative of an interaction with the FACT complex (By similarity). Interacts with CSRP3. - Automatic Text-Mining Approach to Identify Molecular Target Candidates Associated with Metabolic Processes for Myotonic Dystrophy Type 1
Kuntawala, International journal of environmental research and public health 2023 - “...to make a subunit of a structure called a calcium channel. 43 [ 65 ] P15173 MYOG Myogenin Positive regulation of muscle atrophy, regulation of myoblast fusion, skeletal muscle cell differentiation - Plays a role in muscle atrophy, muscle differentiation, and embryonic skeletal fiber muscle differentiation....”
- Characterising the efficacy and bioavailability of bioactive peptides identified for attenuating muscle atrophy within a Vicia faba-derived functional ingredient.
Corrochano, Current research in food science 2021 - “...kinase Human P15172 MYOD1 Myoblast determination protein 1 Human P13349 MYF5 Myogenic factor 5 Human P15173 MYOG Myogenin Human P23760 PAX3 Paired box protein Pax-3 Human P23759 PAX7 Paired box protein Pax-7 Human Q06413 MEF2C Myocyte-specific enhancer factor 2C Human The two approaches were finally combined...”
- Structural Features of Transcription Factors Associating with Nucleosome Binding.
Fernandez, Molecular cell 2019 - “...obtained for each spots. 3D Structural Model Assemblies MYOG, CREM, and ASCL1/E12 structural models (SMR P15173, SMR Q03060, SMR P50553) were constructed based on SWISS-MODEL sequence alignment ( Bienert et al., 2017 ) with MYOD (pdb 1MDY) showing 74.2% DBD sequence identity, CREB1 (pdb 1DH3) showing...”
- “...et al., 2003 ), USF (pdb 1AN4) ( Ferre-DAmare et al., 1994 ), MYOG (SMR P15173), and CREM (SMR Q03060). (C) Group IIB TFs with immunoglobulin-like fold DBDs crystal structures of TBX1 (pdb 4A04) ( El Omari et al., 2012 ), Brachyury (pdb 1XBR) ( Muller...”
- Differentiated evolutionary relationships among chordates from comparative alignments of multiple sequences of MyoD and MyoG myogenic regulatory factors
Oliani, Genetics and molecular research : GMR 2015 (PubMed)- “...(P10085 and P12979), human Homo sapiens (P15172 and P15173), bovine Bos taurus (Q7YS82 and Q7YS81), wild pig Sus scrofa (P49811 and P49812), quail Coturnix...”
- “...(P10085 and P12979), human Homo sapiens (P15172 and P15173), bovine Bos taurus (Q7YS82 and Q7YS81), wild pig Sus scrofa (P49811 and P49812), japanese quail...”
- Prioritizing disease candidate proteins in cardiomyopathy-specific protein-protein interaction networks based on "guilt by association" analysis.
Li, PloS one 2013 - “...26 2449472.494 cardiomyopathy [78] CALM1 P62158 27 2291170.029 DCM [45] ACTB P60709 28 2039574.700 MYOG P15173 29 1304602.403 DNAH8 Q96JB1 30 1247401.222 CKM P06732 31 1139350.347 DCM [49] CAPN3 P20807 32 1108281.072 PRKAG2 Q9UGJ0 33 1068188.085 cardiomyopathy [79] ZMPSTE24 O75844 34 1050441.814 DCM [50] AMY1A P04745...”
- Phylogenetic analysis of the human basic helix-loop-helix proteins
Ledent, Genome biology 2002 - “...Hash3b * Achaete-Scute b ? NT_004680.3 1q31-q32 N009720 Hash3c * Achaete-Scute b ? NT_009720.3 12q23-q24 P15173 Myf4 MyoD Myogenin NT_004662.3 1q31-41 P23409 Myf6 MyoD Myf6 NT_024473.2 12q21 P15172 Myf3 MyoD MyoD NT_009307.3 11p15.4 P13349 Myf5 MyoD Myf5 NT_024473.2 12q21 N011269 E2A * E12/E47 E2A NT_011269.3 19p13.3...”
- “...a P50553 gb|AAB28830.1 Mash2 Achaete-Scute a Q99929 gb|AAD33794.1 Mash3 Achaete-Scute b N024228 sp|CAC37689 Myogenin MyoD P15173 sp|P12979 Myf6 MyoD P23409 ref|NP_032683.1 MyoD MyoD P15172 sp|P10085 Myf5 MyoD P13349 ref|NP_032682.1 E2A E12/E47 N011269 sp|15806 TF12 E12/E47 Q99081 ref|NP_035674.1 TCF4 E12/E47 P15884/P15884 D ref|NP_038713.1 KA1 E12/E47 ? dbj|BAA06218.1...”
- Myogenin suppresses apoptosis induced by angiotensin II in human induced pluripotent stem cell-derived cardiomyocytes.
Gao, Biochemical and biophysical research communications 2021 (PubMed)- GeneRIF: Myogenin suppresses apoptosis induced by angiotensin II in human induced pluripotent stem cell-derived cardiomyocytes.
- CASZ1 induces skeletal muscle and rhabdomyosarcoma differentiation through a feed-forward loop with MYOD and MYOG.
Liu, Nature communications 2020 - GeneRIF: CASZ1 plays a critical role in inducing skeletal myogenesis and co-operating to form a feed-forward loop with MYOD and MYOG that is critical for Embryonal rhabdomyosarcoma differentiation.
- Dual-specificity phosphatase 29 is induced during neurogenic skeletal muscle atrophy and attenuates glucocorticoid receptor activity in muscle cell culture.
Cooper, American journal of physiology. Cell physiology 2020 (PubMed)- GeneRIF: Dual-specificity phosphatase 29 is induced during neurogenic skeletal muscle atrophy and attenuates glucocorticoid receptor activity in muscle cell culture.
- Molecular pathogenesis of esophageal squamous cell carcinoma: Identification of the antitumor effects of miR‑145‑3p on gene regulation.
Shimonosono, International journal of oncology 2019 (PubMed)- GeneRIF: Among these targets, dehydrogenase/reductase member 2 DHRS2 and MYO1B were directly regulated by miR1453p in esophageal squamous cell carcinoma (ESCC) cells by dual luciferase reporter assays. Aberrantly expressed DHRS2 and MYOIB were detected in ESCC clinical specimens, and their overexpression enhanced cancer cell aggressiveness.
- PRMT1 activates myogenin transcription via MyoD arginine methylation at R121.
Liu, Biochimica et biophysica acta. Gene regulatory mechanisms 2019 (PubMed)- GeneRIF: PRMT1 promotes MyoD-mediated myogenin expression, for which the enzymatic activity of PRMT1 is needed. The arginine methylation of MyoD by PRMT1 enhances its DNA binding activity and transactivation.
- The SMYD3 methyltransferase promotes myogenesis by activating the myogenin regulatory network.
Codato, Scientific reports 2019 - GeneRIF: The SMYD3 methyltransferase promotes myogenesis by activating the myogenin regulatory network.
- AKAP6 inhibition impairs myoblast differentiation and muscle regeneration: Positive loop between AKAP6 and myogenin.
Lee, Scientific reports 2015 - GeneRIF: Findings indicate a interplay between A-kinase anchoring protein 6 (AKAP6) and myogenin.
- Muscle disuse atrophy is not accompanied by changes in skeletal muscle satellite cell content.
Snijders, Clinical science (London, England : 1979) 2014 (PubMed)- GeneRIF: Data indicate that muscle MYOG mRNA expression doubled, whereas MSTN protein expression decreased following immobilization.
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MYOG_RAT / P20428 Myogenin from Rattus norvegicus (Rat) (see 3 papers)
77% identity, 21% coverage
- function: Acts as a transcriptional activator that promotes transcription of muscle-specific target genes and plays a role in muscle differentiation, cell cycle exit and muscle atrophy. Essential for the development of functional embryonic skeletal fiber muscle differentiation. However is dispensable for postnatal skeletal muscle growth; phosphorylation by CAMK2G inhibits its transcriptional activity in respons to muscle activity. Required for the recruitment of the FACT complex to muscle-specific promoter regions, thus promoting gene expression initiation. During terminal myoblast differentiation, plays a role as a strong activator of transcription at loci with an open chromatin structure previously initiated by MYOD1. Together with MYF5 and MYOD1, co-occupies muscle-specific gene promoter core regions during myogenesis. Also cooperates with myocyte-specific enhancer factor MEF2D and BRG1-dependent recruitment of SWI/SNF chromatin- remodeling enzymes to alter chromatin structure at myogenic late gene promoters. Facilitates cell cycle exit during terminal muscle differentiation through the up-regulation of miR-20a expression, which in turn represses genes involved in cell cycle progression. Binds to the E-box containing (E1) promoter region of the miR-20a gene. Also plays a role in preventing reversal of muscle cell differentiation. Contributes to the atrophy-related gene expression in adult denervated muscles. Induces fibroblasts to differentiate into myoblasts.
subunit: Homodimer and heterodimer with E12; heterodimerization enhances MYOG DNA-binding and transcriptional activities. Interacts with SMARCA4/BRG1/BAF190A. Interacts (via C-terminal region) with SSRP1 and SUPT16H; the interaction is indicative of an interaction with the FACT complex (By similarity). Interacts with CSRP3. - Differentiated evolutionary relationships among chordates from comparative alignments of multiple sequences of MyoD and MyoG myogenic regulatory factors
Oliani, Genetics and molecular research : GMR 2015 (PubMed)- “...(P16075 and P17920), rat Rattus norvegicus (Q02346 and P20428), domestic water buffalo Bubalus bubalis (D2SP11 and A7L034), and sheep Ovis aries (Q90477 and...”
- High-throughput identification of IMCD proteins using LC-MS/MS.
Pisitkun, Physiological genomics 2006 - A proteomic survey of rat cerebral cortical synaptosomes
Witzmann, Proteomics 2005 - “...P15205 P02688 P04636 P43245 Q08201 P30904 P16036 Q9JLT0 P20428 P13596 P55161 P19804 P07936 P37805 P47971 Q62718 P19234 Q01205 12.72 13.86 15.55 14.20 12.98 8.28...”
- A preliminary gene map for the Van der Woude syndrome critical region derived from 900 kb of genomic sequence at 1q32-q41.
Schutte, Genome research 2000
LOC100303673 myogenin from Meleagris gallopavo
77% identity, 26% coverage
P17920 Myogenin from Gallus gallus
NP_989515 myogenin from Gallus gallus
77% identity, 26% coverage
- Differentiated evolutionary relationships among chordates from comparative alignments of multiple sequences of MyoD and MyoG myogenic regulatory factors
Oliani, Genetics and molecular research : GMR 2015 (PubMed)- “...(P21572 and P34060), chicken Gallus gallus (P16075 and P17920), rat Rattus norvegicus (Q02346 and P20428), domestic water buffalo Bubalus bubalis (D2SP11 and...”
- Impact of strain and duration of thermal stress on carcass yield, metabolic hormones, immunological indices and the expression of HSP90 and Myogenin genes in broilers.
Zaglool, Research in veterinary science 2019 (PubMed)- GeneRIF: Thermal stress for 6h down-regulate the mRNA expression of liver Myogenin, concomitantly with an increase in the expression of HSP90 gene in both broiler strains.
- Expression profiles and association analysis with growth traits of the MyoG and Myf5 genes in the Jinghai yellow chicken.
Genxi, Molecular biology reports 2014 (PubMed)- GeneRIF: Single nucleotide polymorphisms of the MyoG and Myf5 genes had certain effects on growth traits of the Jinghai yellow chicken.
- Changes to daily feed intake during the laying period alters embryonic MSTN and MYOG gene expression in genetically fat and lean lines of chickens.
Li, British poultry science 2013 (PubMed)- GeneRIF: Low daily feed intake did not alter the trend in myostatin (MSTN) mRNA expression levels in either line, but significantly changed the peak values. Myogenin (MYOG) mRNA expression varied by line and over time, with a delay in the Lean line.
- Possible correlation between selenoprotein W and myogenic regulatory factors in chicken embryonic myoblasts.
Wu, Biological trace element research 2012 (PubMed)- GeneRIF: Data suggest that selenium (Se; a dietary factor) promotes differentiation of embryonic myoblasts; up-regulation of selenoprotein W (SelW) and up-regulation of myogenic regulatory factors (myogenin/MYF4; MRF4; MRF5) upon Se treatment are correlated.
- [Correlation analysis of relationships between polymorphisms of high quality chicken myogenin gene and slaughter and meat quality traits].
Wang, Yi chuan = Hereditas 2007 (PubMed)- GeneRIF: MyoG gene is the major gene affect-ing the muscle fiber traits of chicken, and the mutation could be used as the molecular genetic marker to select the chickens for Meat Quality traits.
XP_002717630 myogenin isoform X1 from Oryctolagus cuniculus
77% identity, 24% coverage
NP_001104795 myogenin from Bos taurus
77% identity, 27% coverage
NP_032683 myogenic factor 6 from Mus musculus
79% identity, 24% coverage
- Myf6/MRF4 is a myogenic niche regulator required for the maintenance of the muscle stem cell pool.
Lazure, EMBO reports 2020 - GeneRIF: Myf6/MRF4 is a myogenic niche regulator required for the maintenance of the muscle stem cell pool.
- MicroRNA, miR-374b, directly targets Myf6 and negatively regulates C2C12 myoblasts differentiation.
Ma, Biochemical and biophysical research communications 2015 (PubMed)- GeneRIF: findings identified miR-374b directly targets Myf6 and negatively regulates myogenesis
- Embryonic founders of adult muscle stem cells are primed by the determination gene Mrf4.
Sambasivan, Developmental biology 2013 (PubMed)- GeneRIF: Mrf4 has a role in priming embryonic founder cells to become adult muscle stem cells
- Loss of synaptic vesicles from neuromuscular junctions in aged MRF4-null mice.
Wang, Neuroreport 2011 - GeneRIF: Intrinsic muscle factor MRF4 plays an important role in maintenance of neuromuscular junctions.
- Myogenic regulatory factors transactivate the Tceal7 gene and modulate muscle differentiation.
Shi, The Biochemical journal 2010 (PubMed)- GeneRIF: Data demonstrated that Myf6 is Tceal7 upstream transactivators using transcriptional assays.
- Myogenic regulatory factors regulate M-cadherin expression by targeting its proximal promoter elements.
Hsiao, The Biochemical journal 2010 (PubMed)- GeneRIF: MRF4 targets the proximal region of M-cadherin promoter and bind the E4-box.
- Evidence for a myotomal Hox/Myf cascade governing nonautonomous control of rib specification within global vertebral domains.
Vinagre, Developmental cell 2010 (PubMed)- GeneRIF: Hox genes produce global patterns in the axial skeleton; Myf5 and Myf6 have roles in rib formation
- Opposite roles of MRF4 and MyoD in cell proliferation and myogenic differentiation.
Jin, Biochemical and biophysical research communications 2007 (PubMed)- GeneRIF: Taken together, these results indicate that MRF4 and MyoD play competitive roles in myogenesis by stimulating cell proliferation and differentiation, respectively.
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Q7YS81 Myogenin from Bos taurus
A7L034 Myogenin from Bubalus bubalis
77% identity, 27% coverage
- Differentiated evolutionary relationships among chordates from comparative alignments of multiple sequences of MyoD and MyoG myogenic regulatory factors
Oliani, Genetics and molecular research : GMR 2015 (PubMed)- “...(P15172 and P15173), bovine Bos taurus (Q7YS82 and Q7YS81), wild pig Sus scrofa (P49811 and P49812), quail Coturnix coturnix (P21572 and P34060), chicken Gallus...”
- “...(P15172 and P15173), bovine Bos taurus (Q7YS82 and Q7YS81), wild pig Sus scrofa (P49811 and P49812), japanese quail Coturnix coturnix (P21572 and P34060),...”
- Differentiated evolutionary relationships among chordates from comparative alignments of multiple sequences of MyoD and MyoG myogenic regulatory factors
Oliani, Genetics and molecular research : GMR 2015 (PubMed)- “...P20428), domestic water buffalo Bubalus bubalis (D2SP11 and A7L034), and sheep Ovis aries (Q90477 and D3YKV7) were searched from a non-redundant protein...”
- “...domestic water buffalo Bubalus bubalis (D2SP11 and A7L034), and sheep Ovis aries (Q90477 and D3YKV7). Next, hierarchical dendograms representing the alignments...”
MYF6_XENLA / Q92020 Myogenic factor 6; Myf-6; Muscle-specific regulatory factor 4 from Xenopus laevis (African clawed frog) (see paper)
NP_001081477 myogenic factor 6 from Xenopus laevis
79% identity, 24% coverage
NP_058811 myogenin from Rattus norvegicus
77% identity, 27% coverage
- Regulation of skeletal myogenesis in C2C12 cells through modulation of Pax7, MyoD, and myogenin via different low-frequency electromagnetic field energies.
Bi, Technology and health care : official journal of the European Society for Engineering and Medicine 2022 - GeneRIF: Regulation of skeletal myogenesis in C2C12 cells through modulation of Pax7, MyoD, and myogenin via different low-frequency electromagnetic field energies.
- Comparative effects of low-level laser therapy pre- and post-injury on mRNA expression of MyoD, myogenin, and IL-6 during the skeletal muscle repair.
Alves, Lasers in medical science 2016 (PubMed)- GeneRIF: low-level laser therapy (LLLT) administered following muscle injury modulates the mRNA expression of MyoD and myogenin. Moreover, the both forms of LLLT administration were able to modulate the mRNA expression of IL-6 during the muscle repair process.
- The regulatory mechanisms of myogenin expression in doxorubicin-treated rat cardiomyocytes.
Liu, Oncotarget 2015 - GeneRIF: Suggest that myogenin is the target for doxorubicin-induced cardio-toxicity.
- Myogenin gene expression is not altered in the developing diaphragm of nitrofen-induced congenital diaphragmatic hernia.
Takahashi, Pediatric surgery international 2014 (PubMed)- GeneRIF: Myogenin, which is expressed in MPCs, belongs to a family of basic helix-loop-helix transcription factors that activate skeletal muscle differentiation and thus plays a key role in fetal diaphragmatic development and muscularization.
- Heart failure-induced skeletal myopathy in spontaneously hypertensive rats.
Damatto, International journal of cardiology 2013 (PubMed)- GeneRIF: Myogenin, myostatin, and follistatin expression is lower and MRF4 levels higher in spontaneously hypertensive rats (SHR)
- Comparative analysis of semaphorin 3A in soleus and EDL muscle satellite cells in vitro toward understanding its role in modulating myogenin expression.
Suzuki, The international journal of biochemistry & cell biology 2013 (PubMed)- GeneRIF: Sema3A is a crucial factor that is up-stream of the muscle-specific transcription factor, myogenin.
- Magnesium deficiency up-regulates Myod expression in rat skeletal muscle and C2C12 myogenic cells.
Furutani, Cell biochemistry and function 2011 (PubMed)- GeneRIF: Expression of Myod and myogenin is increased in skeletal muscle of rats fed magnesium-deficient diet.
- Myogenic differentiation in atrium-derived adult cardiac pluripotent cells and the transcriptional regulation of GATA4 and myogenin on ANP promoter.
Kamrul, Genes to cells : devoted to molecular & cellular mechanisms 2010 (PubMed)- GeneRIF: Results describe the involvement of myogenin and GATA4, two tissue-specific transcription factors, and the atrial natriuretic factor promoter, in cardiac transcriptional activity.
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MYF6_RAT / P19335 Myogenic factor 6; Myf-6; Muscle-specific regulatory factor 4 from Rattus norvegicus (Rat) (see paper)
NP_037304 myogenic factor 6 from Rattus norvegicus
79% identity, 24% coverage
MYOG_MOUSE / P12979 Myogenin; MYOD1-related protein from Mus musculus (Mouse) (see 15 papers)
NP_112466 myogenin from Mus musculus
77% identity, 27% coverage
- function: Acts as a transcriptional activator that promotes transcription of muscle-specific target genes and plays a role in muscle differentiation, cell cycle exit and muscle atrophy. Essential for the development of functional embryonic skeletal fiber muscle differentiation. However is dispensable for postnatal skeletal muscle growth; phosphorylation by CAMK2G inhibits its transcriptional activity in respons to muscle activity. Required for the recruitment of the FACT complex to muscle-specific promoter regions, thus promoting gene expression initiation. During terminal myoblast differentiation, plays a role as a strong activator of transcription at loci with an open chromatin structure previously initiated by MYOD1. Together with MYF5 and MYOD1, co-occupies muscle-specific gene promoter core regions during myogenesis. Also cooperates with myocyte-specific enhancer factor MEF2D and BRG1-dependent recruitment of SWI/SNF chromatin- remodeling enzymes to alter chromatin structure at myogenic late gene promoters. Facilitates cell cycle exit during terminal muscle differentiation through the up-regulation of miR-20a expression, which in turn represses genes involved in cell cycle progression. Binds to the E-box containing (E1) promoter region of the miR-20a gene. Also plays a role in preventing reversal of muscle cell differentiation. Contributes to the atrophy-related gene expression in adult denervated muscles. Induces fibroblasts to differentiate into myoblasts.
subunit: Homodimer and heterodimer with E12; heterodimerization enhances MYOG DNA-binding and transcriptional activities. Interacts with SMARCA4/BRG1/BAF190A. Interacts (via C-terminal region) with SSRP1 and SUPT16H; the interaction is indicative of an interaction with the FACT complex. nteracts with CSRP3 (By similarity).
disruption phenotype: Display normal myoblast formation during embryogenesis, but show perinatal lethality because of a deficiency during the later stages of skeletal muscle fiber formation. Show no abnormalities for smooth muscles and cardiocytes differentiation. Conditional mutant with expression abrogated in muscle cells from 15.5 or 17.5 dpc are viable, fertil and exhibit no noticeable muscle growth and reduction of myofiber diameter defects but show smaller body size and mass. Conditional mutant in muscle cells of denervated hindlimb muscles show an inhibition of the denervation-dependent reductions in mass, force and atrophy of slow fiber-type soleus muscles, without increased in satellite cell proliferation and fusion. - Differentiated evolutionary relationships among chordates from comparative alignments of multiple sequences of MyoD and MyoG myogenic regulatory factors
Oliani, Genetics and molecular research : GMR 2015 (PubMed)- “...chordates. Protein sequences from Mus musculus (P10085 and P12979), human Homo sapiens (P15172 and P15173), bovine Bos taurus (Q7YS82 and Q7YS81), wild pig Sus...”
- “...from nine specimens: mouse Mus musculus (P10085 and P12979), human Homo sapiens (P15172 and P15173), bovine Bos taurus (Q7YS82 and Q7YS81), wild pig Sus...”
- Production of soluble mammalian proteins in Escherichia coli: identification of protein features that correlate with successful expression
Dyson, BMC biotechnology 2004 - “...0.0 0.0 124 RelB Q04863 RHD, TIG 102418/558 35.8 4.0 0.0 46.0 25.9 125 myog P12979 HLH, Basic 2224/224 25.1 3.0 1.0 25.8 12.4 Features listed as Table 1 except: a PfamA domains contained within expressed protein and b na no PfamA domains annotated....”
- IL-4 Signaling Promotes Myoblast Differentiation and Fusion by Enhancing the Expression of MyoD, Myogenin, and Myomerger.
Kurosaka, Cells 2023 - GeneRIF: IL-4 Signaling Promotes Myoblast Differentiation and Fusion by Enhancing the Expression of MyoD, Myogenin, and Myomerger.
- Foxo3 Knockdown Mediates Decline of Myod1 and Myog Reducing Myoblast Conversion to Myotubes.
Gellhaus, Cells 2023 - GeneRIF: Foxo3 Knockdown Mediates Decline of Myod1 and Myog Reducing Myoblast Conversion to Myotubes.
- Protective effects of hachimijiogan (HJG), a Japanese Kampo medicine, on cancer cachectic muscle wasting in mice.
Kametaka, Biomedical research (Tokyo, Japan) 2023 (PubMed)- GeneRIF: Protective effects of hachimijiogan (HJG), a Japanese Kampo medicine, on cancer cachectic muscle wasting in mice.
- Myogenin is required for assembly of the transcription machinery on muscle genes during skeletal muscle differentiation.
Adhikari, PloS one 2021 - GeneRIF: Myogenin is required for assembly of the transcription machinery on muscle genes during skeletal muscle differentiation.
- PUFA Treatment Affects C2C12 Myocyte Differentiation, Myogenesis Related Genes and Energy Metabolism.
Risha, Genes 2021 - GeneRIF: PUFA Treatment Affects C2C12 Myocyte Differentiation, Myogenesis Related Genes and Energy Metabolism.
- USP7-dependent control of myogenin stability is required for terminal differentiation in skeletal muscle progenitors.
de, The FEBS journal 2020 (PubMed)- GeneRIF: USP7-dependent control of myogenin stability is required for terminal differentiation in skeletal muscle progenitors.
- Dissecting myogenin-mediated retinoid X receptor signaling in myogenic differentiation.
Khilji, Communications biology 2020 - GeneRIF: Dissecting myogenin-mediated retinoid X receptor signaling in myogenic differentiation.
- The SMYD3 methyltransferase promotes myogenesis by activating the myogenin regulatory network.
Codato, Scientific reports 2019 - GeneRIF: The SMYD3 methyltransferase promotes myogenesis by activating the myogenin regulatory network.
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P34060 Myogenin from Coturnix japonica
73% identity, 27% coverage
XP_972025 transcription factor SUM-1 from Tribolium castaneum
72% identity, 29% coverage
NP_861527 myogenic factor 6 from Bos taurus
Q7YS80 Myogenic factor 6 from Bos taurus
80% identity, 23% coverage
NP_001231601 myogenic factor 6 from Sus scrofa
80% identity, 23% coverage
P23409 Myogenic factor 6 from Homo sapiens
NP_002460 myogenic factor 6 from Homo sapiens
80% identity, 23% coverage
- The role of HR-HPV integration in the progression of premalignant lesions into different cancer types.
Catalán-Castorena, Heliyon 2024 - “...CNKSR2 (Q8WXI2) CAGE1 (Q8TC20) RBL1 (P28749) TP63 (O88898) TRAF1 (Q13077) DCDC1 (M0R2J8) PTPRQ (Q9UMZ3) MYF6 (P23409) [ 157 ] Cytology samples 12 LSIL 2 HSIL 3 ASCUS HPV 39, 52,51, 51, 52 and 45 HIVID-NGS HPV L1, L2, E7, E1, E2, E5 and E6 Intergenic regions,...”
- Phylogenetic analysis of the human basic helix-loop-helix proteins
Ledent, Genome biology 2002 - “...1q31-q32 N009720 Hash3c * Achaete-Scute b ? NT_009720.3 12q23-q24 P15173 Myf4 MyoD Myogenin NT_004662.3 1q31-41 P23409 Myf6 MyoD Myf6 NT_024473.2 12q21 P15172 Myf3 MyoD MyoD NT_009307.3 11p15.4 P13349 Myf5 MyoD Myf5 NT_024473.2 12q21 N011269 E2A * E12/E47 E2A NT_011269.3 19p13.3 Q99081 TF12 E12/E47 TF12 NT_010289.3 15q21...”
- “...Achaete-Scute a Q99929 gb|AAD33794.1 Mash3 Achaete-Scute b N024228 sp|CAC37689 Myogenin MyoD P15173 sp|P12979 Myf6 MyoD P23409 ref|NP_032683.1 MyoD MyoD P15172 sp|P10085 Myf5 MyoD P13349 ref|NP_032682.1 E2A E12/E47 N011269 sp|15806 TF12 E12/E47 Q99081 ref|NP_035674.1 TCF4 E12/E47 P15884/P15884 D ref|NP_038713.1 KA1 E12/E47 ? dbj|BAA06218.1 Math1 Atonal Q92858 dbj|BAA07791.1...”
- Single exchanges of amino acids in the basic region change the specificity of N-Myc
Feldmann, Nucleic acids research 1993 - “...(Accession number: P1 1420), MYF6 (Accession number: P23409), MYOD.(Accession number: P10085), SCL (Accession number: P22091), TWIST (Accession number: P10627),...”
- Expression of the muscle-associated gene MYF6 in hairy cell leukemia.
Arons, PloS one 2020 - GeneRIF: Hypomethylation status of MYF6 supported expression in Hairy cell leukemia more than Hairy cell leukemia variant.
- High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men.
Yerges, Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2009 - GeneRIF: Observational study of gene-disease association. (HuGE Navigator)
- Efficacy of 3 days/wk resistance training on myofiber hypertrophy and myogenic mechanisms in young vs. older adults.
Kosek, Journal of applied physiology (Bethesda, Md. : 1985) 2006 (PubMed)- GeneRIF: Myogenin and myogenic differentiation factor D (MyoD) mRNAs increased (P < 0.05) in young and old, whereas myogenic factor (myf)-5 mRNA increased in young only (P < 0.05). Myf-6 protein increased (P < 0.05) in both young and old.
- The myogenic basic helix-loop-helix family of transcription factors shows similar requirements for SWI/SNF chromatin remodeling enzymes during muscle differentiation in culture.
Roy, The Journal of biological chemistry 2002 (PubMed)- GeneRIF: The myogenic basic helix-loop-helix family of transcription factors, MyoD, Myf5, myogenin, and MRF4, can each activate the muscle differentiation program.
MYOD1_CAEEL / P22980 Myoblast determination protein 1 homolog; MyoD protein 1; Helix-loop-helix protein 1 from Caenorhabditis elegans (see 4 papers)
NP_001021892 Myoblast determination protein 1 homolog from Caenorhabditis elegans
74% identity, 18% coverage
- function: Involved in myogenesis, in cooperation with transcription factors unc-120 and hnd-1 (PubMed:15892873, PubMed:17142668, PubMed:2175254). Acts redundantly with fozi-1 to promote body wall muscle cell and coelomocyte specification in postembryonic mesoderm progenitors, probably through suppression of sem-2 (PubMed:21307099).
subunit: Efficient DNA binding requires dimerization with another bHLH protein
disruption phenotype: RNAi-mediated knockdown results in a low frequency of embryonic lethality, with embryos arresting paralyzed at the two-fold stage; increases in frequency significantly on an hnd-1 or unc-120 mutant background (PubMed:15892873). Many embryos that survive to hatch become uncoordinated, dumpy larvae (PubMed:15892873). Double RNAi-mediated knockdown with sem-2 results in no sex myoblast production (PubMed:21307099). - Imaging of native transcription and transcriptional dynamics in vivo using a tagged Argonaute protein.
Toudji-Zouaz, Nucleic acids research 2021 - GeneRIF: Imaging of native transcription and transcriptional dynamics in vivo using a tagged Argonaute protein.
- Multilevel regulation of muscle-specific transcription factor hlh-1 during Caenorhabditis elegans embryogenesis.
Guan, Development genes and evolution 2020 - GeneRIF: Multilevel regulation of muscle-specific transcription factor hlh-1 during Caenorhabditis elegans embryogenesis.
- A Differentiation Transcription Factor Establishes Muscle-Specific Proteostasis in Caenorhabditis elegans.
Bar-Lavan, PLoS genetics 2016 - GeneRIF: We found that HLH-1-dependent myogenic conversion specifically induced the expression of putative HLH-1-regulated chaperones in differentiating muscle cells. Moreover, disrupting the putative HLH-1-binding sites on ubiquitously expressed daf-21(Hsp90) and muscle-enriched hsp-12.2(sHsp) promoters abolished their myogenic-dependent expressio
- Caudal-like PAL-1 directly activates the bodywall muscle module regulator hlh-1 in C. elegans to initiate the embryonic muscle gene regulatory network.
Lei, Development (Cambridge, England) 2009 - GeneRIF: hlh-1 is indeed a direct target of PAL-1 in the posterior embryonic C. elegans muscle lineages, defining a novel in vivo binding site for this crucial developmental regulator
- Defining the transcriptional redundancy of early bodywall muscle development in C. elegans: evidence for a unified theory of animal muscle development.
Fukushige, Genes & development 2006 - GeneRIF: findings demonstrate that UNC-120/SRF and HND-1/HAND act in concert with HLH-1 to regulate myogenesis
- The myogenic potency of HLH-1 reveals wide-spread developmental plasticity in early C. elegans embryos.
Fukushige, Development (Cambridge, England) 2005 (PubMed)- GeneRIF: CeMyoD (HLH-1) is a myogenic regulatory factor that can convert almost all cells to a muscle-like fate, regardless of their lineage of origin.
NP_001003982 myogenic factor 6 from Danio rerio
77% identity, 23% coverage
XP_009860817 transcription factor protein isoform X1 from Ciona intestinalis
70% identity, 9% coverage
LOC118406750 myogenic factor 5-like from Branchiostoma floridae
74% identity, 25% coverage
- A Preliminary Single-Cell RNA-Seq Analysis of Embryonic Cells That Express Brachyury in the Amphioxus, Branchiostoma japonicum
Satoh, Frontiers in cell and developmental biology 2021 - “...ID, LOC118406741), MyoD1 (AY154744; LOC118407021), an uncharacterized copy (LOC118407176, tentatively called MDF-candidate ), MyoD2 (AY154745; LOC118406750), and a gene for myoblast determination protein (LOC118406791, tentatively called MDP ) ( Figure 3Aa ). A survey of the Branchiostoma belcheri genome ( Huang et al., 2014 ) showed...”
LOC109480333 myogenic factor 5-like from Branchiostoma belcheri
70% identity, 27% coverage
LOC118406741 myogenic factor 5-like from Branchiostoma floridae
74% identity, 26% coverage
LOC109480315 myogenic factor 5-like from Branchiostoma belcheri
70% identity, 20% coverage
LOC118406791 myogenic factor 6-like from Branchiostoma floridae
67% identity, 25% coverage
LOC109480330 myoblast determination protein 1 homolog B-like from Branchiostoma belcheri
68% identity, 26% coverage
NP_731326 salivary gland-expressed bHLH, isoform C from Drosophila melanogaster
45% identity, 22% coverage
PTF1A_MOUSE / Q9QX98 Pancreas transcription factor 1 subunit alpha; Pancreas-specific transcription factor 1a; bHLH transcription factor p48; p48 DNA-binding subunit of transcription factor PTF1; PTF1-p48 from Mus musculus (Mouse) (see 7 papers)
NP_061279 pancreas transcription factor 1 subunit alpha from Mus musculus
46% identity, 17% coverage
- function: Transcription factor implicated in the cell fate determination in various organs (PubMed:11562365, PubMed:12185368, PubMed:15543146, PubMed:17075007, PubMed:9851981). Binds to the E-box consensus sequence 5'-CANNTG-3' (PubMed:11562365, PubMed:12185368, PubMed:9851981). Plays a role in early and late pancreas development and differentiation (PubMed:11562365, PubMed:21852532). Important for determining whether cells allocated to the pancreatic buds continue towards pancreatic organogenesis or revert back to duodenal fates (PubMed:11562365, PubMed:12185368, PubMed:9851981). May be involved in the maintenance of exocrine pancreas-specific gene expression including ELA1 and amylase (PubMed:11562365, PubMed:12185368, PubMed:9851981). Required for the formation of pancreatic acinar and ductal cells (PubMed:11562365). Plays an important role in cerebellar development (PubMed:15543146). Directly regulated by FOXN4 and RORC during retinal development, FOXN4-PTF1A pathway plays a central role in directing the differentiation of retinal progenitors towards horizontal and amacrine fates (PubMed:17075007).
subunit: Component of the pancreas transcription factor 1 complex (PTF1) which is composed of TCF3/p75, TCF12/p64 and PTF1A/p48. TCF3 is responsible for the nuclear import of the p48/p64 complex. Interacts with TCF3 and RBPSUH/RBP-Jkappa.
disruption phenotype: Early postnatal lethal phenotype characterized by a lack of the exocrine pancreas, however, islet-like endocrine cell clusters are formed. A redirection of pancreatic precursors to intestinal fates is seen. At 16.5 dpc embryos show reduced size of cerebellar primordium and cerebellar aplasia. - Ptf1a expression is necessary for correct targeting of spiral ganglion neurons within the cochlear nuclei.
Elliott, Neuroscience letters 2023 - GeneRIF: Ptf1a expression is necessary for correct targeting of spiral ganglion neurons within the cochlear nuclei.
- Positive autofeedback regulation of Ptf1a transcription generates the levels of PTF1A required to generate itch circuit neurons.
Mona, Genes & development 2020 - GeneRIF: Positive autofeedback regulation of Ptf1a transcription generates the levels of PTF1A required to generate itch circuit neurons.
- Interleukin 22 disrupts pancreatic function in newborn mice expressing IL-23.
Chen, Nature communications 2019 - GeneRIF: Study show that necrotizing enterocolitis in neonate mice is accompanied by elevation of IL-23 and IL-22 and decreased production of pancreatic enzymes. Mechanistically, IL-22 acts directly at the level of pancreatic acinar cells to decrease expression of the PTF1a. These results show that augmented production of IL-23 and IL-22 in early life has a negative impact on pancreatic enzyme secretion and food absorption.
- Induced PTF1a expression in pancreatic ductal adenocarcinoma cells activates acinar gene networks, reduces tumorigenic properties, and sensitizes cells to gemcitabine treatment.
Jakubison, Molecular oncology 2018 - GeneRIF: PTF1a induced gene expression of digestive enzymes and acinar-specific transcription factors.
- Forebrain Ptf1a Is Required for Sexual Differentiation of the Brain.
Fujiyama, Cell reports 2018 (PubMed)- GeneRIF: forebrain Ptf1a is one of the earliest regulators for sexual differentiation of the brain.
- Direct reprogramming of fibroblasts into neural stem cells by single non-neural progenitor transcription factor Ptf1a.
Xiao, Nature communications 2018 - GeneRIF: non-neural progenitor transcription factor Ptf1a alone is sufficient to directly reprogram mouse and human fibroblasts into self-renewable induced neural stem cells capable of differentiating into functional neurons, astrocytes and oligodendrocytes, and improving cognitive dysfunction of Alzheimer's disease mouse models when transplanted
- Ptf1a inactivation in adult pancreatic acinar cells causes apoptosis through activation of the endoplasmic reticulum stress pathway.
Sakikubo, Scientific reports 2018 - GeneRIF: The homozygous model helps clarify the role PTF1A has on the homeostasis and pathogenesis of exocrine pancreas in mice.
- c-Jun N-terminal kinase in pancreatic tumor stroma augments tumor development in mice.
Sato, Cancer science 2017 - GeneRIF: We crossed Ptf1a(Cre/+) ;Kras(G12D/+) mice with JNK1(-/-) mice to generate Ptf1a(Cre/+) ;Kras(G12D/+) ;JNK1(-/-) (Kras;JNK1(-/-) ) mice. Tumor weight was significantly lower in Kras;JNK1(-/-) mice than in Kras;JNK1(+/-) mice, whereas histopathological features were similar.we concluded that inhibition of activated JNK in pancreatic tumor stroma could be a potential therapeutic target to increase Ccl20 secretion
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- Identification of Sec23ip, Part of 14-3-3γ Protein Network, as a Regulator of Acute Steroidogenesis in MA-10 Leydig Cells.
Aghazadeh, Endocrinology 2020 - Identification of regulatory factors for mesenchymal stem cell-derived salivary epithelial cells in a co-culture system
Park, PloS one 2014 - “...33.20 5.54 3 13.0% 50 Q91VJ5 Pqbp1 protein PQBP1 263 30.60 5.86 3 25.0% 51 Q9QX98 ptf1a PTF1A 301 35.60 4.99 3 9.0% 52 Q3TZ89 Isoform 2 of Protein transport protein Sec31B SEC31B 1158 125.63 8.00 2 4.0% 53 Q01063 cAMP-specific 3,5-cyclic phosphodiesterase 4D PDE4D 747...”
PTF1A_RAT / Q64305 Pancreas transcription factor 1 subunit alpha; Pancreas-specific transcription factor 1a; bHLH transcription factor p48; p48 DNA-binding subunit of transcription factor PTF1; PTF1-p48 from Rattus norvegicus (Rat) (see 3 papers)
NP_446416 pancreas transcription factor 1 subunit alpha from Rattus norvegicus
46% identity, 17% coverage
- function: Transcription factor implicated in the cell fate determination in various organs. Binds to the E-box consensus sequence 5'-CANNTG-3'. Plays a role in early and late pancreas development and differentiation. Important for determining whether cells allocated to the pancreatic buds continue towards pancreatic organogenesis or revert back to duodenal fates. May be involved in the maintenance of exocrine pancreas-specific gene expression including ELA1 and amylase. Required for the formation of pancreatic acinar and ductal cells. Plays an important role in cerebellar development. Directly regulated by FOXN4 and RORC during retinal development, FOXN4-PTF1A pathway plays a central role in directing the differentiation of retinal progenitors towards horizontal and amacrine fates.
subunit: Component of the pancreas transcription factor 1 complex (PTF1) which is composed of TCF3/p75, TCF12/p64 and PTF1A/p48. TCF3 is responsible for the nuclear import of the p48/p64 complex. Interacts with TCF3 and RBPSUH/RBP-Jkappa (By similarity). - Viral-mediated coexpression of Pdx1 and p48 regulates exocrine pancreatic differentiation in mouse ES cells.
Rovira, Cloning and stem cells 2007 (PubMed)- GeneRIF: combined expression of key genes (Pdx1 and p48) involved in pancreatic development may be a promising approach to generate mature pancreatic exocrine cells.
- Interactions between hairy/enhancer of split-related proteins and the pancreatic transcription factor Ptf1-p48 modulate function of the PTF1 transcriptional complex.
Ghosh, The Biochemical journal 2006 - GeneRIF: The ability of truncated versions of Hes1 to bind Ptf1-p48 correlates with their ability to down-regulate the activity of the PTF1 transcriptional complex.
PTF1A_HUMAN / Q7RTS3 Pancreas transcription factor 1 subunit alpha; Class A basic helix-loop-helix protein 29; bHLHa29; Pancreas-specific transcription factor 1a; bHLH transcription factor p48; p48 DNA-binding subunit of transcription factor PTF1; PTF1-p48 from Homo sapiens (Human) (see 3 papers)
NP_835455 pancreas transcription factor 1 subunit alpha from Homo sapiens
46% identity, 17% coverage
- function: Transcription factor implicated in the cell fate determination in various organs. Binds to the E-box consensus sequence 5'-CANNTG-3'. Plays a role in early and late pancreas development and differentiation. Important for determining whether cells allocated to the pancreatic buds continue towards pancreatic organogenesis or revert back to duodenal fates. May be involved in the maintenance of exocrine pancreas-specific gene expression including ELA1 and amylase. Required for the formation of pancreatic acinar and ductal cells. Plays an important role in cerebellar development. Directly regulated by FOXN4 and RORC during retinal development, FOXN4-PTF1A pathway plays a central role in directing the differentiation of retinal progenitors towards horizontal and amacrine fates.
subunit: Component of the pancreas transcription factor 1 complex (PTF1) which is composed of TCF3/p75, TCF12/p64 and PTF1A/p48. TCF3 is responsible for the nuclear import of the p48/p64 complex. Interacts with TCF3 and RBPSUH/RBP-Jkappa (By similarity). - Identification of CD14 and lipopolysaccharide-binding protein as novel biomarkers for sarcoidosis using proteomics of serum extracellular vesicles.
Futami, International immunology 2022 - “...change P -value P36222 Chitinase-3-like protein1 0.032 O60704 Protein-tyrosine sulfotransferase 2 0.033 Q9NZM1 Myoferlin 0.004 Q7RTS3 Pancreas transcription factor 1 subunit alpha 0.024 Q9Y230 RuvB-like 2 0.034 Q8TAY7 Protein FAM11 D 0.047 Q92522 Histone H1x 0.038 P01040 Cystatin-A 0.040 P06732 Creatine kinase M-type 0.049 P98171 Rho...”
- Quantitative proteomic analysis for high-throughput screening of differential glycoproteins in hepatocellular carcinoma serum
Gao, Cancer biology & medicine 2015 - “...2 OS=Homo sapiens GN=PRODH2 PE=2 SV=1 - [PROD2_HUMAN] 1.31 2 1 1 536 58.8 8.60 Q7RTS3 Pancreas transcription factor 1 subunit alpha OS=Homo sapiens GN=PTF1A PE=1 SV=1 - [PTF1A_HUMAN] 1.83 1 1 1 328 34.9 5.25 A4D1S5 Ras-related protein Rab-19 OS=Homo sapiens GN=RAB19 PE=2 SV=2 -...”
- Genetically identified spinal interneurons integrating tactile afferents for motor control.
Bui, Journal of neurophysiology 2015 - Clinical Characteristics and Long-term Follow-up of Patients with Diabetes Due To PTF1A Enhancer Mutations.
Demirbilek, The Journal of clinical endocrinology and metabolism 2020 - GeneRIF: Clinical Characteristics and Long-term Follow-up of Patients with Diabetes Due To PTF1A Enhancer Mutations.
- Clinical Characteristics, Molecular Features, and Long-Term Follow-Up of 15 Patients with Neonatal Diabetes: A Single-Centre Experience.
Abali, Hormone research in paediatrics 2020 - GeneRIF: Clinical Characteristics, Molecular Features, and Long-Term Follow-Up of 15 Patients with Neonatal Diabetes: A Single-Centre Experience.
- Direct reprogramming of fibroblasts into neural stem cells by single non-neural progenitor transcription factor Ptf1a.
Xiao, Nature communications 2018 - GeneRIF: non-neural progenitor transcription factor Ptf1a alone is sufficient to directly reprogram mouse and human fibroblasts into self-renewable induced neural stem cells capable of differentiating into functional neurons, astrocytes and oligodendrocytes, and improving cognitive dysfunction of Alzheimer's disease mouse models when transplanted
- Loss of Ptf1a Leads to a Widespread Cell-Fate Misspecification in the Brainstem, Affecting the Development of Somatosensory and Viscerosensory Nuclei.
Iskusnykh, The Journal of neuroscience : the official journal of the Society for Neuroscience 2016 - GeneRIF: The results of this study suggested Ptf1a-dependent cell-fate misspecification as a novel mechanism of human brainstem pathology.
- Isolated Pancreatic Aplasia Due to a Hypomorphic PTF1A Mutation.
Houghton, Diabetes 2016 - GeneRIF: Data show isolated Pancreatic Aplasia Due to a Hypomorphic PTF1A Mutation
- Transcriptional Maintenance of Pancreatic Acinar Identity, Differentiation, and Homeostasis by PTF1A.
Hoang, Molecular and cellular biology 2016 - GeneRIF: Study describes the wide range of gene control by PTF1A that maintains the specific characteristics of pancreatic acinar cell identity and differentiation. PTF1A controls the pancreatic acinar transcription program by direct action at a thousand genes and in collaboration with other less cell type-restricted factors to ensure acinar cell homeostasis and to suppress other cell-type-specific programs.
- Mutations in PTF1A are not a common cause for human VATER/VACTERL association or neural tube defects mirroring Danforth's short tail mouse.
Gurung, Molecular medicine reports 2015 (PubMed)- GeneRIF: The results of the present study do not support the hypothesis that high penetrant mutations in these regions of PTF1A are involved in the development of human VATER/VACTERL association or NTDs
- The acinar differentiation determinant PTF1A inhibits initiation of pancreatic ductal adenocarcinoma.
Krah, eLife 2015 - GeneRIF: Loss of Ptf1a alone is sufficient to induce acinar-to-ductal metaplasia, potentiate inflammation, and induce a KRAS-permissive, pancreatic ductal adenocarcinoma-like gene expression profile.
- More
PTF1A_DANRE / Q7ZSX3 Pancreas transcription factor 1 subunit alpha; Pancreas-specific transcription factor 1a; bHLH transcription factor p48 from Danio rerio (Zebrafish) (Brachydanio rerio) (see paper)
NP_997524 pancreas transcription factor 1 subunit alpha from Danio rerio
46% identity, 21% coverage
- function: Transcription factor implicated in the cell fate determination in various organs. Binds to the E-box consensus sequence 5'-CANNTG-3'. Required for exocrine pancreatic development. Plays a central role in directing the differentiation of retinal progenitors towards horizontal and amacrine fates.
- Foxp and Skor family proteins control differentiation of Purkinje cells from Ptf1a- and Neurog1-expressing progenitors in zebrafish.
Itoh, Development (Cambridge, England) 2024 - GeneRIF: Foxp and Skor family proteins control differentiation of Purkinje cells from Ptf1a- and Neurog1-expressing progenitors in zebrafish.
- A novel subset of enteric neurons revealed by ptf1a:GFP in the developing zebrafish enteric nervous system.
Uribe, Genesis (New York, N.Y. : 2000) 2016 - GeneRIF: Results highlight the possibility that Ptf1a may act as an important transcription factor for enteric neuron development.
- Fate mapping of ptf1a-expressing cells during pancreatic organogenesis and regeneration in zebrafish.
Wang, Developmental dynamics : an official publication of the American Association of Anatomists 2015 - GeneRIF: In ptf1a haploinsufficiency, more ptf1a-lineage-labeled cells are traced into the pancreatic Notch-responsive cell and endocrine compartments. More reduction of ptf1a gene dosage converts pancreatic progenitor cells to non-pancreatic cell fates.
- Distinct enhancers of ptf1a mediate specification and expansion of ventral pancreas in zebrafish.
Pashos, Developmental biology 2013 - GeneRIF: Autoregulation of ptf1a is absolutely required for exocrine pancreas formation.
- Suppression of Ptf1a activity induces acinar-to-endocrine conversion.
Hesselson, Current biology : CB 2011 - GeneRIF: Postembryonic antagonism of Ptf1a, a master regulator of pancreatic development and acinar cell fate specification, induced expression of endocrine genes including insulin in the exocrine compartment. Induced insulin+ cells are derived from acinar cells.
- Ptf1a is expressed transiently in all types of amacrine cells in the embryonic zebrafish retina.
Jusuf, Neural development 2009 - GeneRIF: The timing of Ptf1a expression suggests that it is involved in the very early stages or steps in the differentiation of amacrine cells, which can be seen to rapidly diversify into a large number of subtypes.
- Graded levels of Ptf1a differentially regulate endocrine and exocrine fates in the developing pancreas.
Dong, Genes & development 2008 - GeneRIF: We propose that low levels of Ptf1a promote endocrine fate, whereas high levels repress endocrine fate and promote exocrine fate.
- Exdpf is a key regulator of exocrine pancreas development controlled by retinoic acid and ptf1a in zebrafish.
Jiang, PLoS biology 2008 - GeneRIF: Exocrine differentiation and proliferation factor (exdpf) is a direct target gene of pancreas-specific transcription factor 1a (Ptf1a).
- More
XP_973186 helix-loop-helix protein delilah from Tribolium castaneum
43% identity, 28% coverage
PTF1A_XENLA / Q4ZHW1 Pancreas transcription factor 1 subunit alpha; Pancreas-specific transcription factor 1a; Transcription factor Ptf1a/p48 from Xenopus laevis (African clawed frog)
NP_001167491 pancreas transcription factor 1 subunit alpha from Xenopus laevis
45% identity, 20% coverage
- function: Transcription factor implicated in the cell fate determination in various organs. Binds to the E-box consensus sequence 5'-CANNTG-3'. Acts together with pdx1 to induce the pancreatic lineage within the endoderm. Plays a central role in directing the differentiation of retinal progenitors towards horizontal and amacrine fates.
- Prdm13 forms a feedback loop with Ptf1a and is required for glycinergic amacrine cell genesis in the Xenopus Retina.
Bessodes, Neural development 2017 - GeneRIF: Our results demonstrate that Prdm13, downstream of Ptf1a, acts as an important regulator of glycinergic amacrine subtype specification in the Xenopus retina. We also reveal that Prdm13 regulates ptf1a expression through a negative feedback loop.
- Microarray analysis of Xenopus endoderm expressing Ptf1a.
Bilogan, Genesis (New York, N.Y. : 2000) 2012 - GeneRIF: analysis of the gene regulatory network activated by Ptf1a in early pancreas development;results revealed that Ptf1a regulates genes with a wide variety of functions, providing insight into the complexity of the regulatory network required for pancreas specification
- Differential ability of Ptf1a and Ptf1a-VP16 to convert stomach, duodenum and liver to pancreas.
Jarikji, Developmental biology 2007 - GeneRIF: Xenopus Ptf1a is essential for the initial specification of both endocrine and exocrine cells during normal pancreas development.
- Ptf1a triggers GABAergic neuronal cell fates in the retina.
Dullin, BMC developmental biology 2007 - GeneRIF: Ptf1a overexpression leads to an increased ratio of GABAergic subtypes among the whole amacrine and horizontal cell population, highlighting its instructive capacity to promote this specific subtype of inhibitory neurons
DEI_DROME / P41894 Helix-loop-helix protein delilah; Protein taxi from Drosophila melanogaster (Fruit fly) (see paper)
NP_001287543 taxi, isoform B from Drosophila melanogaster
42% identity, 15% coverage
XP_969845 pancreas transcription factor 1 subunit alpha from Tribolium castaneum
44% identity, 24% coverage
TWIST_BRABE / O96642 Twist-related protein; BBtwist from Branchiostoma belcheri (Amphioxus) (see paper)
39% identity, 29% coverage
- function: Probable transcription factor with a role in initial mesoderm differentiation.
subunit: Efficient DNA binding requires dimerization with another bHLH protein. Homodimer (By similarity).
TWIST_DROME / P10627 Protein twist from Drosophila melanogaster (Fruit fly) (see 3 papers)
NP_001286752 twist, isoform C from Drosophila melanogaster
35% identity, 12% coverage
- function: Involved in the establishment and dorsoventral patterning of germ layers in the embryo.
subunit: Efficient DNA binding requires dimerization with another bHLH protein. Homodimer. Interacts with akirin (PubMed:22396663).
disruption phenotype: Embryos fail to form the ventral furrow at gastrulation and lack mesoderm and all internal organs. - Enhancer Priming Enables Fast and Sustained Transcriptional Responses to Notch Signaling.
Falo-Sanjuan, Developmental cell 2019 - GeneRIF: ch-responsive enhancers are activated synchronously in Drosophila embryos; Priming by Twist and Dorsal promotes fast and sustained response to Notch
- The myogenic repressor gene Holes in muscles is a direct transcriptional target of Twist and Tinman in the Drosophila embryonic mesoderm.
Elwell, Developmental biology 2015 - GeneRIF: Findings provide mechanistic insight into the brake on myogenesis that occurs during mesoderm specification: twist and tin expression at early stages in turn activate the myogenic inhibitor Him; yet, once Twist or Tin levels decline at mid-embryogenesis, Him is no longer expressed in the mesoderm, and MEF2-dependent muscle differentiation can proceed.
- Discrete levels of Twist activity are required to direct distinct cell functions during gastrulation and somatic myogenesis.
Wong, PloS one 2014 - GeneRIF: The level of Twi activity determines whether the cellular events of ventral furrow formation, epithelial-to-mesenchymal transition, cell division and mesodermal migration occur.
- Akirin links twist-regulated transcription with the Brahma chromatin remodeling complex during embryogenesis.
Nowak, PLoS genetics 2012 - GeneRIF: Our studies identify Akirin as a nuclear factor that genetically interacts with the BRM complex and is required for optimal expression of the Twist-dependent Dmef2 enhancer
- Specificity of Notch pathway activation: twist controls the transcriptional output in adult muscle progenitors.
Bernard, Development (Cambridge, England) 2010 - GeneRIF: conclude that Twi is an essential Notch co-regulator in myogenic progenitor cells and has the potential to confer specificity on Notch signalling at over 170 genes, showing that a single factor can have a profound effect on the output of the pathway.
- Antagonistic function of Lmd and Zfh1 fine tunes cell fate decisions in the Twi and Tin positive mesoderm of Drosophila melanogaster.
Sellin, Developmental biology 2009 (PubMed)- GeneRIF: Data show that cell fate decisions in the dorsal and lateral Twi- and Tin-positive mesoderm of Drosophila melanogaster depend on the antagonistic action of the transcription factor Lame duck and the zinc finger homeodomain factor Zfh1.
- Tissue deformation modulates twist expression to determine anterior midgut differentiation in Drosophila embryos.
Desprat, Developmental cell 2008 (PubMed)- GeneRIF: These experiments show that mechanically induced Twist upregulation in stomodeal cells is necessary for subsequent midgut differentiation in Drosophila embryos.
- A core transcriptional network for early mesoderm development in Drosophila melanogaster.
Sandmann, Genes & development 2007 - GeneRIF: Twist binds to almost all mesodermal cis-regulatory modules to provide the competence to integrate inputs from more specialized transcription factors.
- More
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 798,070 different protein sequences to 1,261,478 scientific articles. Searches against EuropePMC were last performed on May 12 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory