{ "bcoid": "GLY_000938", "title": "Pig Protein Function (NCBI Refseq)", "description": "The Pig Protein Function (NCBI RefSeq) dataset contains biological function annotation of Sus scrofa ...", "filename": "pig_protein_function_refseq.csv", "filetype": "csv", "categories": { "species": [ "Sus scrofa" ], "molecule": [ "Protein" ], "tag": [ "Protein Function" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "P32196-1...", "NP_001116622..." ], [ "P32196-1...", "NP_001116622..." ] ], "headers": [ "uniprotkb_ca...", "refseq_ac..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "refseq_ac" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "annotation" } ], [ "P32196-1", "NP_001116622", "protein_xref_refseq", "NP_001116622", "Findings showed that PG3 cathelin-like domain (CLD) efficiently activated rather than inhibited human cathepsin L; partial deletion of the L2 loop of PG3 CLD, significantly decreased its activating effect on cathepsin L" ], [ "P32196-1", "NP_001116622", "protein_xref_pubmed", "18289683", "Findings showed that PG3 cathelin-like domain (CLD) efficiently activated rather than inhibited human cathepsin L; partial deletion of the L2 loop of PG3 CLD, significantly decreased its activating effect on cathepsin L" ], [ "P32194-1", "NP_001116621", "protein_xref_refseq", "NP_001116621", "Transgenic Mice Overexpressing PG1 Display Corneal Opacity and Severe Inflammation in the Eye. Publication Status: Online-Only" ], [ "P32194-1", "NP_001116621", "protein_xref_pubmed", "33557346", "Transgenic Mice Overexpressing PG1 Display Corneal Opacity and Severe Inflammation in the Eye. Publication Status: Online-Only" ], [ "P32194-1", "NP_001116621", "protein_xref_refseq", "NP_001116621", "Further study suggested that protegrin-1 activates insulin-like growth factor 1 receptor (IGF1R) and through this receptor it modulates immune activity as well as cell migration. Publication Status: Online-Only" ], [ "P32194-1", "NP_001116621", "protein_xref_pubmed", "30324092", "Further study suggested that protegrin-1 activates insulin-like growth factor 1 receptor (IGF1R) and through this receptor it modulates immune activity as well as cell migration. Publication Status: Online-Only" ], [ "P32194-1", "NP_001116621", "protein_xref_refseq", "NP_001116621", "Analyzed the expression pattern of protegrins in 17 different pig tissues using RT-PCR, and developed an anti-(PG-1) polyclonal IgG. Western blot analysis using the antibody showed that protegrins are mainly present as prepropeptide forms in normal tissue" ], [ "P32194-1", "NP_001116621", "protein_xref_pubmed", "25264901", "Analyzed the expression pattern of protegrins in 17 different pig tissues using RT-PCR, and developed an anti-(PG-1) polyclonal IgG. Western blot analysis using the antibody showed that protegrins are mainly present as prepropeptide forms in normal tissue" ], [ "P32194-1", "NP_001116621", "protein_xref_refseq", "NP_001116621", "Despite the absence of stabilizing disulfide bridges CDP-1 shows broad-spectrum antibacterial activity and assumes beta-hairpin like structure in complex with LPS." ], [ "P32194-1", "NP_001116621", "protein_xref_pubmed", "24997421", "Despite the absence of stabilizing disulfide bridges CDP-1 shows broad-spectrum antibacterial activity and assumes beta-hairpin like structure in complex with LPS." ], [ "P67937-1", "NP_999500", "protein_xref_refseq", "NP_999500", "Upregulation of tropomyosin 4 (TM4) mRNA is a relevant marker of dedifferentiation in vascular smooth muscle cells." ], [ "P67937-1", "NP_999500", "protein_xref_pubmed", "14582535", "Upregulation of tropomyosin 4 (TM4) mRNA is a relevant marker of dedifferentiation in vascular smooth muscle cells." ], [ "Q5D891-1", "NP_001012974", "protein_xref_refseq", "NP_001012974", "These results suggest that LEPR, MC4R, PIK3C3 and VRTN are useful markers for accurately predicting breeding values in Duroc pigs." ], [ "Q5D891-1", "NP_001012974", "protein_xref_pubmed", "24128088", "These results suggest that LEPR, MC4R, PIK3C3 and VRTN are useful markers for accurately predicting breeding values in Duroc pigs." ], [ "Q5D891-1", "NP_001012974", "protein_xref_refseq", "NP_001012974", "Confirmed that the polymorphism in PIK3C3 (C2604T) has the potential to be a genetic marker for production traits in Duroc pigs" ], [ "Q5D891-1", "NP_001012974", "protein_xref_pubmed", "21269358", "Confirmed that the polymorphism in PIK3C3 (C2604T) has the potential to be a genetic marker for production traits in Duroc pigs" ], [ "B4ZYI5-1", "NP_001127830", "protein_xref_refseq", "NP_001127830", "The authors performed methylome and transcriptome analyses of pig induced pluripotent stem cells and associated cloned embryos, and revealed that aberrant silencing of imprinted genes, in particular the retrotransposon-derived RTL1 gene, is the principal epigenetic cause of pregnancy failure." ], [ "B4ZYI5-1", "NP_001127830", "protein_xref_pubmed", "30381455", "The authors performed methylome and transcriptome analyses of pig induced pluripotent stem cells and associated cloned embryos, and revealed that aberrant silencing of imprinted genes, in particular the retrotransposon-derived RTL1 gene, is the principal epigenetic cause of pregnancy failure." ], [ "B4ZYI5-1", "NP_001127830", "protein_xref_refseq", "NP_001127830", "We did not observe significantly different expression of DLK1, MEG3 or PEG11 mRNA in any of analyzed breeds." ], [ "B4ZYI5-1", "NP_001127830", "protein_xref_pubmed", "21414727", "We did not observe significantly different expression of DLK1, MEG3 or PEG11 mRNA in any of analyzed breeds." ], [ "E9LHE5-1", "NP_001188414", "protein_xref_refseq", "NP_001188414", "Results indicated that BMP and activin membrane-bound inhibitor homolog(BAMBI) is an FSH-repressed gene in porcine luteinizing granulosa cells and it may be involved in the regulation of ovarian follicle development and oocyte maturation" ], [ "E9LHE5-1", "NP_001188414", "protein_xref_pubmed", "25168722", "Results indicated that BMP and activin membrane-bound inhibitor homolog(BAMBI) is an FSH-repressed gene in porcine luteinizing granulosa cells and it may be involved in the regulation of ovarian follicle development and oocyte maturation" ], [ "Q8MHY0-1", "NP_998956", "protein_xref_refseq", "NP_998956", "We show that the phosphorylation of cTnI and alphaTm vary in the different chambers of the heart, whereas the phosphorylation of MLC2 and cTnT does not." ], [ "Q8MHY0-1", "NP_998956", "protein_xref_pubmed", "26268593", "We show that the phosphorylation of cTnI and alphaTm vary in the different chambers of the heart, whereas the phosphorylation of MLC2 and cTnT does not." ], [ "D2ST34-1", "NP_001165223", "protein_xref_refseq", "NP_001165223", "The polymorphism and association analysis of FBXL4 was analyzed." ], [ "D2ST34-1", "NP_001165223", "protein_xref_pubmed", "19768576", "The polymorphism and association analysis of FBXL4 was analyzed." ], [ "B3SP85-1", "NP_001124518", "protein_xref_refseq", "NP_001124518", "The cloning and characterization of porcine gamma-interferon-inducible lysosomal thiol reductase (GILT) are reported." ], [ "B3SP85-1", "NP_001124518", "protein_xref_pubmed", "18722674", "The cloning and characterization of porcine gamma-interferon-inducible lysosomal thiol reductase (GILT) are reported." ], [ "P21692-1", "NP_001159701", "protein_xref_refseq", "NP_001159701", "The identification of MMP1 and MMP10 genes in swine is reported." ], [ "P21692-1", "NP_001159701", "protein_xref_pubmed", "19639408", "The identification of MMP1 and MMP10 genes in swine is reported." ], [ "P21692-1", "NP_001159701", "protein_xref_refseq", "NP_001159701", "Results indicate that leukemia inhibitory factor (LIF) and Oncostatin M increase the expression of MMP-1, MMP-3, and TIMP-1 several fold, and that their expression is reduced to basal levels in the presence of the LIF antagonist MH35-BD." ], [ "P21692-1", "NP_001159701", "protein_xref_pubmed", "19342253", "Results indicate that leukemia inhibitory factor (LIF) and Oncostatin M increase the expression of MMP-1, MMP-3, and TIMP-1 several fold, and that their expression is reduced to basal levels in the presence of the LIF antagonist MH35-BD." ], [ "P21692-1", "NP_001159701", "protein_xref_refseq", "NP_001159701", "Increased interstitial MMP1 activity during ischemia and reperfusion is a result of the endothelin protein kinase c pathway and may be due to enhanced phosphorylation of mmp1" ], [ "P21692-1", "NP_001159701", "protein_xref_pubmed", "18065523", "Increased interstitial MMP1 activity during ischemia and reperfusion is a result of the endothelin protein kinase c pathway and may be due to enhanced phosphorylation of mmp1" ], [ "B8XSJ7-1", "NP_001137189", "protein_xref_refseq", "NP_001137189", "The swine MAPKAPK3 gene might play an important role in the growth and development differences between mini-type Diannan small-ear pigs and large-type Diannan small-ear pigs." ], [ "B8XSJ7-1", "NP_001137189", "protein_xref_pubmed", "19921547", "The swine MAPKAPK3 gene might play an important role in the growth and development differences between mini-type Diannan small-ear pigs and large-type Diannan small-ear pigs." ], [ "A0A4X1VSV5-1", "NP_001231341", "protein_xref_refseq", "NP_001231341", "Heme-oxygenase-2 immunoreactivity was found in neurons of myenteric ganglia and in nerve fibers in the circular and longitudinal muscle layers." ], [ "A0A4X1VSV5-1", "NP_001231341", "protein_xref_pubmed", "19232687", "Heme-oxygenase-2 immunoreactivity was found in neurons of myenteric ganglia and in nerve fibers in the circular and longitudinal muscle layers." ], [ "A0A4X1VSV5-1", "NP_001231341", "protein_xref_refseq", "NP_001231341", "HO-2 is critical for protection of cerebrovascular endothelium against apoptotic changes induced by oxidative stress and cytokine-mediated inflammation." ], [ "A0A4X1VSV5-1", "NP_001231341", "protein_xref_pubmed", "16822952", "HO-2 is critical for protection of cerebrovascular endothelium against apoptotic changes induced by oxidative stress and cytokine-mediated inflammation." ], [ "Q29106-1", "NP_998958", "protein_xref_refseq", "NP_998958", "Novel shuttling domain in a regulator (RSC1A1) of transporter SGLT1 steers cell cycle-dependent nuclear location." ], [ "Q29106-1", "NP_998958", "protein_xref_pubmed", "19765263", "Novel shuttling domain in a regulator (RSC1A1) of transporter SGLT1 steers cell cycle-dependent nuclear location." ], [ "Q0R678-1", "NP_001072131", "protein_xref_refseq", "NP_001072131", "The PARK7 gene was demonstrated to be located on porcine chromosome 6" ], [ "Q0R678-1", "NP_001072131", "protein_xref_pubmed", "17268184", "The PARK7 gene was demonstrated to be located on porcine chromosome 6" ], [ "A0AAS4-1", "NP_001090907", "protein_xref_refseq", "NP_001090907", "A Genome-Wide CRISPR/Cas9 Screen Reveals the Requirement of Host Sphingomyelin Synthase 1 for Infection with Pseudorabies Virus Mutant gD(-)Pass. Publication Status: Online-Only" ], [ "A0AAS4-1", "NP_001090907", "protein_xref_pubmed", "34452438", "A Genome-Wide CRISPR/Cas9 Screen Reveals the Requirement of Host Sphingomyelin Synthase 1 for Infection with Pseudorabies Virus Mutant gD(-)Pass. Publication Status: Online-Only" ], [ "B3F0B7-1", "NP_001121964", "protein_xref_refseq", "NP_001121964", "Chromosome mapping of CRABP1 AND CRABP2 in swine." ], [ "B3F0B7-1", "NP_001121964", "protein_xref_pubmed", "16276655", "Chromosome mapping of CRABP1 AND CRABP2 in swine." ], [ "B2ZI34-1", "NP_001121961", "protein_xref_refseq", "NP_001121961", "In sow estrous cycle, the hypothalamic levels of both NMB and NMBR mRAN were similar, but the expression levels of the pituitary were negatively correlated. Publication Status: Online-Only" ], [ "B2ZI34-1", "NP_001121961", "protein_xref_pubmed", "27010315", "In sow estrous cycle, the hypothalamic levels of both NMB and NMBR mRAN were similar, but the expression levels of the pituitary were negatively correlated. Publication Status: Online-Only" ], [ "P49151-1", "NP_999249", "protein_xref_refseq", "NP_999249", "The Influence of Melatonin and Light on VEGF Secretion in Primary RPE Cells. Publication Status: Online-Only" ], [ "P49151-1", "NP_999249", "protein_xref_pubmed", "33467052", "The Influence of Melatonin and Light on VEGF Secretion in Primary RPE Cells. Publication Status: Online-Only" ], [ "P49151-1", "NP_999249", "protein_xref_refseq", "NP_999249", "Epidural Stimulation Combined with Triple Gene Therapy for Spinal Cord Injury Treatment. Publication Status: Online-Only" ], [ "P49151-1", "NP_999249", "protein_xref_pubmed", "33255323", "Epidural Stimulation Combined with Triple Gene Therapy for Spinal Cord Injury Treatment. Publication Status: Online-Only" ], [ "P49151-1", "NP_999249", "protein_xref_refseq", "NP_999249", "Inhibition of ssc-microRNA-140-5p ameliorates the Clostridium perfringens beta2 toxin-induced inflammatory response in IPEC-J2 cells via the ERK1/2 and JNK pathways by targeting VEGFA." ], [ "P49151-1", "NP_999249", "protein_xref_pubmed", "32905904", "Inhibition of ssc-microRNA-140-5p ameliorates the Clostridium perfringens beta2 toxin-induced inflammatory response in IPEC-J2 cells via the ERK1/2 and JNK pathways by targeting VEGFA." ], [ "P49151-1", "NP_999249", "protein_xref_refseq", "NP_999249", "MMP9 and VEGF, but not MMP13 or FGF23 may have roles in bone lesions in the hypovitaminosis D kyphotic pig model" ], [ "P49151-1", "NP_999249", "protein_xref_pubmed", "29991364", "MMP9 and VEGF, but not MMP13 or FGF23 may have roles in bone lesions in the hypovitaminosis D kyphotic pig model" ], [ "P49151-1", "NP_999249", "protein_xref_refseq", "NP_999249", "Results are consistent with a participation of (VEFG) in the regulation of the dynamics of oviductal fluid secretion and the oviduct contractibility" ], [ "P49151-1", "NP_999249", "protein_xref_pubmed", "28257866", "Results are consistent with a participation of (VEFG) in the regulation of the dynamics of oviductal fluid secretion and the oviduct contractibility" ], [ "P49151-1", "NP_999249", "protein_xref_refseq", "NP_999249", "Data demonstrate that lipopolysaccharides evoke a heat shock response, with an increase heat shock proteins 70 and Hsp32) and of VEGF, a specific endothelial cell growth factor." ], [ "P49151-1", "NP_999249", "protein_xref_pubmed", "16333987", "Data demonstrate that lipopolysaccharides evoke a heat shock response, with an increase heat shock proteins 70 and Hsp32) and of VEGF, a specific endothelial cell growth factor." ], [ "P49151-1", "NP_999249", "protein_xref_refseq", "NP_999249", "VEGF upregulation in the proliferative zone after ischemic damage may play a role in stimulating vascular invasion and granulation tissue formation in the necrotic hypertrophic zone of the epiphyseal cartilage" ], [ "P49151-1", "NP_999249", "protein_xref_pubmed", "15537448", "VEGF upregulation in the proliferative zone after ischemic damage may play a role in stimulating vascular invasion and granulation tissue formation in the necrotic hypertrophic zone of the epiphyseal cartilage" ], [ "P49151-1", "NP_999249", "protein_xref_refseq", "NP_999249", "Contrast media did not affect bone marrow cell viability/VEGF secretion." ], [ "P49151-1", "NP_999249", "protein_xref_pubmed", "15274157", "Contrast media did not affect bone marrow cell viability/VEGF secretion." ], [ "P49151-1", "NP_999249", "protein_xref_refseq", "NP_999249", "The earlier increase in VEGF protein and mRNA expression in the Meishan versus the Yorkshire conceptus may explain the previously reported increased vascularity and increased placental efficiency of this breed compared the Yorkshire breed." ], [ "P49151-1", "NP_999249", "protein_xref_pubmed", "14998908", "The earlier increase in VEGF protein and mRNA expression in the Meishan versus the Yorkshire conceptus may explain the previously reported increased vascularity and increased placental efficiency of this breed compared the Yorkshire breed." ], [ "Q9MYP4-1", "NP_999242", "protein_xref_refseq", "NP_999242", "Findings indicate that the genetic basis of muscle residual glycogen in swine can be mainly attributed to two major genes PRKAG3 and PHKG1 Publication Status: Online-Only" ], [ "Q9MYP4-1", "NP_999242", "protein_xref_pubmed", "31443641", "Findings indicate that the genetic basis of muscle residual glycogen in swine can be mainly attributed to two major genes PRKAG3 and PHKG1 Publication Status: Online-Only" ], [ "Q9MYP4-1", "NP_999242", "protein_xref_refseq", "NP_999242", "Activity of glycogen synthase without the allosteric activator glucose 6-phosphate was decreased in gain of function AMPKgamma3(R200Q) relative to all other genotypes" ], [ "Q9MYP4-1", "NP_999242", "protein_xref_pubmed", "27302990", "Activity of glycogen synthase without the allosteric activator glucose 6-phosphate was decreased in gain of function AMPKgamma3(R200Q) relative to all other genotypes" ], [ "Q9MYP4-1", "NP_999242", "protein_xref_refseq", "NP_999242", "Greater net lactate accumulation postmortem (i.e., glycolytic flux) coupled with a lower buffering capacity explains the lower ultimate pH of meat from AMPKgamma3(R200Q) mutant pigs." ], [ "Q9MYP4-1", "NP_999242", "protein_xref_pubmed", "26241465", "Greater net lactate accumulation postmortem (i.e., glycolytic flux) coupled with a lower buffering capacity explains the lower ultimate pH of meat from AMPKgamma3(R200Q) mutant pigs." ], [ "Q9MYP4-1", "NP_999242", "protein_xref_refseq", "NP_999242", "Allelic frequencies of PRKAG3 in several pig breeds" ], [ "Q9MYP4-1", "NP_999242", "protein_xref_pubmed", "24074175", "Allelic frequencies of PRKAG3 in several pig breeds" ], [ "Q9MYP4-1", "NP_999242", "protein_xref_refseq", "NP_999242", "The variation in the promoter region of the porcine PRKAG3 gene has associations with meat quality phenotypes, including traits which are influenced by glycolytic potential and muscle metabolism in a breed-dependent manner. Publication Status: Online-Only" ], [ "Q9MYP4-1", "NP_999242", "protein_xref_pubmed", "22831392", "The variation in the promoter region of the porcine PRKAG3 gene has associations with meat quality phenotypes, including traits which are influenced by glycolytic potential and muscle metabolism in a breed-dependent manner. Publication Status: Online-Only" ], [ "Q9MYP4-1", "NP_999242", "protein_xref_refseq", "NP_999242", "The R225Q mutation of PRKAG3 is associated with higher basal AMPK activity and diminished AMP dependence" ], [ "Q9MYP4-1", "NP_999242", "protein_xref_pubmed", "15247217", "The R225Q mutation of PRKAG3 is associated with higher basal AMPK activity and diminished AMP dependence" ], [ "Q9MYP4-1", "NP_999242", "protein_xref_refseq", "NP_999242", "Findings suggest that the R200Q mutation results in a constitutively active enzyme, leading to hyperaccumulation of glycogen due to the increased influx of glucose" ], [ "Q9MYP4-1", "NP_999242", "protein_xref_pubmed", "15274139", "Findings suggest that the R200Q mutation results in a constitutively active enzyme, leading to hyperaccumulation of glycogen due to the increased influx of glucose" ], [ "Q9MYP4-1", "NP_999242", "protein_xref_refseq", "NP_999242", "Genetic variation of PRKAG3 was studied in indigenous breeds of China." ], [ "Q9MYP4-1", "NP_999242", "protein_xref_pubmed", "15231235", "Genetic variation of PRKAG3 was studied in indigenous breeds of China." ] ] }, "readme": "Name\n - Pig Protein Function (NCBI Refseq)\n\nVersion\n - v-2.4.1\n\nCreated on\n - \n\nModified on\n - \n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - The Pig Protein Function (NCBI RefSeq) dataset contains biological function annotation of Sus scrofa [taxid:9823] genes from GeneRIF section in the NCBI RefSeq database. If you use this dataset please provide proper attribution to NCBI RefSeq and GlyGen.\n\nDescription Domain\n Keywords\n - protein function\n - NCBI RefSeq\n - geneRIF\n - PMID\n\n Pipeline Steps\n - Step-1: The script parses the NCBI RefSeq gpff files to extract the geneRIFs that contain protein function. The script also maps RefSeq accession to the UniProtKB Canonical accessions\n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/dataset-maker/make-protein-dataset.py\n\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Input Subdomain\n Name: pig_protein_xref_refseq.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/pig_protein_xref_refseq.csv\n Name: refseq_protein_all_9823.gpff\n URI: https:/data.glygen.org/ln2downloads/ncbi/refseq/2024_02_18/refseq_protein_all_9823.gpff\n Output Subdomain\n Name: pig_protein_function_refseq.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/pig_protein_function_refseq.csv\n Name: pig_protein_function_refseq.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/pig_protein_function_refseq.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"763\"\n Name: \"refseq_ac\"\n Description: \"Accession in the NCBI RefSeq database\"\n Unique Values: \"763\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"2\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"2408\"\n Name: \"annotation\"\n Description: \"Function annotation from UniProtKB|RefSeq database\"\n Unique Values: \"1720\"", "downloadurl": "/ln2data/releases/data/v-2.4.1/reviewed/pig_protein_function_refseq.csv" }