{ "bcoid": "GLY_000249", "title": "Rat Protein Function (NCBI RefSeq)", "description": "The Rat Protein Function (NCBI RefSeq) dataset contains biological function annotation of rat [taxid:10116] ...", "filename": "rat_protein_function_refseq.csv", "filetype": "csv", "categories": { "species": [ "Rattus norvegicus" ], "molecule": [ "Protein" ], "tag": [ "Protein Function" ], "file_type": [ "csv" ], "status": [ "Reviewed" ], "scope": [ "internal" ] }, "minitable": { "content": [ [ "Q8R512-1...", "NP_620208..." ], [ "Q8R512-1...", "NP_620208..." ] ], "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" } ], [ "Q8R512-1", "NP_620208", "protein_xref_refseq", "NP_620208", "Socius is a novel Rnd GTPase-interacting protein involved in disassembly of actin stress fibers" ], [ "Q8R512-1", "NP_620208", "protein_xref_pubmed", "11940653", "Socius is a novel Rnd GTPase-interacting protein involved in disassembly of actin stress fibers" ], [ "Q6ZXC8-1", "NP_998793", "protein_xref_refseq", "NP_998793", "Expression of St8sia5 increases over 15 fold at night in the rat pineal gland." ], [ "Q6ZXC8-1", "NP_998793", "protein_xref_pubmed", "19103603", "Expression of St8sia5 increases over 15 fold at night in the rat pineal gland." ], [ "Q6REY9-1", "NP_998794", "protein_xref_refseq", "NP_998794", "RARhoGAP expression was found in differentiating male germ cells and in the testis, suggesting that it may be involved in rearrangements of the cytoskeleton and cell signaling events that occur during spermatogenesis." ], [ "Q6REY9-1", "NP_998794", "protein_xref_pubmed", "15234003", "RARhoGAP expression was found in differentiating male germ cells and in the testis, suggesting that it may be involved in rearrangements of the cytoskeleton and cell signaling events that occur during spermatogenesis." ], [ "Q6PNM1-1", "NP_998795", "protein_xref_refseq", "NP_998795", "Combined Immunotherapy With Belatacept and BTLA Overexpression Attenuates Acute Rejection Following Kidney Transplantation. Publication Status: Online-Only" ], [ "Q6PNM1-1", "NP_998795", "protein_xref_pubmed", "33732243", "Combined Immunotherapy With Belatacept and BTLA Overexpression Attenuates Acute Rejection Following Kidney Transplantation. Publication Status: Online-Only" ], [ "Q9Z1Z6-1", "NP_072128", "protein_xref_refseq", "NP_072128", "Distinct functions for mGluR2 and mGluR3 and dynamic regulation of mGluR3 by PP2C" ], [ "Q9Z1Z6-1", "NP_072128", "protein_xref_pubmed", "14663150", "Distinct functions for mGluR2 and mGluR3 and dynamic regulation of mGluR3 by PP2C" ], [ "P20646-1", "NP_001128373", "protein_xref_refseq", "NP_001128373", "PAP-immunoreactivity was present in type I and one of type III taste cells of taste buds. Thus, it is suggested that PAP might be a responsible ectoenzyme for metabolism of extracellular nucleotides, being involved in the regulation of taste signaling in taste buds. Publication Status: Online-Only" ], [ "P20646-1", "NP_001128373", "protein_xref_pubmed", "27348306", "PAP-immunoreactivity was present in type I and one of type III taste cells of taste buds. Thus, it is suggested that PAP might be a responsible ectoenzyme for metabolism of extracellular nucleotides, being involved in the regulation of taste signaling in taste buds. Publication Status: Online-Only" ], [ "P20646-1", "NP_001128373", "protein_xref_refseq", "NP_001128373", "Acpp plays an important role in growth and development of the penis of rats, and its expression is modulated at epigenomic levels via specific miRs" ], [ "P20646-1", "NP_001128373", "protein_xref_pubmed", "25482440", "Acpp plays an important role in growth and development of the penis of rats, and its expression is modulated at epigenomic levels via specific miRs" ], [ "P20646-1", "NP_001128373", "protein_xref_refseq", "NP_001128373", "Our findings suggest that the decrease of PAP in dorsal root ganglion neurons is involved in pathophysiological mechanisms of neuropathic pain Publication Status: Online-Only" ], [ "P20646-1", "NP_001128373", "protein_xref_pubmed", "25674224", "Our findings suggest that the decrease of PAP in dorsal root ganglion neurons is involved in pathophysiological mechanisms of neuropathic pain Publication Status: Online-Only" ], [ "O88794-1", "NP_072123", "protein_xref_refseq", "NP_072123", "PNPO may play a role in activity-dependent regulation of PLP level in the brain, which is involved in LTP induction and paired-pulse facilitation but not in enhancement of GABAergic inhibition." ], [ "O88794-1", "NP_072123", "protein_xref_pubmed", "18680158", "PNPO may play a role in activity-dependent regulation of PLP level in the brain, which is involved in LTP induction and paired-pulse facilitation but not in enhancement of GABAergic inhibition." ], [ "O88794-1", "NP_072123", "protein_xref_refseq", "NP_072123", "Pnpo is a candidate gene responsible for hypertension in Dahl-S rats" ], [ "O88794-1", "NP_072123", "protein_xref_pubmed", "14697241", "Pnpo is a candidate gene responsible for hypertension in Dahl-S rats" ], [ "P97682-1", "NP_072126", "protein_xref_refseq", "NP_072126", "Peripheral blood ESM-1 mRNA and ESM-1 protein expression in kidney grafts can reflect the severity of endothelial cell impairment" ], [ "P97682-1", "NP_072126", "protein_xref_pubmed", "23850961", "Peripheral blood ESM-1 mRNA and ESM-1 protein expression in kidney grafts can reflect the severity of endothelial cell impairment" ], [ "P50609-1", "NP_542429", "protein_xref_refseq", "NP_542429", "Transfer RNA-derived small RNA tRF-Glu-CTC attenuates neointimal formation via inhibition of fibromodulin. Publication Status: Online-Only" ], [ "P50609-1", "NP_542429", "protein_xref_pubmed", "38172726", "Transfer RNA-derived small RNA tRF-Glu-CTC attenuates neointimal formation via inhibition of fibromodulin. Publication Status: Online-Only" ], [ "P50609-1", "NP_542429", "protein_xref_refseq", "NP_542429", "Downregulation of fibromodulin attenuates inflammatory signaling and atrial fibrosis in spontaneously hypertensive rats with atrial fibrillation via inhibiting TLR4/NLRP3 signaling pathway." ], [ "P50609-1", "NP_542429", "protein_xref_pubmed", "37904680", "Downregulation of fibromodulin attenuates inflammatory signaling and atrial fibrosis in spontaneously hypertensive rats with atrial fibrillation via inhibiting TLR4/NLRP3 signaling pathway." ], [ "P50609-1", "NP_542429", "protein_xref_refseq", "NP_542429", "The fibromodulin (Fm)-transforming growth factor (TGF)-beta1 nexus plays a crucial in fetal-type scarless skin repair." ], [ "P50609-1", "NP_542429", "protein_xref_pubmed", "27665369", "The fibromodulin (Fm)-transforming growth factor (TGF)-beta1 nexus plays a crucial in fetal-type scarless skin repair." ], [ "Q71RP1-1", "NP_072127", "protein_xref_refseq", "NP_072127", "We identified Hpse as a previously unexplored candidate, being up-regulated following injury. We confirmed these results and demonstrated inhibition of Hpse led to an acceleration of axonal degeneration, accompanied by an increase in b-catenin Publication Status: Online-Only" ], [ "Q71RP1-1", "NP_072127", "protein_xref_pubmed", "29581478", "We identified Hpse as a previously unexplored candidate, being up-regulated following injury. We confirmed these results and demonstrated inhibition of Hpse led to an acceleration of axonal degeneration, accompanied by an increase in b-catenin Publication Status: Online-Only" ], [ "Q71RP1-1", "NP_072127", "protein_xref_refseq", "NP_072127", "Heparanase plays an important role in mediating the neuroinflammatory response after subarachnoid hemorrhage. Publication Status: Online-Only" ], [ "Q71RP1-1", "NP_072127", "protein_xref_pubmed", "28720149", "Heparanase plays an important role in mediating the neuroinflammatory response after subarachnoid hemorrhage. Publication Status: Online-Only" ], [ "Q71RP1-1", "NP_072127", "protein_xref_refseq", "NP_072127", "Endothelial cell-to-cardiomyocyte transfer of heparanase to modulates the cardiomyocyte cell death signature. This mechanism was observed in the acutely diabetic heart, and its interruption following chronic diabetes may contribute towards the development of diabetic cardiomyopathy." ], [ "Q71RP1-1", "NP_072127", "protein_xref_pubmed", "27979811", "Endothelial cell-to-cardiomyocyte transfer of heparanase to modulates the cardiomyocyte cell death signature. This mechanism was observed in the acutely diabetic heart, and its interruption following chronic diabetes may contribute towards the development of diabetic cardiomyopathy." ], [ "Q71RP1-1", "NP_072127", "protein_xref_refseq", "NP_072127", "The expression of the gene for heparanase was increased in the right and left ventricles after treatment with monocrotaline" ], [ "Q71RP1-1", "NP_072127", "protein_xref_pubmed", "26638897", "The expression of the gene for heparanase was increased in the right and left ventricles after treatment with monocrotaline" ], [ "Q71RP1-1", "NP_072127", "protein_xref_refseq", "NP_072127", "Inhibiting heparanase function could offer a new strategy for managing cardiomyopathy observed after diabetes." ], [ "Q71RP1-1", "NP_072127", "protein_xref_pubmed", "24608441", "Inhibiting heparanase function could offer a new strategy for managing cardiomyopathy observed after diabetes." ], [ "Q71RP1-1", "NP_072127", "protein_xref_refseq", "NP_072127", "Characterization of rat heparanase activity in a parathyroid cell line" ], [ "Q71RP1-1", "NP_072127", "protein_xref_pubmed", "12077130", "Characterization of rat heparanase activity in a parathyroid cell line" ], [ "Q71RP1-1", "NP_072127", "protein_xref_refseq", "NP_072127", "Characterization of a novel intracellular heparanase that has a FERM domain." ], [ "Q71RP1-1", "NP_072127", "protein_xref_pubmed", "11988100", "Characterization of a novel intracellular heparanase that has a FERM domain." ], [ "Q6ZM99-1", "NP_998897", "protein_xref_refseq", "NP_998897", "Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]." ], [ "Q6ZMA0-1", "NP_998896", "protein_xref_refseq", "NP_998896", "Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]." ], [ "P06536-1", "NP_036708", "protein_xref_refseq", "NP_036708", "Glucocorticoid receptor-NECAB1 axis can negatively regulate insulin secretion in pancreatic beta-cells. Publication Status: Online-Only" ], [ "P06536-1", "NP_036708", "protein_xref_pubmed", "37863964", "Glucocorticoid receptor-NECAB1 axis can negatively regulate insulin secretion in pancreatic beta-cells. Publication Status: Online-Only" ], [ "P06536-1", "NP_036708", "protein_xref_refseq", "NP_036708", "Role of glucocorticoid receptor (GR) in white adipose tissue beiging." ], [ "P06536-1", "NP_036708", "protein_xref_pubmed", "37040814", "Role of glucocorticoid receptor (GR) in white adipose tissue beiging." ], [ "P06536-1", "NP_036708", "protein_xref_refseq", "NP_036708", "Regulatory Effects of Maternal Immune Activation and Environmental Enrichment on Glucocorticoid Receptor and FKBP5 Expression in Stress-sensitive Regions of the Offspring Brain." ], [ "P06536-1", "NP_036708", "protein_xref_pubmed", "36116554", "Regulatory Effects of Maternal Immune Activation and Environmental Enrichment on Glucocorticoid Receptor and FKBP5 Expression in Stress-sensitive Regions of the Offspring Brain." ], [ "P06536-1", "NP_036708", "protein_xref_refseq", "NP_036708", "Glucocorticoid Receptor/HCN4 Channels Interaction in Spinal Dorsal Horn Participates in the Regulation of Neuropathic Pain after Peripheral Nerve Injury in Rats." ], [ "P06536-1", "NP_036708", "protein_xref_pubmed", "36214984", "Glucocorticoid Receptor/HCN4 Channels Interaction in Spinal Dorsal Horn Participates in the Regulation of Neuropathic Pain after Peripheral Nerve Injury in Rats." ], [ "P06536-1", "NP_036708", "protein_xref_refseq", "NP_036708", "Hypothalamic NR3C1 DNA methylation in rats exposed to prenatal stress." ], [ "P06536-1", "NP_036708", "protein_xref_pubmed", "35661969", "Hypothalamic NR3C1 DNA methylation in rats exposed to prenatal stress." ], [ "Q00960-1", "NP_036706", "protein_xref_refseq", "NP_036706", "Cellular mechanisms of contextual fear memory reconsolidation: Role of hippocampal SFKs, TrkB receptors and GluN2B-containing NMDA receptors." ], [ "Q00960-1", "NP_036706", "protein_xref_pubmed", "37700085", "Cellular mechanisms of contextual fear memory reconsolidation: Role of hippocampal SFKs, TrkB receptors and GluN2B-containing NMDA receptors." ], [ "Q00960-1", "NP_036706", "protein_xref_refseq", "NP_036706", "Transcranial Direct Current Stimulation Attenuates the Chronic Pain of Osteoarthritis in Rats via Reducing NMDAR2B Expressions in the Spinal Cord." ], [ "Q00960-1", "NP_036706", "protein_xref_pubmed", "38037367", "Transcranial Direct Current Stimulation Attenuates the Chronic Pain of Osteoarthritis in Rats via Reducing NMDAR2B Expressions in the Spinal Cord." ], [ "Q00960-1", "NP_036706", "protein_xref_refseq", "NP_036706", "Activation of the N-methyl-D-aspartate receptor and calcium/calmodulin-dependent protein kinase IIalpha signal in the rostral anterior cingulate cortex is involved in pain-related aversion in rats with peripheral nerve injury." ], [ "Q00960-1", "NP_036706", "protein_xref_pubmed", "37394125", "Activation of the N-methyl-D-aspartate receptor and calcium/calmodulin-dependent protein kinase IIalpha signal in the rostral anterior cingulate cortex is involved in pain-related aversion in rats with peripheral nerve injury." ], [ "Q00960-1", "NP_036706", "protein_xref_refseq", "NP_036706", "Activation of CB1R alleviates central sensitization by regulating HCN2-pNR2B signaling in a chronic migraine rat model. Publication Status: Online-Only" ], [ "Q00960-1", "NP_036706", "protein_xref_pubmed", "37085778", "Activation of CB1R alleviates central sensitization by regulating HCN2-pNR2B signaling in a chronic migraine rat model. Publication Status: Online-Only" ], [ "Q00960-1", "NP_036706", "protein_xref_refseq", "NP_036706", "Hyperthyroidism leads learning and memory impairment possibly via GRIN2B expression alterations." ], [ "Q00960-1", "NP_036706", "protein_xref_pubmed", "36563833", "Hyperthyroidism leads learning and memory impairment possibly via GRIN2B expression alterations." ], [ "Q01812-1", "NP_036704", "protein_xref_refseq", "NP_036704", "The structure of a high-affinity kainate receptor gluk4 ligand-binding domain crystallized with kainite has been presented." ], [ "Q01812-1", "NP_036704", "protein_xref_pubmed", "27524200", "The structure of a high-affinity kainate receptor gluk4 ligand-binding domain crystallized with kainite has been presented." ], [ "Q01812-1", "NP_036704", "protein_xref_refseq", "NP_036704", "Presynaptic kainate receptors on GABAergic nerve terminals appear to modulate GABAergic transmission, and in doing so may play an important role in the regulation of PAG neuron excitability." ], [ "Q01812-1", "NP_036704", "protein_xref_pubmed", "20303934", "Presynaptic kainate receptors on GABAergic nerve terminals appear to modulate GABAergic transmission, and in doing so may play an important role in the regulation of PAG neuron excitability." ], [ "Q01812-1", "NP_036704", "protein_xref_refseq", "NP_036704", "Adrenalectomy results in increased expression of hippocampal KA1 mRNA, an effect which is reversed by treatment with corticosterone..." ], [ "Q01812-1", "NP_036704", "protein_xref_pubmed", "19180187", "Adrenalectomy results in increased expression of hippocampal KA1 mRNA, an effect which is reversed by treatment with corticosterone..." ], [ "Q00959-1", "NP_036705", "protein_xref_refseq", "NP_036705", "GluN2A Mediates PS-Induced Depressive-Like Behavior by Activating CaMKII and Inhibiting Myelinization." ], [ "Q00959-1", "NP_036705", "protein_xref_pubmed", "38179739", "GluN2A Mediates PS-Induced Depressive-Like Behavior by Activating CaMKII and Inhibiting Myelinization." ], [ "Q00959-1", "NP_036705", "protein_xref_refseq", "NP_036705", "RAGE signaling pathway is involved in CUS-induced depression-like behaviors by regulating the expression of NR2A and NR2B in rat hippocampus DG." ], [ "Q00959-1", "NP_036705", "protein_xref_pubmed", "36521778", "RAGE signaling pathway is involved in CUS-induced depression-like behaviors by regulating the expression of NR2A and NR2B in rat hippocampus DG." ], [ "Q00959-1", "NP_036705", "protein_xref_refseq", "NP_036705", "Differential effects of memory enhancing and impairing doses of methylphenidate on serotonin metabolism and 5-HT1A, GABA, glutamate receptor expression in the rat prefrontal cortex." ], [ "Q00959-1", "NP_036705", "protein_xref_pubmed", "34454977", "Differential effects of memory enhancing and impairing doses of methylphenidate on serotonin metabolism and 5-HT1A, GABA, glutamate receptor expression in the rat prefrontal cortex." ], [ "Q00959-1", "NP_036705", "protein_xref_refseq", "NP_036705", "Knockdown of astrocytic Grin2a aggravates beta-amyloid-induced memory and cognitive deficits through regulating nerve growth factor." ], [ "Q00959-1", "NP_036705", "protein_xref_pubmed", "34291567", "Knockdown of astrocytic Grin2a aggravates beta-amyloid-induced memory and cognitive deficits through regulating nerve growth factor." ], [ "Q00959-1", "NP_036705", "protein_xref_refseq", "NP_036705", "Regulation of NMDA receptor trafficking and gating by activity-dependent CaMKIIalpha phosphorylation of the GluN2A subunit." ], [ "Q00959-1", "NP_036705", "protein_xref_pubmed", "34233182", "Regulation of NMDA receptor trafficking and gating by activity-dependent CaMKIIalpha phosphorylation of the GluN2A subunit." ], [ "P10860-1", "NP_036702", "protein_xref_refseq", "NP_036702", "GDH promotes isoprenaline-induced cardiac hypertrophy by activating mTOR signaling via elevation of alpha-ketoglutarate level." ], [ "P10860-1", "NP_036702", "protein_xref_pubmed", "35904584", "GDH promotes isoprenaline-induced cardiac hypertrophy by activating mTOR signaling via elevation of alpha-ketoglutarate level." ], [ "P10860-1", "NP_036702", "protein_xref_refseq", "NP_036702", "Findings demonstrate that hippocampal synapse assembly and maintenance require a tripartite molecular complex in which the ligand Cbln2 binds with presynaptic neurexin 1beta (+S4) and postsynaptic GluD1." ], [ "P10860-1", "NP_036702", "protein_xref_pubmed", "29784783", "Findings demonstrate that hippocampal synapse assembly and maintenance require a tripartite molecular complex in which the ligand Cbln2 binds with presynaptic neurexin 1beta (+S4) and postsynaptic GluD1." ] ] }, "readme": "Name\n - Rat Protein Function (NCBI RefSeq)\n\nVersion\n - v-2.4.1\n\nCreated on\n - 2019-09-06T14:06:38.975527\n\nModified on\n - 2022-09-26T09:04:47.890686\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Luke Johnson [luke.johnson@email.gwu.edu], Urnisha Bhuiyan [sbhuiyan28@email.gwu.edu], Cyrus Au-Yeung [cyruschauyeung@gwu.edu], Jingyue Wu [jingyue.wu@email.gwu.edu]\n\nAuthors\n - Not Applicable []\n\nChecksum\n - \n\nUsability Domain\n - The Rat Protein Function (NCBI RefSeq) dataset contains biological function annotation of rat [taxid:10116] genes from GeneRIF section in the NCBI RefSeq database. The dataset is derived from NCBI RefSeq Release 96, September 9, 2019. 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 accessions 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: rat_protein_xref_refseq.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/rat_protein_xref_refseq.csv\n Name: refseq_protein_all_10116.gpff\n URI: https:/data.glygen.org/ln2downloads/ncbi/refseq/2024_02_18/refseq_protein_all_10116.gpff\n Output Subdomain\n Name: rat_protein_function_refseq.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/rat_protein_function_refseq.csv\n Name: rat_protein_function_refseq.stat.csv\n URI: https:/data.glygen.org/ln2releases/data/v-2.4.1/reviewed/rat_protein_function_refseq.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"5843\"\n Name: \"refseq_ac\"\n Description: \"Accession in the NCBI RefSeq database\"\n Unique Values: \"5843\"\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: \"18142\"\n Name: \"annotation\"\n Description: \"Function annotation from UniProtKB|RefSeq database\"\n Unique Values: \"12612\"", "downloadurl": "/ln2data/releases/data/v-2.4.1/reviewed/rat_protein_function_refseq.csv" }