{ "bcoid": "GLY_000249", "title": "Rat Refseq Protein Function", "description": "The Rat NCBI RefSeq Protein Function dataset contains biological function annotaion of rat [taxid:10116] ...", "filename": "rat_protein_function_refseq.csv", "filetype": "csv", "categories": { "species": "Rattus Norvegicus", "molecule": "Protein", "tags": "Protein Function", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "Q63366-1...", "RefSeq..." ], [ "Q63366-1...", "RefSeq..." ] ], "headers": [ "uniprotkb_ca...", "database_nam..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "database_name" }, { "type": "string", "label": "database_id" }, { "type": "string", "label": "evidence" }, { "type": "string", "label": "annotation" } ], [ "Q63366-1", "RefSeq", "NP_037126.1", "25420124", "NRXN1alpha KO rats were found to present with large and persistent nonsocial deficits, including hyperactivity, deficits in simple instrumental learning, latent inhibition, and spatial-dependent learning." ], [ "Q63366-1", "RefSeq", "NP_037126.1", "25157101", "Dystroglycan binding to alpha-neurexin competes with neurexophilin-1 and neuroligin in the brain." ], [ "Q63366-1", "RefSeq", "NP_037126.1", "12141453", "Study on the expression of NXPH1 in the developing and adult olfactory bulb" ], [ "D3ZKJ8-1", "RefSeq", "NP_001163817.1", "22564741", "These results suggest that DNA glycosylases OGG1 and NEIL3 play multiple roles in governing essential neural stem cell characteristics." ], [ "B4F775-1", "RefSeq", "NP_001101101.1", "21953547", "Distribution of Gopc/PIST suggests that the protein serves distinctive roles in specific neuronal populations, establishing functionally distinct zones, for instance, in the hippocampus." ], [ "Q62921-1", "RefSeq", "NP_068532.2", "15833741", "RBCK1 (human C20orf18 and rat Pkcbpb15) is involved in transcriptional machinery in the nuclear bodies, and its transcriptional activity is regulated by nucleocytoplasmic shuttling." ], [ "Q8VHU4-1", "RefSeq", "NP_543175.1", "20184874", "Organ culture of bronchi induces IkappaB kinase mediated inflammatory changes resulting in airway hyperresponsiveness to bradykinin via the up-regulation of bradykinin receptors." ], [ "Q62868-1", "RefSeq", "NP_037154.2", "30747210", "These results demonstrate that miR335 promotes stress granule formation and inhibits apoptosis by reducing ROCK2 expression in acute ischemic stroke." ], [ "Q62868-1", "RefSeq", "NP_037154.2", "30363018", "Inhibition of ROCK2 promotes autophagy and reduces the injury in the hippocampus, leading to the recovery of learning and memory ability following subarachnoid hemorrhage" ], [ "Q62868-1", "RefSeq", "NP_037154.2", "29791873", "Together, the results of this study reveal a novel mechanism through which RhoA/ROCK signaling regulates smooth muscle phenotypic modulation and vascular remodeling via the JNK pathway and vimentin cytoskeleton" ], [ "Q62868-1", "RefSeq", "NP_037154.2", "29219181", "Suggest an essential role for Rock1/2 activity in the insulin signaling and glucose homeostasis improvement in exercising skeletal muscle." ], [ "Q62868-1", "RefSeq", "NP_037154.2", "11867620", "RhoA and Rho kinase-dependent phosphorylation of moesin at Thr-558 in hippocampal neuronal cells by glutamate" ], [ "Q8VID6-1", "RefSeq", "NP_543169.1", "19445908", "We here present, for the first time, the expression of PDE9A, PDE10A, and PDE11A in the trigeminovascular system; localisation indicates that they may have a role in pain pathways" ], [ "Q8VID6-1", "RefSeq", "NP_543169.1", "17696499", "This report is the first to describe an inhibitory effect of the N-terminal region of PDE11A4 on the affinity of the catalytic domain for both substrates and inhibitors and the first to define the quaternary structure." ], [ "P01257-1", "RefSeq", "NP_059034.1", "29846865", "CGRP gene-modified rat bone mesenchymal stem cells show better osteogenic differentiation capacity." ], [ "P01257-1", "RefSeq", "NP_059034.1", "29730242", "We analysed the modulation of capsaicin (CAP)-induced neurogenic inflammation in the rat hind paw by the selective 5-HT7 receptor agonist, LP-44, and the involvement of calcitonin gen-related peptide (CGRP) in this effect" ], [ "P01257-1", "RefSeq", "NP_059034.1", "28599085", "Remote hind limb preconditioning stimulus probably activates TRPV1 channels which subsequently induces CGRP release to produce cardioprotective effects." ], [ "P01257-1", "RefSeq", "NP_059034.1", "28560441", "Data suggest that CGRP can partly protect AECII cells from hyperoxia-induced injury, and the upregulation of CGRP may be a potential therapeutic approach with which to combat hyperoxia-induced lung injury, which may be associated with the activation of the SHH signaling pathway." ], [ "P01257-1", "RefSeq", "NP_059034.1", "28393079", "Tyrosine phosphorylation of NR2B decreased the mechanical threshold and increased migraine attacks via upregulated CGRP expression in the rat model of chronic migraines (CM). Thus, tyrosine phosphorylation of NR2B may be a potential therapeutic target for treatment of CM" ], [ "Q62667-1", "RefSeq", "NP_073206.2", "16441665", "Data show that the interaction between Src and major vault protein (MVP) is critically dependent on Src activity and protein (MVP) tyrosyl phosphorylation, which are induced by epidermal growth factor stimulation. Erratum:[FEBS J. 2006 Jun;273(11):2577]" ], [ "Q62667-1", "RefSeq", "NP_073206.2", "11727830", "Casein kinase II enhances the phosphorylation of MVP in PC12 cells.Our results suggest that cell-specific phosphorylation of MVP may play a critical role in vault function." ], [ "P97639-1", "RefSeq", "NP_113946.1", "27579857", "Data suggest a dual role of MCH and the MCH1-R in regulation of alcohol intake, possibly through mechanisms involving caloric intake and reward motivation." ], [ "P97639-1", "RefSeq", "NP_113946.1", "26456505", "MCH levels in the CSF, brain preproMCH and MCHR1 gene expression during paradoxical sleep deprivation, sleep rebound and chronic sleep restriction were studied in rats." ], [ "P97639-1", "RefSeq", "NP_113946.1", "25617691", "The study identified the amino acids that are selectively involved in Gi/o activation by rat melanin-concentrating hormone receptor 1." ], [ "Q8K4B1-1", "RefSeq", "NP_663705.1", "23819906", "CXCL9 is involved in the modulation of pancreatic fibrogenesis in trinitrobenzene sulfonic acid-induced chronic pancreatitis in rats, and may be a therapeutic target in pancreatic fibrosis." ], [ "Q8K4B1-1", "RefSeq", "NP_663705.1", "14568964", "Has an important role in the recruitment of mononuclear cells, a pivotal event in the pathogenesis of acute lung allograft rejection" ], [ "Q2VUH7-1", "RefSeq", "NP_001032743.1", "27873129", "Up-regulation of Dixdc1 protein expression is potentially involved in astrocyte proliferation after traumatic brain injury in the rat." ], [ "Q2VUH7-1", "RefSeq", "NP_001032743.1", "27521891", "These data demonstrated that Dixdc1 might participate in Schwann cell proliferation by targeting CyclinD1 and p21 at least partially through the PI3K/AKT activation." ], [ "Q2VUH7-1", "RefSeq", "NP_001032743.1", "19339625", "Findings define a novel SnoN-Ccd1 link that promotes axonal growth in the mammalian brain, with important implications for axonal development and regeneration" ], [ "Q2VUH7-1", "RefSeq", "NP_001032743.1", "17554179", "The DIX domain of rat axin, which is important for its homooligomerization and interactions with other regulators in the Wnt pathway, has been purified and crystallized." ], [ "Q91XV6-1", "RefSeq", "NP_071288.1", "17676640", "FXYD6 is expressed in the inner ear and may have a role in endolymph homeostasis and neuronal activity" ], [ "Q91XV6-1", "RefSeq", "NP_071288.1", "15193427", "Findings suggest that Php may play an important role in the excitability of neurons in the central nervous system during postnatal development, as well as those in the adult brain" ], [ "Q793F9-1", "RefSeq", "NP_663711.1", "28064406", "Vps4A was involved in promoting neuronal apoptosis via inhibiting Akt phosphorylation after intracerebral hemorrhage" ], [ "Q08603-1", "RefSeq", "NP_619715.1", "23114750", "SiRNA-mediated knockdown of alpha- or beta-subunits of RGGT and REP1 markedly attenuates glucose-stimulated insulin secretion in insulin 832/13 cells" ], [ "Q2PWT8-1", "RefSeq", "NP_001033066.1", "24486887", "AP4M1 is not only down-regulated at both the mRNA and protein levels, but also redistributed from dendrites to axons in oxygen-glucose deprived hippocampal neurons." ], [ "Q63484-1", "RefSeq", "NP_113763.1", "27821807", "Suggest that when cardiomyocytes incur oxidative stress under diabetic conditions, it subsequently activates the PI3Kgamma/Akt cell-signaling pathway and further increases HMGB1 expression." ], [ "Q63484-1", "RefSeq", "NP_113763.1", "11907032", "Overexpression of calreticulin modulates protein kinase B/Akt signaling to promote apoptosis" ], [ "Q7TT49-1", "RefSeq", "NP_446072.2", "18854160", "Study reports that MRCK and myosin II-related MYO18A linked by the adaptor protein LRAP35a form a functional tripartite complex, which is responsible for the assembly of lamellar actomyosin bundles and of a subnuclear actomyosin network." ], [ "P0C5J5-1", "RefSeq", "NP_001123248.1", "15497143", "OC29 may have a role in the early development of the inner ear sensory organ, particularly in the formation of the cristae of the semicircular canals [OC29]" ], [ "P46844-1", "RefSeq", "NP_446302.1", "23722043", "BVR contributes to the inhibitory process of hypoxia on pulmonary arterial smooth muscle cell apoptosis, which is mediated by bilirubin through ERK1/2 pathway." ], [ "P46844-1", "RefSeq", "NP_446302.1", "20876213", "Data show that siRNA blockage of BVR protein expression in cardiomyocytes inhibits HO-2 protein induction but not vice versa." ], [ "P46844-1", "RefSeq", "NP_446302.1", "17402939", "Results describe the activation of biliverdin-IXalpha reductase by inorganic phosphate and related anions." ], [ "P46844-1", "RefSeq", "NP_446302.1", "12079357", "X-ray crystal structures of apo rat BVR and its complex with NADH at 1.2 A and 1.5 A resolution, respectively" ], [ "Q62865-1", "RefSeq", "NP_059033.1", "27975297", "PDE3A is a low-affinity and high-velocity enzyme for hydrolysis of cUMP in cardiac myocytes." ], [ "Q62865-1", "RefSeq", "NP_059033.1", "21224496", "Observations suggest that NO modulates PDE3A gene expression via mechanisms dependent upon cGMP synthesis and gene transcription." ], [ "D4ADE6-1", "RefSeq", "NP_001100732.1", "19131967", "These data establish Sall2 as a link between p75 neurotrophin receptor and transcriptional events that regulate the growth and development of neuronal cells." ], [ "Q62747-1", "RefSeq", "NP_067691.1", "28111077", "The slowed endocytosis phenotype previously reported after syt1 loss of function can also be triggered by other manipulations that promote asynchronous release such as Sr(2+) substitution and complexin loss of function. The link between asynchronous release and slowed endocytosis was due to selective targeting of fused synaptic vesicles toward slow retrieval by the asynchronous release Ca(2+) sensor synaptotagmin-7." ], [ "Q62747-1", "RefSeq", "NP_067691.1", "27771350", "In somata of Purkinje neurons in the cerebellar cortex, both SYT7 (and SYNCRIP) were expressed and co-localized." ], [ "Q920R4-1", "RefSeq", "NP_599213.1", "16298334", "Nuclear translocation of PIPS is involved in NGF mediated neuronal survival via TrkA, PI3K, and Gab1 signaling pathway" ], [ "Q920R4-1", "RefSeq", "NP_599213.1", "12409294", "Ca(2+)/cAMP response element-binding protein (CREB) and Per1 are integral components of the pathway transducing light-stimulated GLU neurotransmission into phase advance of the circadian clock" ], [ "Q920R4-1", "RefSeq", "NP_599213.1", "12176169", "Per1 gene product in the rat suprachiasmatic nucleus is modulated by seasonal changes in daylength." ], [ "Q5XIF5-1", "RefSeq", "NP_445775.2", "22139871", "The myristic acid-associated increase in DES1 activity slightly enhanced the number of apoptotic cells" ], [ "Q5XIF5-1", "RefSeq", "NP_445775.2", "21914808", "Overexpression of DEGS1 or DEGS2 attenuates the DHC accumulation and increased cell proliferation during hypoxia Erratum:[J Biol Chem. 2012 May 18;287(21):17425]" ], [ "Q9WUF4-1", "RefSeq", "NP_114015.1", "28242757", "Acute inhibition of VAMP8-mediated secretion during pancreatitis triggers intracellular trypsin accumulation and loss of the early endosomal compartment" ], [ "Q9WUF4-1", "RefSeq", "NP_114015.1", "27402227", "The authors took a proteomics approach using a PKCB knockout mast cell model and found that the key mast cell secretory protein VAMP8 becomes phosphorylated by PKC at multiple residues in the SNARE domain." ], [ "B2RZ98-1", "RefSeq", "NP_001120776.1", "25224032", "The levels of cytosolic p67Phox, p47Phox, and p40Phox were increased in membrane fractions following traumatic brain injury." ], [ "P43428-1", "RefSeq", "NP_037230.2", "22214556", "We demonstrate an essential role for fructose 2,6-bisphosphate in the induction of glucose-6-phosphatase and other ChREBP target genes" ], [ "P43428-1", "RefSeq", "NP_037230.2", "21402051", "An increase in G6Pase activity was observed in liver microsomes from rats starved overnight, which presented a ~15% decrease in hepatic Mg(2+) content." ], [ "P43428-1", "RefSeq", "NP_037230.2", "18717264", "The lower sensitivity of the liver nuclear envelope G-6-Pase to N-ethylmaleimide suggests that the catalytic subunit of this system has some differences from the microsomal isoform." ], [ "P43428-1", "RefSeq", "NP_037230.2", "18304430", "Calorie restriction can inhibit the expressions of FoxO1, PEPCK and G-6-P, strengthen insulin signal conduction, suppress gluconeogenesis and thus regulate glycometabolism." ], [ "P43428-1", "RefSeq", "NP_037230.2", "17931592", "The effect, which is lost when G6P has readily access to the ER lumen, requires physiological endoplasmic reticulum Mg(2+) content." ], [ "G3V802-1", "RefSeq", "NP_446154.3", "27414783", "SPINK3 along with Ccna2 and EGFR accelerated cell proliferation during rat liver regeneration via P38 MAPK, PKC, JAK-STAT and AKT pathways." ], [ "O55005-1", "RefSeq", "NP_071524.1", "28973045", "The alteration of Slit2 and Robo1 expression in the retinas of diabetic rats and patients with proliferative diabetic retinopathy suggests a role for the Slit-Robo signal in the various stages diabetic retinopathy. Publication Status: Online-Only" ], [ "O55005-1", "RefSeq", "NP_071524.1", "27893610", "This study showed that Robo1 and RhoA were increased in the same surviving neurons in the spinal cord following spinal cord injury." ], [ "O55005-1", "RefSeq", "NP_071524.1", "27686659", "Data revealed a selective and sustained induction of Slit2 and Robo in astrocytes localized throughout the astroglial scar after ischemic stroke, suggesting that Slit2/Robo signaling participates in glial scar formation and brain remodeling following ischemic injury." ], [ "O55005-1", "RefSeq", "NP_071524.1", "26764532", "Results suggest that Slit2/Robo signaling may be involved in regulating the astroglial reaction via autocrine or paracrine mechanisms in post-ischemic processes." ], [ "Q9EQL5-1", "RefSeq", "NP_446237.1", "17069928", "Rat TM4SF4 is overexpressed in acutely injured liver induced by CCl4 and plays a crucial role in accelerating liver injury, which may be mediated by the TNF-alpha and HGF/c-met signaling pathways." ], [ "D3Z8Q6-1", "RefSeq", "NP_001099554.2", "28628258", "Studied role of tankyrase and effect of tankyrase inhibitor XAV939 on corpus luteum development , luteal function, and Wnt/beta-catenin signaling in gonadotropin-treated prepubertal rats." ], [ "D3Z8Q6-1", "RefSeq", "NP_001099554.2", "25876076", "Tankyrase-mediated PARsylation is promoted by nutritional energy stimulated NAD+ in insulinoma cells Publication Status: Online-Only" ], [ "Q62638-1", "RefSeq", "NP_058907.1", "19148508", "Under hypoxia, ESL-1 is shed from activated hepatic stellate cells" ], [ "P02665-1", "RefSeq", "NP_058816.2", "21621605", "4-Vinylcyclohexene diepoxide administration to 1-month rats acutely decreased mammary alveolar bud number and expression of beta-casein." ], [ "P02665-1", "RefSeq", "NP_058816.2", "18462607", "Mammary tissue from late pregnant Restricted rats had elevated alpha-lactalbumin, but not beta-casein mRNA." ], [ "P35572-1", "RefSeq", "NP_037236.1", "28044240", "IGFBP-6 was significantly up-regulated adjacent to the hematoma following intracerebral hemorrhage." ], [ "P35572-1", "RefSeq", "NP_037236.1", "27888466", "Following spinal cord injury, IGFBP6 was significantly up-regulated." ], [ "P35572-1", "RefSeq", "NP_037236.1", "21598309", "IGFs/IGFBPs may have important roles not only in fracture healing but also in nonunion formation." ], [ "Q9ES19-1", "RefSeq", "NP_077379.1", "28188284", "Glucagon plus insulin increases FGF21 transcription by stimulating ATF4 expression" ], [ "Q9ES19-1", "RefSeq", "NP_077379.1", "27841340", "Results find that ATF4 down-regulation in both hippocampal and cortical neuron cultures reduces protein and RNA levels of RhoGDIalpha. The study identified a new cellular pathway in which ATF4 regulates the expression of RhoGDIalpha that in turn affects Rho GTPase protein levels, and thereby, controls cellular functions as diverse as memory and cell motility. Publication Status: Online-Only" ], [ "Q63673-1", "RefSeq", "NP_058917.1", "30391523", "Reintroduction of sonic hedgehog protein in an aged prostatectomy model is even more effective in promoting neurite formation/cavernous nerve regeneration than in adult." ], [ "Q63673-1", "RefSeq", "NP_058917.1", "29721855", "These results revealed the critical roles of Id1 and SHH mediating Abeta-dependent cell cycle reentry and subsequently caspase-dependent apoptosis in the fully differentiated post-mitotic neurons." ], [ "Q63673-1", "RefSeq", "NP_058917.1", "28560441", "Data suggest that CGRP can partly protect AECII cells from hyperoxia-induced injury, and the upregulation of CGRP may be a potential therapeutic approach with which to combat hyperoxia-induced lung injury, which may be associated with the activation of the SHH signaling pathway." ], [ "Q63673-1", "RefSeq", "NP_058917.1", "28262835", "Data show that sonic hedgehog protein (SHH) was expressed mainly in the synaptic vesicles of hippocampus in both young postnatal and adult rats. Publication Status: Online-Only" ], [ "Q63673-1", "RefSeq", "NP_058917.1", "27639396", "A positive role for Shh signaling, through the activator Smo, in oligodendrocyte differentiation after lineage specification." ], [ "Q9EPI8-1", "RefSeq", "NP_445951.1", "15087485", "The DNA-binding activity of mTERF is unaffected by the phosphorylation or dephosphorylation state, however, only the phosphorylated form of the protein is active for termination activity. Publication Status: Online-Only" ], [ "Q923Y4-1", "RefSeq", "NP_783177.1", "17556730", "Expression of Taar family members is limited to specific tissue subpopulations and developmental stages in mouse." ] ] }, "readme": "Name\n - Rat Refseq Protein Function\n\nVersion\n - 1.4.5\n\nCreated on\n - 2019-09-06T14:06:38.975527\n\nModified on\n - \n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Xavier Holmes [xavierh@email.gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - The Rat NCBI RefSeq Protein Function dataset contains biological function annotaion of rat [taxid:10116] genes from GeneRIF section in the NCBI RefSeq database. The data is downloaded from NCBI RefSeq and is processed into a dataset by GlyGen. 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 accesion to the UniProtKB Canonical accessions\n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/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: refseq_protein_all_10116.gpff\n URI: https://data.glygen.org/ln2data/releases/data/v-1.4.5/source/refseq_protein_all_10116.gpff\n Name: rat_protein_xref_refseq.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.4.5/reviewed/rat_protein_xref_refseq.csv\n Output Subdomain\n Name: rat_protein_function_refseq.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.4.5/reviewed/rat_protein_function_refseq.csv\n Name: rat_protein_function_refseq.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.4.5/reviewed/rat_protein_function_refseq.stat.csv\n\nFields\n Name: \"database_id\"\n Description: \"Identifier in the database\"\n Unique Values: \"3760\"\n Name: \"uniprotkb_canonical_ac\"\n Description: \"Accession assigned to the protein isoform chosen to be the canonical sequence to which all positional annotation refers in UniProtKB database\"\n Unique Values: \"3760\"\n Name: \"database_name\"\n Description: \"The name of the source database\"\n Unique Values: \"1\"\n Name: \"annotation\"\n Description: \"Function annotation from UniProtKB|RefSeq database\"\n Unique Values: \"9090\"\n Name: \"evidence\"\n Description: \"NCBI PubMed Id (PMID) as evidence for the entry/annotation\"\n Unique Values: \"8933\"", "downloadurl": "/ln2data/releases/data/v-1.4.5/reviewed/rat_protein_function_refseq.csv" }