{ "bcoid": "GLY_000249", "title": "Rat Protein Function (NCBI RefSeq)", "description": "The Rat Protein Function (NCBI RefSeq) 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...", "protein_xref..." ], [ "Q63366-1...", "protein_xref..." ] ], "headers": [ "uniprotkb_ca...", "xref_key..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "evidence" }, { "type": "string", "label": "annotation" } ], [ "Q63366-1", "protein_xref_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", "protein_xref_refseq", "NP_037126.1", "25157101", "Dystroglycan binding to alpha-neurexin competes with neurexophilin-1 and neuroligin in the brain." ], [ "Q63366-1", "protein_xref_refseq", "NP_037126.1", "12141453", "Study on the expression of NXPH1 in the developing and adult olfactory bulb" ], [ "D3ZKJ8-1", "protein_xref_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", "protein_xref_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", "protein_xref_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", "protein_xref_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", "protein_xref_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", "protein_xref_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", "protein_xref_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", "protein_xref_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", "protein_xref_refseq", "NP_037154.2", "11867620", "RhoA and Rho kinase-dependent phosphorylation of moesin at Thr-558 in hippocampal neuronal cells by glutamate" ], [ "D4A3M8-1", "protein_xref_refseq", "NP_001101686.1", "17591694", "Results suggest that Nckbeta maintains paxillin stability during neuritogenesis." ], [ "P01257-1", "protein_xref_refseq", "NP_059034.1", "31035923", "The expression of CGRPO and (PACAP1-38) simultaneously increases in the trigeminovascular system and influences the formation of mechanical hyperalgesia. Publication Status: Online-Only" ], [ "P01257-1", "protein_xref_refseq", "NP_059034.1", "29846865", "CGRP gene-modified rat bone mesenchymal stem cells show better osteogenic differentiation capacity." ], [ "P01257-1", "protein_xref_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", "protein_xref_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", "protein_xref_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." ], [ "D3ZTD8-1", "protein_xref_refseq", "NP_001101129.1", "16144627", "Semaphorin5A expression in the developing chick telencephalon." ], [ "Q62667-1", "protein_xref_refseq", "NP_073206.2", "29093465", "The predicted docking shows that the vault-interacting domain of vault poly(ADP-ribose)-polymerase (INT) interaction sites are located between MVP domains 3 and 5. Publication Status: Online-Only" ], [ "Q62667-1", "protein_xref_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", "protein_xref_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", "protein_xref_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", "protein_xref_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", "protein_xref_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", "protein_xref_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." ], [ "Q2VUH7-1", "protein_xref_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", "protein_xref_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", "protein_xref_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", "protein_xref_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", "protein_xref_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", "protein_xref_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", "protein_xref_refseq", "NP_663711.1", "28064406", "Vps4A was involved in promoting neuronal apoptosis via inhibiting Akt phosphorylation after intracerebral hemorrhage" ], [ "Q08603-1", "protein_xref_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" ], [ "P16177-1", "protein_xref_refseq", "NP_058749.1", "30207304", "The different impacts of diverse long-term exercise intensities on the male pituitary-gonadal axis maybe relay by the various changes in hypothalamic Nkb and Pdyn gene expressions." ], [ "P16177-1", "protein_xref_refseq", "NP_058749.1", "26851555", "Results give support to the involvement of NK3 receptors in the anxiogenic-like actions of SP6-11(C-terminal), where this metabolite seems to behave as an antagonist, in a way similar to SR142801." ], [ "P16177-1", "protein_xref_refseq", "NP_058749.1", "25825817", "Median preoptic nucleus NK3R neurons facilitate cutaneous vasodilation, an important heat-dissipation effector." ], [ "P16177-1", "protein_xref_refseq", "NP_058749.1", "24863620", "Data suggest that endogenous NeuroKinin B-Neurokinin 3 Receptor signalling plays a role in controlling the timing of puberty." ], [ "P16177-1", "protein_xref_refseq", "NP_058749.1", "24708241", "Data indicate that the suppression of the GnRH pulse generator by acute systemic stress equires hypothalamic NKB/neurokinin B (NKB) receptor (NK3R) signaling." ], [ "Q2PWT8-1", "protein_xref_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", "protein_xref_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", "protein_xref_refseq", "NP_113763.1", "11907032", "Overexpression of calreticulin modulates protein kinase B/Akt signaling to promote apoptosis" ], [ "Q7TT49-1", "protein_xref_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", "protein_xref_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", "protein_xref_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", "protein_xref_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", "protein_xref_refseq", "NP_446302.1", "17402939", "Results describe the activation of biliverdin-IXalpha reductase by inorganic phosphate and related anions." ], [ "P46844-1", "protein_xref_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" ], [ "Q920L7-1", "protein_xref_refseq", "NP_599209.1", "25046614", "Results show that genes with the highest expression in the mammary gland, liver and adipose tissue were Elovl5, Fads2, and Fasn, respectively, in a low-lipid diet than in adequate-lipid diet." ], [ "Q920L7-1", "protein_xref_refseq", "NP_599209.1", "23873268", "Critical residues in Elovl2 and Elovl5 define their substrate specificities and their ability to elongate docosapentaenoic acid." ], [ "Q62865-1", "protein_xref_refseq", "NP_059033.1", "27975297", "PDE3A is a low-affinity and high-velocity enzyme for hydrolysis of cUMP in cardiac myocytes." ], [ "Q62865-1", "protein_xref_refseq", "NP_059033.1", "21224496", "Observations suggest that NO modulates PDE3A gene expression via mechanisms dependent upon cGMP synthesis and gene transcription." ], [ "D3ZCS4-1", "protein_xref_refseq", "NP_001178638.1", "29522098", "Naturally occurring cytokinesis failure in primary cardiomyocytes is due to an aberrant mitotic microtubule apparatus and mislocalization of RhoA and IQGAP3 resulting in inefficient anchorage of the actomyosin ring to the plasma cell membrane." ], [ "D3ZCS4-1", "protein_xref_refseq", "NP_001178638.1", "17244649", "Iqgap3, a novel effector of Rac1 and Cdc42, regulates neurite outgrowth." ], [ "D4ADE6-1", "protein_xref_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." ], [ "Q8R426-1", "protein_xref_refseq", "NP_001248318.1", "25917026", "KChIP1 plays a neuroprotective role against 4-AP acute induced cell death in primary hippocampal cells through regulation of Kv 4.3 and GABA transmission but this is lost after long term exposure." ], [ "Q8R426-1", "protein_xref_refseq", "NP_001248318.1", "24037673", "This study demonistrared that the expression and function of KCHIP1 channels in neurons of the rat bed nucleus of the stria terminalis." ], [ "Q8R426-1", "protein_xref_refseq", "NP_001248318.1", "20849929", "KChIP1 is selectively expressed in BLA interneurons where it may function to regulate the activity of A-type potassium channels. Hence, KChIP1 might be considered as a specific regulator of GABAergic inhibitory circuits in the basolateral amygdala." ], [ "Q8R426-1", "protein_xref_refseq", "NP_001248318.1", "19896980", "Aph1b and KCnIP1 are significantly differentially expressed in a number of brain tissues of a schizophrenia model; KCnIP1 is an attractive novel candidate gene that may play a role in the complex phenotype" ], [ "Q8R426-1", "protein_xref_refseq", "NP_001248318.1", "12646414", "The features of KChIP1b modulation of Kv4 channels are likely to be conserved in mammals and demonstrate a role for the KChIP1 NH2-terminal region in the regulation of closed inactivation gating." ], [ "Q8R426-1", "protein_xref_refseq", "NP_001248318.1", "12138168", "Hypothesis that occlusion of the inner vestibule of the Na(+) channel by the fast inactivation gate inhibits ultra-slow inactivation (mu1 sodium channel)" ], [ "Q62747-1", "protein_xref_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", "protein_xref_refseq", "NP_067691.1", "27771350", "In somata of Purkinje neurons in the cerebellar cortex, both SYT7 (and SYNCRIP) were expressed and co-localized." ], [ "Q6IN38-1", "protein_xref_refseq", "NP_446190.1", "26637809", "Data show that microRNA miR-17-5p over-expression promoted the activation of hepatic stellate cell (HSC) and contributed to the reduction of Wnt inhibitory factor 1 (WIF1) levels." ], [ "Q6IN38-1", "protein_xref_refseq", "NP_446190.1", "21986617", "Downregulation of Smad1/Wif1 gene expression may contribute to pulmonary hypoplasia in the nitrofen CDH model by retardation of lung development during saccular stage." ], [ "Q6IN38-1", "protein_xref_refseq", "NP_446190.1", "19621428", "Wif-1 inhibits proliferation of neoplastic choroid plexus epithelial cells" ], [ "Q6IN38-1", "protein_xref_refseq", "NP_446190.1", "12470708", "GLT mRNA was translated in Wnt-1-expressing C6 cells when the GLT mRNA required no splicing before translation occurred" ], [ "Q920R4-1", "protein_xref_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", "protein_xref_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", "protein_xref_refseq", "NP_599213.1", "12176169", "Per1 gene product in the rat suprachiasmatic nucleus is modulated by seasonal changes in daylength." ], [ "Q5XIF5-1", "protein_xref_refseq", "NP_445775.2", "22139871", "The myristic acid-associated increase in DES1 activity slightly enhanced the number of apoptotic cells" ], [ "Q5XIF5-1", "protein_xref_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]" ], [ "P29315-1", "protein_xref_refseq", "NP_001257691.1", "24288130", "RNH1 protein is upregulated after spinal cord injury." ], [ "P29315-1", "protein_xref_refseq", "NP_001257691.1", "23624614", "Rnh1-mediated RhoA inactivation enhances the differentiation and myelination in oligodendrocytes." ], [ "Q03344-1", "protein_xref_refseq", "NP_037047.2", "29380352", "Results indicate that IF1 is a negative regulator of insulin secretion involved in pancreatic beta-cell glucose sensing." ], [ "Q03344-1", "protein_xref_refseq", "NP_037047.2", "26484591", "These data suggest that in mammalian neurons mitochondria adapt to respiratory stress by upregulating IF1, which exerts a protective role by coordinating pro-survival cell mitophagy and bioenergetics resilience" ], [ "Q03344-1", "protein_xref_refseq", "NP_037047.2", "24380588", "The subunit c of F0F1-ATPase is a structural and/or regulatory component of the mPTP complex, whose activity might be modulated bycalcium-dependent phosphorylation." ], [ "Q9WUF4-1", "protein_xref_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", "protein_xref_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." ], [ "Q8VD50-1", "protein_xref_refseq", "NP_536324.1", "23193052", "An immobilization-induced attenuation of mTORC1 signaling mediated by induction of REDD1/2 and defective p70S6K1 phosphorylation." ], [ "Q8VD50-1", "protein_xref_refseq", "NP_536324.1", "15607738", "SMHS1 was found to be mainly expressed in skeletal muscle, and comparisons of its expression in atrophied versus hypertrophied muscles and in oxidative versus glycolytic muscles suggested that SMHS1 contributes to the muscle energy metabolism phenotypes." ], [ "B2RZ98-1", "protein_xref_refseq", "NP_001120776.1", "25224032", "The levels of cytosolic p67Phox, p47Phox, and p40Phox were increased in membrane fractions following traumatic brain injury." ], [ "G3V802-1", "protein_xref_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." ], [ "D4A7E1-1", "protein_xref_refseq", "NP_001100218.1", "30498928", "Hepatitis B virus markedly upregulated hepatic BATF expression and promoted Th17 cell activation." ] ] }, "readme": "Name\n - Rat Protein Function (NCBI RefSeq)\n\nVersion\n - 1.7.10\n\nCreated on\n - 2019-09-06T14:06:38.975527\n\nModified on\n - 2020-04-10T11:59:41.589685\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 Protein Function (NCBI RefSeq) dataset contains biological function annotaion 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 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/ln2wwwdata/source/refseq_protein_all_10116.gpff\n Name: rat_protein_xref_refseq.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/rat_protein_xref_refseq.csv\n Output Subdomain\n Name: rat_protein_function_refseq.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/rat_protein_function_refseq.csv\n Name: rat_protein_function_refseq.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/rat_protein_function_refseq.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"4912\"\n Name: \"evidence\"\n Description: \"NCBI PubMed Id (PMID) or DOI (Digital Object Identifier) as evidence for the entry/annotation\"\n Unique Values: \"11356\"\n Name: \"annotation\"\n Description: \"Function annotation from UniProtKB|RefSeq database\"\n Unique Values: \"11633\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"4912\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.7.10/reviewed/rat_protein_function_refseq.csv" }