{ "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", "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", "", "a neuronal protein that binds neurexin l alpha [RGD, Feb 2006]." ], [ "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." ], [ "P29598-1", "protein_xref_refseq", "NP_037217.3", "", "displays a post-transcriptional increase in enzyme levels in chemically induced mammary carcinoma; may play a role in tumor invasion and metastasis [RGD, Feb 2006]." ], [ "P29598-1", "protein_xref_refseq", "NP_037217.3", "30671487", "That study shows that urokinase attenuates pulmonary thromboembolism in an animal model by inhibition of inflammatory response Publication Status: Online-Only" ], [ "P29598-1", "protein_xref_refseq", "NP_037217.3", "26363453", "Autophagy could regulate the EPCs migration through mTOR-P70 S6K pathway, and MMP2, MMP9 and uPA may also involve in the regulation mechanism" ], [ "Q62921-1", "protein_xref_refseq", "NP_068532.2", "", "PKC binding protein; may play a role in protein kinase C mediated signaling [RGD, Feb 2006]." ], [ "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", "", "mutation of gene is associated with autosomal recessive disorder familial dysautonomia (FD) [RGD, Feb 2006]." ], [ "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", "", "a Rho kinase that is involved in inducing membrane blebbing and chromatin condensation [RGD, Feb 2006]." ], [ "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." ], [ "M0R669-1", "protein_xref_refseq", "NP_001000372.1", "", "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]." ], [ "D4A4L3-1", "protein_xref_refseq", "NP_001000223.1", "", "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]." ], [ "P01257-1", "protein_xref_refseq", "NP_059034.1", "", "an inhibitor of lactotroph function and a potent vasodilator [RGD, Feb 2006]." ], [ "P01257-1", "protein_xref_refseq", "NP_059034.1", "31386894", "CGRP has a protective role in high-glucose-induced oxidative injury in rat aorta endothelial cells." ], [ "P01257-1", "protein_xref_refseq", "NP_059034.1", "32212492", "The expressions of CGRP and VIP were significantly down-regulated in the erectile dysfunction rat model" ], [ "Q5USB9-1", "protein_xref_refseq", "NP_001000424.1", "", "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]." ], [ "O88272-1", "protein_xref_refseq", "NP_446058.1", "", "may play a role in degrading and remodeling components of extracellular matrix [RGD, Feb 2006]." ], [ "D3ZTD8-1", "protein_xref_refseq", "NP_001101129.1", "16144627", "Semaphorin5A expression in the developing chick telencephalon." ], [ "Q62667-1", "protein_xref_refseq", "NP_073206.2", "", "member of a large cytosolic ribonucleoprotein particle; may play a role in vault function [RGD, Feb 2006]." ], [ "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." ], [ "D4ACZ8-1", "protein_xref_refseq", "NP_001000308.1", "", "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]." ], [ "P14173-1", "protein_xref_refseq", "NP_001257782.1", "", "catalyzes the decarboxylation of L-5-hydroxytryptophan to serotonin and L-3,4-dihydroxyphenylalanine to dopamine [RGD, Feb 2006]." ], [ "P14173-1", "protein_xref_refseq", "NP_001257782.1", "22829864", "The data show that endothelial AADC plays an important role in cardiac synthesis of 5-HT and possibly in 5-HT-dependent regulation of nitric oxide generation." ], [ "P14173-1", "protein_xref_refseq", "NP_001257782.1", "20232137", "The expression of striatal L: -amino-acid decarboxylase (AADC) in L: -DOPA-induced dyskinesia rats, even though tyrosine hydroxylase (TH) expression did not increase." ], [ "D3ZSC7-1", "protein_xref_refseq", "NP_001000093.1", "", "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]." ], [ "P97639-1", "protein_xref_refseq", "NP_113946.1", "", "receptor for melanin-concentrating hormone (MCH); may mediate intracellular Ca2+ levels, forskolin-stimulated cyclic AMP production, and activation of mitogen-activated protein kinase; may play role in energy homeostasis [RGD, Feb 2006]." ], [ "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." ], [ "D3ZVM8-1", "protein_xref_refseq", "NP_001001038.1", "", "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]." ], [ "A0A096MJG3-1", "protein_xref_refseq", "NP_001102582.1", "27196292", "CP-25 attenuates the inflammatory response of fibroblast-like synoviocytes from arthritic rats co-cultured with BAFF-activated CD4(+) T cells." ], [ "A0A096MJG3-1", "protein_xref_refseq", "NP_001102582.1", "26688104", "Increased spleen levels at early stage of adjuvant induced arthritis" ], [ "A0A096MJG3-1", "protein_xref_refseq", "NP_001102582.1", "26417991", "Role of TLR3/BAFF axis in IgA class-switch recombination of IgA nephropathy" ], [ "D3ZLZ1-1", "protein_xref_refseq", "NP_001000562.1", "", "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]." ], [ "Q8K4B1-1", "protein_xref_refseq", "NP_663705.1", "32061390", "Upregulation of lncRNA-NONRATT021203.2 in the dorsal root ganglion contributes to cancer-induced pain via CXCL9 in rats." ], [ "Q8K4B1-1", "protein_xref_refseq", "NP_663705.1", "31550444", "Results reveal that Cxcl9 is a negative modulator of angiogenesis and osteogenesis, and its inhibition could promote pre-vascularization of bone tissue engineering" ], [ "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." ], [ "D3Z984-1", "protein_xref_refseq", "NP_001000286.1", "", "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]." ], [ "Q91XV6-1", "protein_xref_refseq", "NP_071288.1", "", "This reference sequence was derived from multiple replicate ESTs and a deposited cDNA, and validated by similar human genomic sequence. This gene encodes a member of a family of small membrane proteins that share a 35-amino acid signature sequence domain, beginning with the sequence PFXYD and containing 7 invariant and 6 highly conserved amino acids. The approved human gene nomenclature for the family is FXYD-domain containing ion transport regulator. FXYD2, also known as the gamma subunit of the Na,K-ATPase, regulates the properties of that enzyme. FXYD1 (phospholemman), FXYD2 (gamma), FXYD3 (MAT-8), FXYD4 (CHIF), and FXYD5 (RIC) have been shown to induce channel activity in experimental expression systems. Transmembrane topology has been established for two family members (FXYD1 and FXYD2), with the N-terminus extracellular and the C-terminus on the cytoplasmic side of the membrane. This gene product, FXYD6, is novel and has not been characterized as a protein. The name 'phosphohippolin' has been used in GenBank, but there is no evidence yet of protein phosphorylation. [RefSeq curation by Kathleen J. Sweadner, Ph.D., sweadner@helix.mgh.harvard.edu., Dec 2000]." ], [ "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", "", "binds Rho family GTPase Rnd2; may play a role in endosomal trafficking [RGD, Feb 2006]." ], [ "Q793F9-1", "protein_xref_refseq", "NP_663711.1", "28064406", "Vps4A was involved in promoting neuronal apoptosis via inhibiting Akt phosphorylation after intracerebral hemorrhage" ], [ "M0RAV4-1", "protein_xref_refseq", "NP_001000013.1", "", "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]." ], [ "Q08603-1", "protein_xref_refseq", "NP_619715.1", "", "subunit of Rab geranylgeranyl transferase, which catalyses the transfer of geranylgeranyl groups to Rab protein cysteine residues [RGD, Feb 2006]." ], [ "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", "", "receptor for the tachykinin neuromedin K (neurokinin B); couples with G protein that activates the phosphatidylinositol-calcium second mesenger system [RGD, Feb 2006]." ], [ "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." ], [ "P48679-1", "protein_xref_refseq", "NP_001002016.2", "", "a component of the nuclear membrane on the nucleoplasmic side or lamina [RGD, Feb 2006]." ], [ "P48679-1", "protein_xref_refseq", "NP_001002016.2", "29040816", "Lamin A/C interacts with Notch signaling, thereby influencing cellular differentiation, and point mutation in LMNA could halt this interaction" ], [ "P48679-1", "protein_xref_refseq", "NP_001002016.2", "27114541", "Our findings establish the pathogenetic role of emerin and lamin A/C repression in stretch-induced VSMC proliferation and suggest mechanobiological mechanism underlying this process that involves the sequence-specific binding of emerin and lamin A/C to specific transcription factor motifs." ], [ "P48679-1", "protein_xref_refseq", "NP_001002016.2", "26769003", "The knockdown of prelamin A and lamin A inhibited the increase of Runx2, osteocalcin and osteopontin gene expression, calcium deposition, nuclear abnormalities and the RUNX2 protein translocation into the nucleus of the cell." ], [ "Q7TT49-1", "protein_xref_refseq", "NP_446072.2", "", "serine/threonine protein kinase; mediates myosin light chain phosphorylation [RGD, Feb 2006]." ], [ "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." ], [ "P30349-1", "protein_xref_refseq", "NP_001025202.1", "30745237", "Gliotoxin suppresses the biosynthesis of the potent neutrophil chemoattractant LTB4 by direct interference with LTA4H thereby impairing neutrophil functions in invasive aspergillosis." ], [ "P30349-1", "protein_xref_refseq", "NP_001025202.1", "24701582", "The involvement of compartmentalized and coupled changes of LTB4 and LTA4H in the resistance and development of arthritis in CIA model was demonstrated for the first time." ], [ "Q63636-1", "protein_xref_refseq", "NP_599159.1", "", "serine protease in activated lymphocytes required for lymphocyte cytotoxic granules to lyse target cells [RGD, Feb 2006]." ], [ "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]" ], [ "Q63148-1", "protein_xref_refseq", "NP_476475.1", "", "secreted protein; human homolog binds TGF-beta and similar morphogenetic proteins; may be important for organogenesis and dorsal/ventral pattern specification of neural crest [RGD, Feb 2006]." ], [ "Q63148-1", "protein_xref_refseq", "NP_476475.1", "27546891", "Chordin and noggin were intensely expressed throughout the trigeminal nuclei. chordin prefers dendritic expression than noggin, suggesting that chordin is involved in the regulation of dendritic morphology and synaptic homeostasis. Furthermore, chordin and noggin were differentially expressed in the neuropil of the trigeminal nuclei." ], [ "Q63148-1", "protein_xref_refseq", "NP_476475.1", "24231736", "Data indicate that chordin is more widely expressed throughout the adult CNS than previously reported, and its continued abundant expression in the adult brain strongly supports the idea that chordin plays pivotal roles also in the adult brain" ], [ "Q920L7-1", "protein_xref_refseq", "NP_599209.1", "", "human homolog is involved in the elongation of long-chain polyunsaturated fatty acids [RGD, Feb 2006]." ], [ "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", "", "plays a role in cyclic nucleotide degradation; may be involved in oocyte maturation [RGD, Feb 2006]." ] ] }, "readme": "Name\n - Rat Protein Function (NCBI RefSeq)\n\nVersion\n - 1.11.2\n\nCreated on\n - 2019-09-06T14:06:38.975527\n\nModified on\n - 2022-01-19T13:13:56.046976\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], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@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/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-1.11.2/source/refseq_protein_all_10116.gpff\n Name: rat_protein_xref_refseq.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.11.2/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-1.11.2/reviewed/rat_protein_function_refseq.csv\n Name: rat_protein_function_refseq.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.11.2/reviewed/rat_protein_function_refseq.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"16\"\n Name: \"motif_start\"\n Description: \"\"\n Unique Values: \"23\"\n Name: \"filter_flags\"\n Description: \"Filter tags/flags assigned to the mutation entries that have passed the mutation filter criteria\"\n Unique Values: \"19\"\n Name: \"sift_prediction\"\n Description: \"The SIFT qualitative prediction is derived from this score such that substitutions with a score < 0.05 are called 'deleterious' and all others are called 'tolerated\"\n Unique Values: \"3\"\n Name: \"somatic_status\"\n Description: \"The status of the variant whether it is germline (somatic status =0) or somatic (somatic status =1) variant\"\n Unique Values: \"1\"\n Name: \"chr_pos\"\n Description: \"Chromosome Position of a gene\"\n Unique Values: \"19\"\n Name: \"chr_id\"\n Description: \"\"\n Unique Values: \"10\"\n Name: \"dbsnp_id\"\n Description: \"\"A reference SNP ID number\"\n Unique Values: \"19\"\n Name: \"evidence_ECO:0000313\"\n Description: \"A type of evidence that is imported information used in an automatic assertion\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"19\"\n Name: \"mim_id\"\n Description: \"Disease ID from the OMIM database\"\n Unique Values: \"1\"\n Name: \"description\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"begin_aa_pos\"\n Description: \"Start position of the amino acid in the sequence of a protein in UniProtKB\"\n Unique Values: \"18\"\n Name: \"cytogenic_band\"\n Description: \"One of the subregions of a chromosome visible microscopically after special staining\"\n Unique Values: \"14\"\n Name: \"aa_pos\"\n Description: \"Position of the amino acid in canonical sequence of protein in the UniProtKB database\"\n Unique Values: \"18\"\n Name: \"ref_aa\"\n Description: \"Reference amino acid residue\"\n Unique Values: \"9\"\n Name: \"sift_score\"\n Description: \"SIFT predicts whether an amino acid substitution is likely to affect protein function based on sequence homology and the physico-chemical similarity between the alternate amino acids. The data we provide for each amino acid substitution is a score and a qualitative prediction (either 'tolerated' or 'deleterious'). The score is the normalized probability that the amino acid change is tolerated so scores nearer zero are more likely to be deleterious. The qualitative prediction is derived from this score such that substitutions with a score < 0.05 are called 'deleterious' and all others are called 'tolerated\"\n Unique Values: \"10\"\n Name: \"alt_motif\"\n Description: \"Altered motif\"\n Unique Values: \"24\"\n Name: \"disease_xrefs\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"polyphen_score\"\n Description: \"The score assigned to a amino acid substitution by a tool called as PolyPhen (=Polymorphism Phenotyping) which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. The PolyPhen score ranges from 0.0 (tolerated) to 1.0 (deleterious). Variants with scores of 0.0 are predicted to be benign. Values closer to 1.0 are more confidently predicted to be deleterious\"\n Unique Values: \"1\"\n Name: \"polyphen_prediction\"\n Description: \"\"The PolyPhen prediction values are - greater than 0.908 - \"\"Probably Damaging\"\"; greater than 0.446 and less than or equal to 0.908 - \"\"Possibly Damaging\"\"; less than or equal to 0.446 - \"\"Benign\"\"\"\n Unique Values: \"1\"\n Name: \"is_known_glycoprotein\"\n Description: \"Yes or no flag to denote if a protein is experimentally proven glycoprotein\"\n Unique Values: \"1\"\n Name: \"alt_nt\"\n Description: \"Alternative nucleotide\"\n Unique Values: \"1\"\n Name: \"protein_name\"\n Description: \"Protein name in the UniProtKB\"\n Unique Values: \"16\"\n Name: \"disease_evidence_ECO:0000313\"\n Description: \"The evidence that could be a PMID or a ClinVar ID that associates disease with the variant\"\n Unique Values: \"1\"\n Name: \"effect\"\n Description: \"The effect on glycosylation or N-sequon due to variation at site of glycosylated amino acid.\"\n Unique Values: \"3\"\n Name: \"end_aa_pos\"\n Description: \"End position of the amino acid in the sequence of a protein in UniProtKB\"\n Unique Values: \"18\"\n Name: \"mutation_type\"\n Description: \"Denotes whether mutation was reported with reference to amino acid or nucleotide\"\n Unique Values: \"1\"\n Name: \"disease_description\"\n Description: \"The disease description and/or definition \"\n Unique Values: \"1\"\n Name: \"do_id\"\n Description: \"Disease Ontology identifier\"\n Unique Values: \"1\"\n Name: \"evidence_ECO:0000269\"\n Description: \"A type of experimental evidence that is used in a manual assertion. Usually the values are PMIDs\"\n Unique Values: \"1\"\n Name: \"ref_nt\"\n Description: \"Reference nucleotide\"\n Unique Values: \"4\"\n Name: \"disease\"\n Description: \"The disease name for the cell line\"\n Unique Values: \"1\"\n Name: \"alt_aa\"\n Description: \"Altered amino acid residue\"\n Unique Values: \"10\"\n Name: \"cosmic_id\"\n Description: \"Legacy mutation identifier (COSM) in Catalogue of Somatic Mutations in Cancer (COSMIC) represents existing COSM mutation identifiers. This identifier remains the same between different assemblies (GRCh37 and GRCh38). All the COSM ids at the same genomic location have been collapsed into one representative COSM id. These ids are maintained to help track existing mutations\"\n Unique Values: \"1\"\n Name: \"ref_motif\"\n Description: \"Reference motif\"\n Unique Values: \"20\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"2\"\n Name: \"minor_allelic_frequency\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"gene_name\"\n Description: \"\"Official gene name/symbol assigned to the gene. Human gene name/symbol are approved by the HUGO Gene Nomenclature Committee (HGNC) and mouse gene name are approved by the Mouse Genome Informatics (MGI)\"\n Unique Values: \"17\"\n Name: \"disease_evidence_ECO:0000269\"\n Description: \"The PMID evidence for the association of the disease with the variant.\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.11.2/reviewed/rat_protein_function_refseq.csv" }