{ "bcoid": "GLY_000021", "title": "Human RefSeq Protein Information", "description": "The Human RefSeq Protein Information dataset contains human [taxid:9606] protein information such as ...", "filename": "human_protein_refseq_protein_info.csv", "filetype": "csv", "categories": { "status": "Reviewed" }, "minitable": { "content": [ [ "Q8TBF5-1...", "NP_001159776..." ], [ "Q8TBF4-1...", "NP_149105.3..." ] ], "headers": [ "uniprotkb_ca...", "p_refseq_ac_..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "p_refseq_ac_best_match" }, { "type": "string", "label": "refseq_protein_name" }, { "type": "string", "label": "refseq_protein_length" }, { "type": "string", "label": "refseq_protein_summary" } ], [ "Q8TBF5-1", "NP_001159776.1", "phosphatidylinositol-glycan biosynthesis class X protein isoform 1 precursor", "276", "This gene encodes a type I transmembrane protein in the endoplasmic reticulum (ER). The protein is an essential component of glycosylphosphatidylinositol-mannosyltransferase I, which transfers the first of the four mannoses in the GPI-anchor precursors during GPI-anchor biosynthesis. Studies in rat indicate that the protein is translated from a non-AUG translation initiation site. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]. " ], [ "Q8TBF4-1", "NP_149105.3", "zinc finger CCHC-type and RNA-binding motif-containing protein 1", "217", "Pre-mRNA splicing is catalyzed by the spliceosome. U12-type spliceosome binds U12-type pre-mRNAs and recognizes the 5' splice site and branch-point sequence. U11 and U12 snRNPs are components of U12-type spliceosome and function as a molecular bridge connecting both ends of the intron. The protein encoded by this gene contains a RNA recognition motif. It was identified as one of the protein components of U11/U12 snRNPs. This protein and many other U11/U12 snRNP proteins are highly conserved in organisms known to contain U12-type introns. These proteins have been shown to be essential for cell viability, suggesting the key roles in U12-type splicing. [provided by RefSeq, Jul 2008]. " ], [ "Q9NQ79-1", "NP_001193457.1", "cartilage acidic protein 1 isoform B precursor", "645", "This gene encodes a glycosylated extracellular matrix protein that is found in the interterritorial matrix of articular deep zone cartilage. This protein is used as a marker to distinguish chondrocytes from osteoblasts and mesenchymal stem cells in culture. The presence of FG-GAP motifs and an RGD integrin-binding motif suggests that this protein may be involved in cell-cell or cell-matrix interactions. Copy number alterations in this gene have been observed in neurofibromatosis type 1-associated glomus tumors. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]. " ], [ "Q9NVL8-1", "NP_001269985.1", "uncharacterized protein CCDC198 isoform 1", "336", "" ], [ "P30613-1", "NP_000289.1", "pyruvate kinase PKLR isoform 1", "574", "The protein encoded by this gene is a pyruvate kinase that catalyzes the transphosphorylation of phohsphoenolpyruvate into pyruvate and ATP, which is the rate-limiting step of glycolysis. Defects in this enzyme, due to gene mutations or genetic variations, are the common cause of chronic hereditary nonspherocytic hemolytic anemia (CNSHA or HNSHA). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]. " ], [ "Q5H9L4-1", "NP_001161946.1", "transcription initiation factor TFIID subunit 7-like isoform 2", "376", "This gene is similar to a mouse gene that encodes a TATA box binding protein-associated factor, and shows testis-specific expression. The encoded protein could be a spermatogenesis-specific component of the DNA-binding general transcription factor complex TFIID. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2009]. " ], [ "Q9BZL4-1", "NP_001258547.1", "protein phosphatase 1 regulatory subunit 12C isoform b", "780", "The gene encodes a subunit of myosin phosphatase. The encoded protein regulates the catalytic activity of protein phosphatase 1 delta and assembly of the actin cytoskeleton. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Oct 2012]. " ], [ "Q9NVL1-1", "NP_001093123.1", "protein FAM86C1 isoform 3", "158", "" ], [ "Q9NQ75-1", "NP_001157586.1", "cas scaffolding protein family member 4 isoform b", "732", "" ], [ "F8VUJ3-1", "NP_001186710.1", "POC1B-GALNT4 protein isoform 1", "575", "This locus represents naturally occurring transcripts that splice the 5' exons of the POC1B (POC1 centriolar protein homolog B) gene on chromosome 12 to the GALNT4 (UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4) gene, which is located within a POC1B intron. Alternative splicing results in two transcript variants, one of which encodes a fusion isoform that shares sequence identity with the products of each individual gene. [provided by RefSeq, Dec 2010]. " ], [ "P20933-1", "NP_000018.2", "N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase isoform 1 preproprotein", "346", "This gene encodes a member of the N-terminal nucleophile (Ntn) hydrolase family of proteins. The encoded preproprotein is proteolytically processed to generate alpha and beta chains that comprise the mature enzyme. This enzyme is involved in the catabolism of N-linked oligosaccharides of glycoproteins. It cleaves asparagine from N-acetylglucosamines as one of the final steps in the lysosomal breakdown of glycoproteins. Mutations in this gene are associated with the lysosomal storage disease aspartylglycosaminuria that results in progressive neurodegeneration. Alternative splicing results in multiple transcript variants, at least one of which encodes an isoform that is subject to proteolytic processing. [provided by RefSeq, Nov 2015]. " ], [ "P20936-1", "NP_002881.1", "ras GTPase-activating protein 1 isoform 1", "1047", "The protein encoded by this gene is located in the cytoplasm and is part of the GAP1 family of GTPase-activating proteins. The gene product stimulates the GTPase activity of normal RAS p21 but not its oncogenic counterpart. Acting as a suppressor of RAS function, the protein enhances the weak intrinsic GTPase activity of RAS proteins resulting in the inactive GDP-bound form of RAS, thereby allowing control of cellular proliferation and differentiation. Mutations leading to changes in the binding sites of either protein are associated with basal cell carcinomas. Mutations also have been associated with hereditary capillary malformations (CM) with or without arteriovenous malformations (AVM) and Parkes Weber syndrome. Alternative splicing results in two isoforms where the shorter isoform, lacking the N-terminal hydrophobic region but retaining the same activity, appears to be abundantly expressed in placental but not adult tissues. [provided by RefSeq, May 2012]. " ], [ "Q9NZV5-1", "NP_065184.2", "selenoprotein N isoform 2", "590", "This gene encodes a glycoprotein that is localized in the endoplasmic reticulum. It plays an important role in cell protection against oxidative stress, and in the regulation of redox-related calcium homeostasis. Mutations in this gene are associated with early onset muscle disorders, referred to as SEPN1-related myopathy. SEPN1-related myopathy consists of 4 autosomal recessive disorders, originally thought to be separate entities: rigid spine muscular dystrophy (RSMD1), the classical form of multiminicore disease, desmin related myopathy with Mallory-body like inclusions, and congenital fiber-type disproportion (CFTD). This protein is a selenoprotein, containing the rare amino acid selenocysteine (Sec). Sec is encoded by the UGA codon, which normally signals translation termination. The 3' UTRs of selenoprotein mRNAs contain a conserved stem-loop structure, designated the Sec insertion sequence (SECIS) element, that is necessary for the recognition of UGA as a Sec codon, rather than as a stop signal. A second stop-codon redefinition element (SRE) adjacent to the UGA codon has been identified in this gene (PMID:15791204). SRE is a phylogenetically conserved stem-loop structure that stimulates readthrough at the UGA codon, and augments the Sec insertion efficiency by SECIS. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2016]. " ], [ "Q6P1J6-1", "NP_001164056.1", "phospholipase B1, membrane-associated isoform 2 precursor", "1447", "This gene encodes a membrane-associated phospholipase that displays lysophospholipase and phospholipase A2 activities through removal of sn-1 and sn-2 fatty acids of glycerophospholipids. In addition, it displays lipase and retinyl ester hydrolase activities. The encoded protein is highly conserved and is composed of a large, glycosylated extracellular domain composed of four tandem homologous domains, followed by a hydrophobic segment that anchors the enzyme to the membrane and a short C-terminal cytoplasmic tail. This gene has been identified as a candidate rheumatoid arthritis risk gene. [provided by RefSeq, Jul 2016]. " ], [ "Q9UM21-1", "NP_001153626.1", "alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase A isoform 2", "423", "This gene encodes a key glycosyltransferase that regulates the formation of tri- and multiantennary branching structures in the Golgi apparatus. The encoded protein, in addition to the related isoenzyme B, catalyzes the transfer of N-acetylglucosamine (GlcNAc) from UDP-GlcNAc in a beta-1,4 linkage to the Man-alpha-1,3-Man-beta-1,4-GlcNAc arm of R-Man-alpha-1,6(GlcNAc-beta-1,2-Man-alpha-1,3)Man-beta-1, 4-GlcNAc-beta-1,4-GlcNAc-beta-1-Asn. The encoded protein may play a role in regulating the availability of serum glycoproteins, oncogenesis, and differentiation. [provided by RefSeq, Jul 2008]. " ], [ "Q496A3-1", "NP_659463.1", "spermatogenesis-associated serine-rich protein 1", "300", "" ], [ "Q9Y2J8-1", "NP_031391.2", "protein-arginine deiminase type-2", "665", "This gene encodes a member of the peptidyl arginine deiminase family of enzymes, which catalyze the post-translational deimination of proteins by converting arginine residues into citrullines in the presence of calcium ions. The family members have distinct substrate specificities and tissue-specific expression patterns. The type II enzyme is the most widely expressed family member. Known substrates for this enzyme include myelin basic protein in the central nervous system and vimentin in skeletal muscle and macrophages. This enzyme is thought to play a role in the onset and progression of neurodegenerative human disorders, including Alzheimer disease and multiple sclerosis, and it has also been implicated in glaucoma pathogenesis. This gene exists in a cluster with four other paralogous genes. [provided by RefSeq, Jul 2008]. " ], [ "P83859-1", "NP_937823.1", "orexigenic neuropeptide QRFP preproprotein", "136", "This gene encodes a preproprotein that is proteolytically processed to generate multiple protein products. The encoded products are members of the RFamide family of neuropeptides, characterized by their common protein C-terminus consisting of an arginine (R) and an amidated phenylalanine (F). These products include the neuropeptides 26RFa and the N-terminally extended form, 43RFa. Both of these neuropeptides bind to the pyroglutamylated RFamide peptide receptor (QRFPR) and may regulate blood pressure, reproduction and food intake in rodents. [provided by RefSeq, Jul 2015]. " ], [ "Q8TBF2-1", "NP_001182665.1", "prostamide/prostaglandin F synthase isoform a", "246", "" ], [ "Q15573-1", "NP_001188465.1", "TATA box-binding protein-associated factor RNA polymerase I subunit A isoform 1", "450", "This gene encodes a subunit of the RNA polymerase I complex, Selectivity Factor I (SLI). The encoded protein is a TATA box-binding protein-associated factor that plays a role in the assembly of the RNA polymerase I preinitiation complex. Alternate splicing results in multiple transcript variants encoding multiple isoforms.[provided by RefSeq, Jan 2011]. " ], [ "Q15572-1", "NP_001230085.1", "TATA box-binding protein-associated factor RNA polymerase I subunit C isoform 3", "843", "Initiation of transcription by RNA polymerase I requires the formation of a complex composed of the TATA-binding protein (TBP) and three TBP-associated factors (TAFs) specific for RNA polymerase I. This complex, known as SL1, binds to the core promoter of ribosomal RNA genes to position the polymerase properly and acts as a channel for regulatory signals. This gene encodes the largest SL1-specific TAF. Multiple alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2011]. " ], [ "Q9H999-1", "NP_078870.1", "pantothenate kinase 3", "370", "This gene encodes a protein belonging to the pantothenate kinase family. Pantothenate kinase is a key regulatory enzyme in the biosynthesis of coenzyme A (CoA) in bacteria and mammalian cells. It catalyzes the first committed step in the universal biosynthetic pathway leading to CoA and is itself subject to regulation through feedback inhibition by CoA. This family member is expressed most abundantly in the liver. [provided by RefSeq, Jul 2008]. " ], [ "P23919-1", "NP_001158503.1", "thymidylate kinase isoform 2", "188", "" ], [ "Q8NHX4-1", "NP_620712.2", "spermatogenesis-associated protein 3", "192", "" ], [ "Q8NHX9-1", "NP_620714.2", "two pore calcium channel protein 2", "752", "This gene encodes a putative cation-selective ion channel with two repeats of a six-transmembrane-domain. The protein localizes to lysosomal membranes and enables nicotinic acid adenine dinucleotide phosphate (NAADP) -induced calcium ion release from lysosome-related stores. This ubiquitously expressed gene has elevated expression in liver and kidney. Two common nonsynonymous SNPs in this gene strongly associate with blond versus brown hair pigmentation.[provided by RefSeq, Dec 2009]. " ], [ "Q6ZNW5-1", "NP_001013679.2", "GDP-D-glucose phosphorylase 1", "385", "" ], [ "Q9NXR8-1", "NP_061944.2", "inhibitor of growth protein 3 isoform 1", "418", "The protein encoded by this gene is similar to ING1, a tumor suppressor protein that can interact with TP53, inhibit cell growth, and induce apoptosis. This protein contains a PHD-finger, which is a common motif in proteins involved in chromatin remodeling. This gene can activate p53 trans-activated promoters, including promoters of p21/waf1 and bax. Overexpression of this gene has been shown to inhibit cell growth and induce apoptosis. Allelic loss and reduced expression of this gene were detected in head and neck cancers. Two alternatively spliced transcript variants encoding different isoforms have been observed. [provided by RefSeq, Jul 2008]. " ], [ "Q9C0H2-1", "NP_079526.1", "protein tweety homolog 3", "523", "This gene encodes a member of the tweety family of proteins. Members of this family function as chloride anion channels. The encoded protein functions as a calcium(2+)-activated large conductance chloride(-) channel. [provided by RefSeq, Jul 2008]. " ], [ "Q9C0H5-1", "NP_001295136.1", "rho GTPase-activating protein 39 isoform 1", "1083", "" ], [ "Q4VXU2-1", "NP_001118228.1", "polyadenylate-binding protein 1-like", "614", "" ], [ "Q00534-1", "NP_001138778.1", "cyclin-dependent kinase 6", "326", "The protein encoded by this gene is a member of the CMGC family of serine/threonine protein kinases. This kinase is a catalytic subunit of the protein kinase complex that is important for cell cycle G1 phase progression and G1/S transition. The activity of this kinase first appears in mid-G1 phase, which is controlled by the regulatory subunits including D-type cyclins and members of INK4 family of CDK inhibitors. This kinase, as well as CDK4, has been shown to phosphorylate, and thus regulate the activity of, tumor suppressor protein Rb. Altered expression of this gene has been observed in multiple human cancers. A mutation in this gene resulting in reduced cell proliferation, and impaired cell motility and polarity, and has been identified in patients with primary microcephaly. [provided by RefSeq, Aug 2017]. " ], [ "Q00537-1", "NP_001163935.1", "cyclin-dependent kinase 17 isoform 2", "523", "The protein encoded by this gene belongs to the cdc2/cdkx subfamily of the ser/thr family of protein kinases. It has similarity to a rat protein that is thought to play a role in terminally differentiated neurons. Alternatively spliced transcript variants encoding different isoforms have been found. [provided by RefSeq, Jul 2010]. " ], [ "Q00536-1", "NP_001163931.1", "cyclin-dependent kinase 16 isoform 3", "570", "The protein encoded by this gene belongs to the cdc2/cdkx subfamily of the ser/thr family of protein kinases. It may play a role in signal transduction cascades in terminally differentiated cells; in exocytosis; and in transport of secretory cargo from the endoplasmic reticulum. This gene is thought to escape X inactivation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2009]. " ], [ "Q9NXR5-1", "NP_001273650.1", "ankyrin repeat domain-containing protein 10 isoform 2", "220", "" ], [ "Q9NXR7-2", "NP_001248769.1", "BRISC and BRCA1-A complex member 2 isoform 4", "379", "This gene encodes an anti-apoptotic, death receptor-associated protein that interacts with tumor necrosis factor-receptor-1. The encoded protein acts as an adapter in several protein complexes, including the BRCA1-A complex and the BRISC complex. The BRCA1-A complex possesses ubiquitinase activity and targets sites of double strand DNA breaks, while the BRISC complex exhibits deubiquitinase activity and is involved in mitotic spindle assembly. This gene is upregulated in several types of cancer. [provided by RefSeq, Jun 2016]. " ], [ "Q96J66-1", "NP_115972.2", "ATP-binding cassette sub-family C member 11 isoform a", "1382", "The protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This ABC full transporter is a member of the MRP subfamily which is involved in multi-drug resistance. The product of this gene participates in physiological processes involving bile acids, conjugated steroids, and cyclic nucleotides. In addition, a SNP in this gene is responsible for determination of human earwax type. This gene and family member ABCC12 are determined to be derived by duplication and are both localized to chromosome 16q12.1. Multiple alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Jul 2008]. " ], [ "O00244-1", "NP_004036.1", "copper transport protein ATOX1", "68", "This gene encodes a copper chaperone that plays a role in copper homeostasis by binding and transporting cytosolic copper to ATPase proteins in the trans-Golgi network for later incorporation to the ceruloplasmin. This protein also functions as an antioxidant against superoxide and hydrogen peroxide, and therefore, may play a significant role in cancer carcinogenesis. Because of its cytogenetic location, this gene represents a candidate gene for 5q-syndrome. [provided by RefSeq, Jul 2008]. " ], [ "Q9UBM8-1", "NP_037376.2", "alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase C isoform c", "478", "" ], [ "Q86U70-1", "NP_001106878.1", "LIM domain-binding protein 1 isoform 1", "411", "" ], [ "O00716-1", "NP_001230005.1", "transcription factor E2F3 isoform 2", "334", "This gene encodes a member of a small family of transcription factors that function through binding of DP interaction partner proteins. The encoded protein recognizes a specific sequence motif in DNA and interacts directly with the retinoblastoma protein (pRB) to regulate the expression of genes involved in the cell cycle. Altered copy number and activity of this gene have been observed in a number of human cancers. There are pseudogenes for this gene on chromosomes 2 and 17. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2013]. " ], [ "Q6VAB6-1", "NP_775869.3", "kinase suppressor of Ras 2", "921", "" ], [ "Q9H8L6-1", "NP_079032.2", "multimerin-2 precursor", "949", "This gene encodes a protein belonging to the member of elastin microfibril interface-located (EMILIN) protein family. This family member is an extracellular matrix glycoprotein that can interfere with tumor angiogenesis and growth. It serves as a transforming growth factor beta antagonist and can interfere with the VEGF-A/VEGFR2 pathway. A related pseudogene has been identified on chromosome 6. [provided by RefSeq, Aug 2012]. " ], [ "Q96KS0-1", "NP_444274.1", "egl nine homolog 2", "407", "The hypoxia inducible factor (HIF) is a transcriptional complex that is involved in oxygen homeostasis. At normal oxygen levels, the alpha subunit of HIF is targeted for degration by prolyl hydroxylation. This gene encodes an enzyme responsible for this post-translational modification. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the upstream RAB4B (RAB4B, member RAS oncogene family) gene. [provided by RefSeq, Feb 2011]. " ], [ "Q9UBM7-1", "NP_001157289.1", "7-dehydrocholesterol reductase", "475", "This gene encodes an enzyme that removes the C(7-8) double bond in the B ring of sterols and catalyzes the conversion of 7-dehydrocholesterol to cholesterol. This gene is ubiquitously expressed and its transmembrane protein localizes to the endoplasmic reticulum membrane and nuclear outer membrane. Mutations in this gene cause Smith-Lemli-Opitz syndrome (SLOS); a syndrome that is metabolically characterized by reduced serum cholesterol levels and elevated serum 7-dehydrocholesterol levels and phenotypically characterized by cognitive disability, facial dysmorphism, syndactyly of second and third toes, and holoprosencephaly in severe cases to minimal physical abnormalities and near-normal intelligence in mild cases. Alternative splicing results in multiple transcript variants that encode the same protein.[provided by RefSeq, Aug 2009]. " ], [ "Q6BEB4-1", "NP_001003845.1", "transcription factor Sp5", "398", "" ], [ "P24522-1", "NP_001186670.1", "growth arrest and DNA damage-inducible protein GADD45 alpha isoform 2", "131", "This gene is a member of a group of genes whose transcript levels are increased following stressful growth arrest conditions and treatment with DNA-damaging agents. The protein encoded by this gene responds to environmental stresses by mediating activation of the p38/JNK pathway via MTK1/MEKK4 kinase. The DNA damage-induced transcription of this gene is mediated by both p53-dependent and -independent mechanisms. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene.[provided by RefSeq, Dec 2010]. " ], [ "P20930-1", "NP_002007.1", "filaggrin", "4061", "The protein encoded by this gene is an intermediate filament-associated protein that aggregates keratin intermediate filaments in mammalian epidermis. It is initially synthesized as a polyprotein precursor, profilaggrin (consisting of multiple filaggrin units of 324 aa each), which is localized in keratohyalin granules, and is subsequently proteolytically processed into individual functional filaggrin molecules. Mutations in this gene are associated with ichthyosis vulgaris.[provided by RefSeq, Dec 2009]. " ], [ "Q9NYS7-1", "NP_001265486.1", "WD repeat and SOCS box-containing protein 2 isoform 1", "421", "This gene encodes a member of the WD-protein subfamily. The encoded protein contains five WD-repeats spanning most of the protein and an SOCS box in the C-terminus. The SOCS box may act as a bridge between specific substrate-binding domains and E3 ubiquitin protein ligases. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2013]. " ], [ "A0AVF1-1", "NP_001138392.1", "intraflagellar transport protein 56 isoform 2", "487", "" ], [ "P40424-1", "NP_001191892.1", "pre-B-cell leukemia transcription factor 1 isoform 3", "420", "This gene encodes a nuclear protein that belongs to the PBX homeobox family of transcriptional factors. Studies in mice suggest that this gene may be involved in the regulation of osteogenesis and required for skeletal patterning and programming. A chromosomal translocation, t(1;19) involving this gene and TCF3/E2A gene, is associated with pre-B-cell acute lymphoblastic leukemia. The resulting fusion protein, in which the DNA binding domain of E2A is replaced by the DNA binding domain of this protein, transforms cells by constitutively activating transcription of genes regulated by the PBX protein family. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2017]. " ], [ "P40425-1", "NP_002577.2", "pre-B-cell leukemia transcription factor 2", "430", "This gene encodes a ubiquitously expressed member of the TALE/PBX homeobox family. It was identified by its similarity to a homeobox gene which is involved in t(1;19) translocation in acute pre-B-cell leukemias. This protein is a transcriptional activator which binds to the TLX1 promoter. The gene is located within the major histocompatibility complex (MHC) on chromosome 6. [provided by RefSeq, Jul 2008]. " ], [ "P09001-1", "NP_009139.1", "39S ribosomal protein L3, mitochondrial", "348", "Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a 39S subunit protein that belongs to the L3P ribosomal protein family. A pseudogene corresponding to this gene is found on chromosome 13q. [provided by RefSeq, Jul 2008]. " ], [ "Q8IZK6-1", "NP_001317576.1", "mucolipin-2 isoform 2", "538", "Mucolipins constitute a family of cation channel proteins with homology to the transient receptor potential superfamily. In mammals, the mucolipin family includes 3 members, MCOLN1 (MIM 605248), MCOLN2, and MCOLN3 (MIM 607400), that exhibit a common 6-membrane-spanning topology. Homologs of mammalian mucolipins exist in Drosophila and C. elegans. Mutations in the human MCOLN1 gene cause mucolipodosis IV (MIM 262650) (Karacsonyi et al., 2007 [PubMed 17662026]).[supplied by OMIM, Sep 2009]. " ], [ "P40429-1", "NP_001257420.1", "60S ribosomal protein L13a isoform 2", "142", "Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a member of the L13P family of ribosomal proteins that is a component of the 60S subunit. The encoded protein also plays a role in the repression of inflammatory genes as a component of the IFN-gamma-activated inhibitor of translation (GAIT) complex. This gene is co-transcribed with the small nucleolar RNA genes U32, U33, U34, and U35, which are located in the second, fourth, fifth, and sixth introns, respectively. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed throughout the genome. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]. " ], [ "Q71RG4-1", "NP_001070142.1", "transmembrane and ubiquitin-like domain-containing protein 2 isoform b", "321", "" ], [ "Q7Z3T8-1", "NP_001271166.1", "zinc finger FYVE domain-containing protein 16 isoform b", "809", "This gene encodes an endosomal protein that belongs to the FYVE zinc finger family of proteins. The encoded protein is thought to regulate membrane trafficking in the endosome. This protein functions as a scaffold protein in the transforming growth factor-beta signaling pathway and is involved in positive and negative feedback regulation of the bone morphogenetic protein signaling pathway. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]. " ], [ "Q13838-1", "NP_004631.1", "spliceosome RNA helicase DDX39B", "428", "This gene encodes a member of the DEAD box family of RNA-dependent ATPases that mediate ATP hydrolysis during pre-mRNA splicing. The encoded protein is an essential splicing factor required for association of U2 small nuclear ribonucleoprotein with pre-mRNA, and it also plays an important role in mRNA export from the nucleus to the cytoplasm. This gene belongs to a cluster of genes localized in the vicinity of the genes encoding tumor necrosis factor alpha and tumor necrosis factor beta. These genes are all within the human major histocompatibility complex class III region. Mutations in this gene may be associated with rheumatoid arthritis. Alternative splicing results in multiple transcript variants. Related pseudogenes have been identified on both chromosomes 6 and 11. Read-through transcription also occurs between this gene and the upstream ATP6V1G2 (ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G2) gene. [provided by RefSeq, Feb 2011]. " ], [ "O00337-1", "NP_001274691.1", "sodium/nucleoside cotransporter 1 isoform 1", "649", "" ], [ "Q8TDW7-3", "NP_001008781.2", "protocadherin Fat 3 precursor", "4557", "" ], [ "Q5M775-1", "NP_001028725.1", "cytospin-B isoform 1", "1068", "The protein encoded by this gene belongs to the cytospin-A family. It is localized in the nucleus, and highly expressed in testis and some cancer cell lines. A chromosomal translocation involving this gene and platelet-derived growth factor receptor, beta gene (PDGFRB) may be a cause of juvenile myelomonocytic leukemia. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2011]. " ], [ "A6H8Z2-1", "NP_001012448.2", "protein FAM221B", "402", "" ], [ "Q9H2I8-1", "NP_114413.1", "leucine-rich melanocyte differentiation-associated protein isoform 2", "198", "This gene encodes a leucine-rich repeat protein. The encoded protein is thought to play a role in melanocyte differentiation. Mutations in this gene have been associated with autosomal recessive oculocutaneous albinism 7 (OCA7). Alternatively spliced transcript variants have been identified. [provided by RefSeq, Mar 2015]. " ], [ "P08842-1", "NP_000342.2", "steryl-sulfatase isoform 1 precursor", "583", "This gene encodes a multi-pass membrane protein that is localized to the endoplasmic reticulum. It belongs to the sulfatase family and hydrolyzes several 3-beta-hydroxysteroid sulfates, which serve as metabolic precursors for estrogens, androgens, and cholesterol. Mutations in this gene are associated with X-linked ichthyosis (XLI). Alternatively spliced transcript variants resulting from the use of different promoters have been described for this gene (PMID:17601726). [provided by RefSeq, Mar 2016]. " ], [ "Q6ZT89-1", "NP_660325.4", "solute carrier family 25 member 48 isoform 2", "157", "" ], [ "Q5VUR7-1", "NP_001012419.1", "ankyrin repeat domain-containing protein 20A3", "823", "" ], [ "P48960-1", "NP_001020331.1", "CD97 antigen isoform 3 preproprotein", "786", "This gene encodes a member of the EGF-TM7 subfamily of adhesion G protein-coupled receptors, which mediate cell-cell interactions. These proteins are cleaved by self-catalytic proteolysis into a large extracellular subunit and seven-span transmembrane subunit, which associate at the cell surface as a receptor complex. The encoded protein may play a role in cell adhesion as well as leukocyte recruitment, activation and migration, and contains multiple extracellular EGF-like repeats which mediate binding to chondroitin sulfate and the cell surface complement regulatory protein CD55. Expression of this gene may play a role in the progression of several types of cancer. Alternatively spliced transcript variants encoding multiple isoforms with 3 to 5 EGF-like repeats have been observed for this gene. This gene is found in a cluster with other EGF-TM7 genes on the short arm of chromosome 19. [provided by RefSeq, Jun 2011]. " ], [ "Q86WA6-1", "NP_001289706.1", "valacyclovir hydrolase isoform 2", "274", "This gene encodes a member of the serine protease family of hydrolytic enzymes which contain a serine in their active site. The encoded protein may play a role in activation of the antiviral prodrug valacyclovir. Alternatively spliced transcript variants have been described.[provided by RefSeq, Jan 2009]. " ], [ "P02768-1", "NP_000468.1", "serum albumin preproprotein", "609", "This gene encodes the most abundant protein in human blood. This protein functions in the regulation of blood plasma colloid osmotic pressure and acts as a carrier protein for a wide range of endogenous molecules including hormones, fatty acids, and metabolites, as well as exogenous drugs. Additionally, this protein exhibits an esterase-like activity with broad substrate specificity. The encoded preproprotein is proteolytically processed to generate the mature protein. A peptide derived from this protein, EPI-X4, is an endogenous inhibitor of the CXCR4 chemokine receptor. [provided by RefSeq, Jul 2016]. " ], [ "P20645-1", "NP_002346.1", "cation-dependent mannose-6-phosphate receptor isoform 1 precursor", "277", "This gene encodes a member of the P-type lectin family. P-type lectins play a critical role in lysosome function through the specific transport of mannose-6-phosphate-containing acid hydrolases from the Golgi complex to lysosomes. The encoded protein functions as a homodimer and requires divalent cations for ligand binding. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. A pseudogene of this gene is located on the long arm of chromosome X. [provided by RefSeq, May 2011]. " ], [ "Q9UNA4-1", "NP_009126.2", "DNA polymerase iota isoform a (long)", "740", "The protein encoded by this gene is an error-prone DNA polymerase involved in DNA repair. The encoded protein promotes DNA synthesis across lesions in the template DNA, which other polymerases cannot do. The encoded polymerase inserts deoxynucleotides across lesions and then relies on DNA polymerase zeta to extend the nascent DNA strand to bypass the lesion. [provided by RefSeq, May 2017]. " ], [ "Q5TAX3-1", "NP_001009881.1", "terminal uridylyltransferase 4 isoform a", "1645", "ZCCHC11 is an RNA uridyltransferase (EC 2.7.7.52) that uses UTP to add uridines to the 3-prime end of substrate RNA molecules (Jones et al., 2009 [PubMed 19701194]).[supplied by OMIM, Jan 2011]. " ], [ "P07902-1", "NP_000146.2", "galactose-1-phosphate uridylyltransferase isoform 1", "379", "Galactose-1-phosphate uridyl transferase (GALT) catalyzes the second step of the Leloir pathway of galactose metabolism, namely the conversion of UDP-glucose + galactose-1-phosphate to glucose-1-phosphate + UDP-galactose. The absence of this enzyme results in classic galactosemia in humans and can be fatal in the newborn period if lactose is not removed from the diet. The pathophysiology of galactosemia has not been clearly defined. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]. " ], [ "P21815-1", "NP_004958.2", "bone sialoprotein 2 precursor", "317", "The protein encoded by this gene is a major structural protein of the bone matrix. It constitutes approximately 12% of the noncollagenous proteins in human bone and is synthesized by skeletal-associated cell types, including hypertrophic chondrocytes, osteoblasts, osteocytes, and osteoclasts. The only extraskeletal site of its synthesis is the trophoblast. This protein binds to calcium and hydroxyapatite via its acidic amino acid clusters, and mediates cell attachment through an RGD sequence that recognizes the vitronectin receptor. [provided by RefSeq, Jul 2008]. " ], [ "P02763-1", "NP_000598.2", "alpha-1-acid glycoprotein 1 precursor", "201", "This gene encodes a key acute phase plasma protein. Because of its increase due to acute inflammation, this protein is classified as an acute-phase reactant. The specific function of this protein has not yet been determined; however, it may be involved in aspects of immunosuppression. [provided by RefSeq, Jul 2008]. " ], [ "P02765-1", "NP_001613.2", "alpha-2-HS-glycoprotein isoform 2 preproprotein", "367", "The protein encoded by this gene is a negatively-charged serum glycoprotein that is synthesized by hepatocytes. The encoded protein consists of two polypeptide chains, which are both cleaved from a proprotein encoded from a single mRNA. It is involved in several processes, including endocytosis, brain development, and the formation of bone tissue. Defects in this gene are a cause of susceptibility to leanness. [provided by RefSeq, Aug 2017]. " ], [ "P82921-1", "NP_061870.1", "28S ribosomal protein S21, mitochondrial", "87", "Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a 28S subunit protein that belongs to the ribosomal protein S21P family. Pseudogenes corresponding to this gene are found on chromosomes 1p, 1q, 9p, 10p, 10q, 16q, and 17q. Available sequence data analyses identified splice variants that differ in the 5' UTR; both transcripts encode the same protein. [provided by RefSeq, Jul 2008]. " ], [ "A8K4G0-1", "NP_777552.3", "CMRF35-like molecule 7 precursor", "201", "CD300LB is a nonclassical activating receptor of the immunoglobulin (Ig) superfamily expressed on myeloid cells (Martinez-Barriocanal and Sayos, 2006 [PubMed 16920917]).[supplied by OMIM, Mar 2008]. " ], [ "Q7L266-1", "NP_001077395.1", "isoaspartyl peptidase/L-asparaginase", "308", "" ], [ "Q9UQ07-1", "NP_001258940.1", "MAPK/MAK/MRK overlapping kinase isoform 2", "389", "This gene belongs to the MAP kinase superfamily. The gene was found to be regulated by caudal type transcription factor 2 (Cdx2) protein. The encoded protein, which is localized to epithelial cells in the intestinal crypt, may play a role in growth arrest and differentiation of cells of upper crypt and lower villus regions. Multiple alternatively spliced transcript variants encoding different isoforms have been observed for this gene. [provided by RefSeq, Dec 2012]. " ], [ "Q9UQ05-1", "NP_036417.1", "potassium voltage-gated channel subfamily H member 4", "1017", "Voltage-gated potassium (Kv) channels represent the most complex class of voltage-gated ion channels from both functional and structural standpoints. Their diverse functions include regulating neurotransmitter release, heart rate, insulin secretion, neuronal excitability, epithelial electrolyte transport, smooth muscle contraction, and cell volume. This gene encodes a member of the potassium channel, voltage-gated, subfamily H. This member is a pore-forming (alpha) subunit. The gene is brain-specific, and located in the neocortex and the striatum. It may be involved in cellular excitability of restricted neurons in the central nervous system. [provided by RefSeq, Jul 2008]. " ], [ "Q9UJ70-1", "NP_060037.3", "N-acetyl-D-glucosamine kinase isoform 1", "390", "This gene encodes a member of the N-acetylhexosamine kinase family. The encoded protein catalyzes the conversion of N-acetyl-D-glucosamine to N-acetyl-D-glucosamine 6-phosphate, and is the major mammalian enzyme which recovers amino sugars. [provided by RefSeq, Nov 2011]. " ], [ "Q9UJ71-1", "NP_056532.4", "C-type lectin domain family 4 member K", "328", "The protein encoded by this gene is expressed only in Langerhans cells which are immature dendritic cells of the epidermis and mucosa. It is localized in the Birbeck granules, organelles present in the cytoplasm of Langerhans cells and consisting of superimposed and zippered membranes. It is a C-type lectin with mannose binding specificity, and it has been proposed that mannose binding by this protein leads to internalization of antigen into Birbeck granules and providing access to a nonclassical antigen-processing pathway. Mutations in this gene result in Birbeck granules deficiency or loss of sugar binding activity. [provided by RefSeq, Aug 2010]. " ], [ "Q9UJ72-1", "NP_009124.2", "annexin A10", "324", "This gene encodes a member of the annexin family. Members of this calcium-dependent phospholipid-binding protein family play a role in the regulation of cellular growth and in signal transduction pathways. The function of this gene has not yet been determined. [provided by RefSeq, Jul 2008]. " ], [ "O15075-1", "NP_001182344.1", "serine/threonine-protein kinase DCLK1 isoform 2", "422", "This gene encodes a member of the protein kinase superfamily and the doublecortin family. The protein encoded by this gene contains two N-terminal doublecortin domains, which bind microtubules and regulate microtubule polymerization, a C-terminal serine/threonine protein kinase domain, which shows substantial homology to Ca2+/calmodulin-dependent protein kinase, and a serine/proline-rich domain in between the doublecortin and the protein kinase domains, which mediates multiple protein-protein interactions. The microtubule-polymerizing activity of the encoded protein is independent of its protein kinase activity. The encoded protein is involved in several different cellular processes, including neuronal migration, retrograde transport, neuronal apoptosis and neurogenesis. This gene is up-regulated by brain-derived neurotrophic factor and associated with memory and general cognitive abilities. Multiple transcript variants generated by two alternative promoter usage and alternative splicing have been reported, but the full-length nature and biological validity of some variants have not been defined. These variants encode different isoforms, which are differentially expressed and have different kinase activities.[provided by RefSeq, Sep 2010]. " ] ] }, "readme": "Name\n - Human RefSeq Protein Information\n\nVersion\n - 1.0.13\n\nCreated on\n - 2019-01-23T17:21:05.888176\n\nModified on\n - 2019-04-23T13:57:53.499636\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu]\n\nAuthors\n - \n\nChecksum\n - \n\nUsability Domain\n - The Human RefSeq Protein Information dataset contains human [taxid:9606] protein information such as protein accession, name, length and protein function summmary from NCBI RefSeq database\n - If you use this dataset please provide proper attribution to NCBI RefSeq and GlyGen\n\nDescription Domain\n Keywords\n - protein information\n - protein length\n\n Pipeline Steps\n - Step-1: This script parses the NCBI RefSeq gpff files to extract the accession, length, protein summary and then maps the NCBI RefSeq accesion to the UniProtKB Canonical accessions\n\nExecution Domain\n Scripts - https://github.com/glygener/glygen-backend-integration/blob/master/pipeline/extractor/extract-from-gp.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_9606.gpff\n URI: https://data.glygen.org/ln2data/releases/data/v-1.0.13/source/refseq_protein_all_9606.gpff\n Name: human_protein_idmapping.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.0.13/reviewed/human_protein_idmapping.csv\n Output Subdomain\n Name: human_protein_refseq_protein_info.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.0.13/reviewed/human_protein_refseq_protein_info.csv\n Name: human_protein_refseq_protein_info.stat.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.0.13/reviewed/human_protein_refseq_protein_info.stat.csv\n\nFields\n Name: \"refseq_protein_summary\"\n Description: \"Function of the protein in NCBI RefSeq database\"\n Unique Values: \"11946\"\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: \"18882\"\n Name: \"p_refseq_ac_best_match\"\n Description: \"Best match NCBI RefSeq protein accession to UniProtKB canonical accession\"\n Unique Values: \"18882\"\n Name: \"refseq_protein_name\"\n Description: \"Name of the protein in NCBI RefSeq database\"\n Unique Values: \"18876\"\n Name: \"refseq_protein_length\"\n Description: \"Length of the protein in NCBI RefSeq database\"\n Unique Values: \"2032\"", "downloadurl": "/ln2data/releases/data/v-1.0.13/reviewed/human_protein_refseq_protein_info.csv" }