{ "bcoid": "GLY_000021", "title": "Human Protein Information (NCBI RefSeq)", "description": "The Human Protein Information (NCBI RefSeq) dataset contains human [taxid:9606] protein information such ...", "filename": "human_protein_info_refseq.csv", "filetype": "csv", "categories": { "species": "Homo Sapiens", "molecule": "Protein", "tags": "Protein Information", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "P03886-1...", "YP_003024026..." ], [ "P03891-1...", "YP_003024027..." ] ], "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" } ], [ "P03886-1", "YP_003024026.1", "NADH dehydrogenase subunit 1", "318", "" ], [ "P03891-1", "YP_003024027.1", "NADH dehydrogenase subunit 2", "347", "" ], [ "P00395-1", "YP_003024028.1", "cytochrome c oxidase subunit I", "513", "" ], [ "P00403-1", "YP_003024029.1", "cytochrome c oxidase subunit II", "227", "" ], [ "P03928-1", "YP_003024030.1", "ATP synthase F0 subunit 8", "68", "" ], [ "P00846-1", "YP_003024031.1", "ATP synthase F0 subunit 6", "226", "" ], [ "P00414-1", "YP_003024032.1", "cytochrome c oxidase subunit III", "261", "" ], [ "P03897-1", "YP_003024033.1", "NADH dehydrogenase subunit 3", "115", "" ], [ "P03901-1", "YP_003024034.1", "NADH dehydrogenase subunit 4L", "98", "" ], [ "P03905-1", "YP_003024035.1", "NADH dehydrogenase subunit 4", "459", "" ], [ "P03915-1", "YP_003024036.1", "NADH dehydrogenase subunit 5", "603", "" ], [ "P03923-1", "YP_003024037.1", "NADH dehydrogenase subunit 6", "174", "" ], [ "P00156-1", "YP_003024038.1", "cytochrome b", "380", "" ], [ "A0A0K2S4Q6-1", "NP_001311005.1", "CD300c molecule-like isoform 2 precursor", "153", "This gene belongs to the CD300 gene family, which in turn, belongs to the immunoglobulin (Ig) superfamily. This gene is located within a CD300 cluster on chromosome 17. The encoded protein may be involved in innate immunity as well as autoimmune response. A G>A mutation, represented by the single nucleotide polymorphism (SNP) rs905709, at the splice donor site of the 5' terminal exon may be associated with lack of expression of this gene in homozygous (AA) individuals. The human reference assembly (GRCh38.p2) represents the 'A' allele at this SNP. [provided by RefSeq, Apr 2016]. " ], [ "P0C869-1", "NP_005081.1", "JMJD7-PLA2G4B protein isoform a", "1012", "This locus represents naturally-occurring readthrough transcription between the neighboring jumonji domain containing 7 (JMJD7) and phospholipase A2, group IVB (cytosolic) (PLA2G4B) genes. Readthrough transcripts encode fusion proteins that share amino acid sequence with each individual gene product, including a partial JmjC domain and downstream C2 and phospholipase A2 domains. Alternatively spliced transcript variants have been observed. [provided by RefSeq, Oct 2013]. " ], [ "Q8IVW1-1", "NP_057716.2", "ADP-ribosylation factor-like 17-like isoform b", "125", "" ], [ "Q8N8H1-1", "NP_001189402.1", "ZNF816-ZNF321 protein", "233", "This locus represents naturally occurring read-through transcription between the zinc finger protein 816 (ZNF816) gene and the zinc finger protein 321 (ZNF321) pseudogene on chromosome 19. The read-through transcript encodes a KRAB domain-containing protein that shares sequence identity with the upstream gene product, but it contains a distinct C-terminus encoded by exon structure from the downstream pseudogene. [provided by RefSeq, Jan 2011]. " ], [ "Q9BTE6-1", "NP_079543.1", "PTGES3L-AARSD1 protein isoform 2", "525", "This locus represents naturally occurring readthrough transcription between the neighboring PTGES3L (prostaglandin E synthase 3 (cytosolic)-like) and AARSD1(alanyl-tRNA synthetase domain containing 1) genes on chromosome 17. The readthrough transcript encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, May 2012]. " ], [ "A5PLL7-1", "NP_954673.1", "TMEM189-UBE2V1 fusion protein", "370", "The TMEM189-UEV mRNA is an infrequent but naturally occurring read-through transcript of the neighboring TMEM189 and UBE2V1 genes. Ubiquitin-conjugating E2 enzyme variant proteins constitute a distinct subfamily within the E2 protein family. They have sequence similarity to other ubiquitin-conjugating enzymes but lack the conserved cysteine residue that is critical for the catalytic activity of E2s. The protein produced by this transcript has UEV1 B domains but the protein is localized to the cytoplasm rather than to the nucleus. The significance of this read-through mRNA and the function of its protein product has not yet been determined. [provided by RefSeq, Oct 2010]. " ], [ "Q6T311-1", "NP_996802.1", "ADP-ribosylation factor-like protein 9 isoform 2", "123", "ARL9 is a member of the small GTPase protein family with a high degree of similarity to ARF (MIM 103180) proteins of the RAS superfamily.[supplied by OMIM, Nov 2008]. " ], [ "Q96T66-1", "NP_835471.1", "nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 isoform 1", "215", "This gene encodes a member of the nicotinamide/nicotinic acid mononucleotide adenylyltransferase family. These enzymes use ATP to catalyze the synthesis of nicotinamide adenine dinucleotide or nicotinic acid adenine dinucleotide from nicotinamide mononucleotide or nicotinic acid mononucleotide, respectively. The encoded protein is localized to mitochondria and may also play a neuroprotective role as a molecular chaperone. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2011]. " ], [ "Q96JK4-1", "NP_115801.3", "HHIP-like protein 1 isoform b precursor", "608", "This gene encodes a protein that belongs to the glucose/sorbosone dehydrogenase family. The encoded protein also contains a domain that binds folate and reduced folic acid derivatives. [provided by RefSeq, Jul 2016]. " ], [ "Q9BRA0-1", "NP_115732.2", "N-alpha-acetyltransferase 38, NatC auxiliary subunit isoform 1 precursor", "173", "" ], [ "Q6NUI2-1", "NP_001308459.1", "glycerol-3-phosphate acyltransferase 2, mitochondrial isoform 5", "724", "" ], [ "Q5TGU0-1", "NP_001153198.1", "translocator protein 2", "170", "" ], [ "Q9Y608-1", "NP_060194.1", "leucine-rich repeat flightless-interacting protein 2 isoform l", "400", "The protein encoded by this gene, along with MYD88, binds to the cytosolic tail of toll-like receptor 4 (TLR4), which results in activation of nuclear factor kappa B signaling. The ubiquitin-like protein FAT10 prevents the interaction of the encoded protein and TLR4, thereby inactivating the nuclear factor kappa B signaling pathway. In addition, this protein can downregulate the NLRP3 inflammasome by recruiting the caspase-1 inhibitor Flightless-I to the inflammasome complex. [provided by RefSeq, Jan 2017]. " ], [ "Q92543-1", "NP_001334856.1", "sorting nexin-19 isoform 12", "232", "Islet antigen-2 (IA-2) is an autoantigen in type 1 diabetes and plays a role in insulin secretion. IA-2 is found in dense-core secretory vesicles and interacts with the product of this gene, a sorting nexin. In mouse pancreatic beta-cells, the encoded protein influenced insulin secretion by stabilizing the number of dense-core secretory vesicles. [provided by RefSeq, Dec 2016]. " ], [ "Q9UJU3-1", "NP_001335212.1", "zinc finger protein 112 isoform 2", "907", "" ], [ "Q8N6R1-1", "NP_001333909.1", "stress-associated endoplasmic reticulum protein 2", "65", "" ], [ "Q7L4E1-1", "NP_116198.3", "mitoguardin 2 isoform 1", "657", "" ], [ "Q5MAI5-1", "NP_001333840.1", "cyclin-dependent kinase-like 4 isoform 1", "379", "" ], [ "A0PK05-1", "NP_001332855.1", "transmembrane protein 72 isoform 2", "157", "This gene encodes a transmembrane protein which may be expressed specifically in the kidney. [provided by RefSeq, Sep 2016]. " ], [ "Q9UQ53-1", "NP_463459.1", "alpha-1,3-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase B isoform 2", "563", "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 A, 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]. " ], [ "Q8N3Z3-1", "NP_612494.1", "GTP-binding protein 8 isoform 2", "251", "" ], [ "Q8NHH1-1", "NP_919228.2", "tubulin polyglutamylase TTLL11 isoform b", "538", "" ], [ "Q8WV35-1", "NP_036295.1", "leucine-rich repeat-containing protein 29", "223", "This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbls class and, in addition to an F-box, contains 9 tandem leucine-rich repeats. Two transcript variants encoding the same protein have been found for this gene. Other variants may occur, but their full-length natures have not been characterized. [provided by RefSeq, Jul 2008]. " ], [ "Q8TD35-1", "NP_001007126.1", "protein LKAAEAR1 isoform 1", "240", "" ], [ "O00534-1", "NP_938057.1", "von Willebrand factor A domain-containing protein 5A isoform 2", "415", "" ], [ "Q3B7T1-1", "NP_056423.2", "erythroid differentiation-related factor 1 isoform 2", "1204", "This gene may play a role in erythroid cell differentiation. The encoded protein inhibits DNA binding of the erythroid transcription factor GATA-1 and may regulate the expression of alpha-globin and gamma-globin. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]. " ], [ "Q8WWF8-1", "NP_653248.3", "calcyphosin-like protein", "208", "" ], [ "Q96KR7-1", "NP_899069.1", "phosphatase and actin regulator 3 isoform 3", "448", "This gene encodes a member of the phosphatase and actin regulator protein family. The encoded protein is associated with the nuclear scaffold in proliferating cells, and binds to actin and the catalytic subunit of protein phosphatase-1, suggesting that it functions as a regulatory subunit of protein phosphatase-1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]. " ], [ "Q9UII6-1", "NP_057448.3", "dual specificity protein phosphatase 13 isoform 6", "198", "Members of the protein-tyrosine phosphatase superfamily cooperate with protein kinases to regulate cell proliferation and differentiation. This superfamily is separated into two families based on the substrate that is dephosphorylated. One family, the dual specificity phosphatases (DSPs) acts on both phosphotyrosine and phosphoserine/threonine residues. This gene encodes different but related DSP proteins through the use of non-overlapping open reading frames, alternate splicing, and presumed different transcription promoters. Expression of the distinct proteins from this gene has been found to be tissue specific and the proteins may be involved in postnatal development of specific tissues. A protein encoded by the upstream ORF was found in skeletal muscle, whereas the encoded protein from the downstream ORF was found only in testis. In mouse, a similar pattern of expression was found. Multiple alternatively spliced transcript variants were described, but the full-length sequence of only some were determined. [provided by RefSeq, Jul 2008]. " ], [ "Q7Z5M8-1", "NP_861535.1", "protein ABHD12B isoform c", "285", "" ], [ "Q6PIL6-1", "NP_671712.1", "Kv channel-interacting protein 4 isoform 4", "229", "This gene encodes a member of the family of voltage-gated potassium (Kv) channel-interacting proteins (KCNIPs), which belong to the recoverin branch of the EF-hand superfamily. Members of the KCNIP family are small calcium binding proteins. They all have EF-hand-like domains, and differ from each other in the N-terminus. They are integral subunit components of native Kv4 channel complexes. They may regulate A-type currents, and hence neuronal excitability, in response to changes in intracellular calcium. This protein member also interacts with presenilin. Multiple alternatively spliced transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]. " ], [ "Q8WXA3-2", "NP_060457.4", "RUN and FYVE domain-containing protein 2 isoform a", "641", "" ], [ "Q8WXC6-2", "NP_612209.1", "COP9 signalosome complex subunit 9 isoform 1", "252", "" ], [ "Q9BST9-1", "NP_149035.1", "rhotekin isoform b", "550", "This gene encodes a scaffold protein that interacts with GTP-bound Rho proteins. Binding of this protein inhibits the GTPase activity of Rho proteins. This protein may interfere with the conversion of active, GTP-bound Rho to the inactive GDP-bound form by RhoGAP. Rho proteins regulate many important cellular processes, including cytokinesis, transcription, smooth muscle contraction, cell growth and transformation. Dysregulation of the Rho signal transduction pathway has been implicated in many forms of cancer. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]. " ], [ "Q8NBD8-1", "NP_872332.1", "transmembrane protein 229B isoform b", "167", "" ], [ "Q6ICG6-1", "NP_056079.1", "uncharacterized protein KIAA0930 isoform a", "409", "" ], [ "Q68DY1-1", "NP_660340.1", "zinc finger protein 626 isoform 2", "92", "" ], [ "Q7Z5G4-1", "NP_057183.2", "golgin subfamily A member 7 isoform a", "137", "" ], [ "Q8TD91-1", "NP_803251.1", "melanoma-associated antigen C3 isoform 2", "346", "This gene is a member of the MAGEC gene family. The members of this family are not expressed in normal tissues, except for testis, and are expressed in tumors of various histological types. The MAGEC genes are clustered on chromosome Xq26-q27. Two transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]. " ], [ "Q9H609-1", "NP_077303.1", "zinc finger protein 576", "170", "" ], [ "Q8NEF3-1", "NP_689762.2", "coiled-coil domain-containing protein 112 isoform 2", "446", "" ], [ "Q6ZN01-1", "NP_872380.1", "MEF2-activating motif and SAP domain-containing transcriptional regulator isoform 2", "312", "" ], [ "Q96LL3-1", "NP_001103130.1", "uncharacterized protein C16orf92 isoform 2", "132", "" ], [ "P51522-1", "NP_060770.3", "zinc finger protein 83", "516", "" ], [ "Q7LBE3-1", "NP_599152.2", "solute carrier family 26 member 9 isoform b", "887", "This gene is one member of a family of sulfate/anion transporter genes. Family members are well conserved in their genomic (number and size of exons) and protein (aa length among species) structures yet have markedly different tissue expression patterns. The product of this gene is a highly selective chloride ion channel regulated by WNK kinases. Alternative splicing results in multiple transcript variants encoding differing isoforms.[provided by RefSeq, Dec 2008]. " ], [ "Q7Z4V0-1", "NP_877432.1", "zinc finger protein 438 isoform a", "828", "" ], [ "Q9C0I3-1", "NP_997374.1", "serine-rich coiled-coil domain-containing protein 1 isoform 2", "677", "" ], [ "Q6UWN5-1", "NP_872379.2", "ly6/PLAUR domain-containing protein 5 isoform B", "208", "" ], [ "O75123-1", "NP_055604.3", "zinc finger protein 623 isoform 1", "536", "" ], [ "Q8N0U4-1", "NP_001138741.1", "protein FAM185A isoform 2", "275", "" ], [ "Q7L3S4-1", "NP_057727.2", "zinc finger protein 771", "317", "" ], [ "Q8N7R7-1", "NP_689736.1", "cyclin-Y-like protein 1 isoform 2", "289", "" ], [ "Q8N841-1", "NP_775894.2", "tubulin polyglutamylase TTLL6 isoform 2", "584", "" ], [ "Q96ET8-1", "NP_660344.2", "Golgi apparatus membrane protein TVP23 homolog C isoform 1", "276", "" ], [ "Q9ULK2-1", "NP_689962.1", "ataxin-7-like protein 1 isoform 2", "146", "" ], [ "Q5JUW0-1", "NP_060246.2", "KRAB domain-containing protein 4 isoform 2", "166", "This encodes a zinc finger protein with an N-terminal KRAB (Kruppel-associated) domain found in transcriptional repressors. This gene is located in a region of the X chromosome thought to be involved in nonsyndromic X-linked cognitive disability. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]. " ], [ "Q6PI97-1", "NP_997313.2", "UPF0722 protein C11orf88 isoform 1", "196", "" ], [ "Q9NVL1-1", "NP_689776.1", "protein FAM86C1 isoform 2", "131", "" ], [ "Q8NEB5-1", "NP_115872.2", "phospholipid phosphatase 5 isoform 2", "216", "" ], [ "Q5JZY3-1", "NP_775912.2", "ephrin type-A receptor 10 isoform 2 precursor", "295", "Ephrin receptors, the largest subfamily of receptor tyrosine kinases (RTKs), and their ephrin ligands are important mediators of cell-cell communication regulating cell attachment, shape, and mobility in neuronal and epithelial cells (Aasheim et al., 2005 [PubMed 15777695]). See MIM 179610 for additional background on Eph receptors and ephrins.[supplied by OMIM, Mar 2008]. " ], [ "Q96EN9-1", "NP_001093889.1", "required for excision 1-B domain-containing protein isoform 2", "179", "" ], [ "A0AVI4-1", "NP_612394.1", "E3 ubiquitin-protein ligase TM129 isoform b", "232", "" ], [ "Q9Y236-1", "NP_004328.1", "oxidative stress-induced growth inhibitor 2 isoform 2", "505", "" ], [ "Q6P2M8-1", "NP_001129212.1", "calcium/calmodulin-dependent protein kinase type 1B isoform b", "360", "PNCK is a member of the calcium/calmodulin-dependent protein kinase family of protein serine/threonine kinases (see CAMK1; MIM 604998) (Gardner et al., 2000 [PubMed 10673339]).[supplied by OMIM, Mar 2008]. " ], [ "Q8N4H5-1", "NP_001127957.1", "mitochondrial import receptor subunit TOM5 homolog isoform 2", "85", "" ], [ "Q8N309-1", "NP_689972.3", "leucine-rich repeat-containing protein 43 isoform 2", "471", "" ], [ "Q96BR6-1", "NP_079080.2", "zinc finger protein 669 isoform 1", "464", "" ], [ "Q96KR4-1", "NP_149018.2", "leishmanolysin-like peptidase isoform 2", "655", "This gene encodes a zinc-metallopeptidase. The encoded protein may play a role in cell migration and invasion. Studies of a similar protein in Drosophila indicate a potential role in mitotic progression. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2009]. " ], [ "A4QPB2-1", "NP_872298.1", "low-density lipoprotein receptor-related protein 5-like protein", "252", "" ], [ "Q6UXU4-1", "NP_653276.1", "germ cell-specific gene 1-like protein isoform 2", "176", "" ], [ "Q6ZT89-1", "NP_660325.4", "solute carrier family 25 member 48 isoform 2", "157", "" ] ] }, "readme": "Name\n - Human Protein Information (NCBI RefSeq)\n\nVersion\n - 1.5.12\n\nCreated on\n - 2019-01-23T17:21:05.888176\n\nModified on\n - 2019-12-03T10:10:53.391808\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 Human Protein Information (NCBI RefSeq) dataset contains human [taxid:9606] protein information such as protein accession, name, length and protein function summary from NCBI RefSeq database. The dataset is derived from NCBI RefSeq Release 96, September 9, 2019. 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 information\n - protein length\n - NCBI RefSeq\n - protein summary\n\n Pipeline Steps\n - Step-1: The 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/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_9606.gpff\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.12/source/refseq_protein_all_9606.gpff\n Name: human_protein_info_refseq.csv\n URI: https://data.glygen.org/ln2data/releases/data/v-1.5.12/reviewed/human_protein_info_refseq.csv\n Output Subdomain\n Name: human_protein_info_refseq.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.5.12/reviewed/human_protein_info_refseq.csv\n Name: human_protein_info_refseq.stat.csv\n URI: http://data.glygen.org/ln2data/releases/data/v-1.5.12/reviewed/human_protein_info_refseq.stat.csv\n\nFields\n Name: \"refseq_protein_summary\"\n Description: \"Function of the protein in NCBI RefSeq database\"\n Unique Values: \"11639\"\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: \"18311\"\n Name: \"p_refseq_ac_best_match\"\n Description: \"Best match NCBI RefSeq protein accession to UniProtKB canonical accession\"\n Unique Values: \"18311\"\n Name: \"refseq_protein_name\"\n Description: \"Name of the protein in NCBI RefSeq database\"\n Unique Values: \"18310\"\n Name: \"refseq_protein_length\"\n Description: \"Length of the protein in NCBI RefSeq database\"\n Unique Values: \"2025\"", "downloadurl": "/ln2data/releases/data/v-1.5.12/reviewed/human_protein_info_refseq.csv" }