{ "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", "" ], [ "Q9BTE6-1", "NP_001129514.2", "PTGES3L-AARSD1 protein isoform 1", "586", "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]. " ], [ "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]. " ], [ "B7Z3J9-1", "NP_001306966.1", "uncharacterized protein LOC730098", "87", "" ], [ "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_001186976.1", "nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 isoform 2", "163", "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]. " ], [ "Q8IV50-1", "NP_001137389.1", "lysM and putative peptidoglycan-binding domain-containing protein 2 isoform 2", "124", "" ], [ "Q9HAE3-1", "NP_001136329.1", "EF-hand calcium-binding domain-containing protein 1 isoform b", "159", "" ], [ "Q9UN30-3", "NP_001032624.1", "sex comb on midleg-like protein 1 isoform c", "208", "" ], [ "Q562E7-1", "NP_001157145.1", "WD repeat-containing protein 81 isoform 3", "738", "This gene encodes a multi-domain transmembrane protein which is predominantly expressed in the brain and is thought to play a role in endolysosomal trafficking. Mutations in this gene are associated with an autosomal recessive form of a syndrome exhibiting cerebellar ataxia, cognitive disability, and disequilibrium (CAMRQ2). Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]. " ], [ "Q96K17-1", "NP_001129969.1", "transcription factor BTF3 homolog 4 isoform 2", "100", "" ], [ "Q9Y608-1", "NP_001127841.1", "leucine-rich repeat flightless-interacting protein 2 isoform k", "424", "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]. " ], [ "Q6R2W3-1", "NP_001316545.1", "SCAN domain-containing protein 3 isoform 2", "1174", "" ], [ "Q9NWW7-1", "NP_001335687.1", "uncharacterized protein C2orf42", "574", "" ], [ "Q8NDP4-1", "NP_001335653.1", "zinc finger protein 439 isoform f", "363", "" ], [ "Q14094-1", "NP_001335061.1", "cyclin-I isoform a", "377", "The protein encoded by this gene belongs to the highly conserved cyclin family, whose members are characterized by a dramatic periodicity in protein abundance through the cell cycle. Cyclins function as regulators of CDK kinases. Different cyclins exhibit distinct expression and degradation patterns which contribute to the temporal coordination of each mitotic event. This cyclin shows the highest similarity with cyclin G. The transcript of this gene was found to be expressed constantly during cell cycle progression. [provided by RefSeq, Jan 2017]. " ], [ "Q8TAB5-1", "NP_001335620.1", "UPF0500 protein C1orf216", "229", "" ], [ "Q7Z5U6-1", "NP_001332835.1", "WD repeat-containing protein 53 isoform a", "358", "This gene encodes a protein containing WD domains. The function of this gene is unknown. [provided by RefSeq, Jul 2008]. " ], [ "Q5T197-1", "NP_001137159.1", "E3 ubiquitin-protein ligase DCST1 isoform 2", "681", "This gene encodes a protein with a domain similar to one found in dendritic cells (PMID:11169400) which play a key role in antigen processing and display for immune responses. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]. " ], [ "P0C7X2-1", "NP_001019854.1", "zinc finger protein 688 isoform b", "262", "" ], [ "Q96B23-1", "NP_001008240.1", "uncharacterized protein C18orf25 isoform b", "343", "" ], [ "Q8TD35-1", "NP_001007126.1", "protein LKAAEAR1 isoform 1", "240", "" ], [ "Q6PIL6-1", "NP_001030175.1", "Kv channel-interacting protein 4 isoform 5", "225", "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]. " ], [ "Q9NYT6-1", "NP_001027544.1", "zinc finger protein 226 isoform a", "803", "" ], [ "Q6P3X8-1", "NP_001017434.1", "piggyBac transposable element-derived protein 2 isoform b", "341", "The piggyBac family of proteins, found in diverse animals, are transposases related to the transposase of the canonical piggyBac transposon from the moth, Trichoplusia ni. This family also includes genes in several genomes, including human, that appear to have been derived from the piggyBac transposons. This gene belongs to the subfamily of piggyBac transposable element derived (PGBD) genes. The PGBD proteins appear to be novel, with no obvious relationship to other transposases, or other known protein families. The exact function of this gene is not known. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]. " ], [ "Q8TCJ0-1", "NP_036305.2", "F-box only protein 25 isoform 3", "291", "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 Fbxs class. Three alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]. " ], [ "Q8WXA3-2", "NP_001035882.1", "RUN and FYVE domain-containing protein 2 isoform b", "403", "" ], [ "Q9Y5V0-1", "NP_001035975.1", "zinc finger protein 706", "76", "" ], [ "Q9NRR8-1", "NP_001033796.1", "CDC42 small effector protein 1", "79", "" ], [ "Q8IYN2-1", "NP_001006685.1", "transcription elongation factor A protein-like 8", "117", "This gene encodes a member of the transcription elongation factor A (SII)-like (TCEAL) gene family. Members of this family contain TFA domains and may function as nuclear phosphoproteins that modulate transcription in a promoter context-dependent manner. Multiple family members are located on the X chromosome. Alternative splicing results in multiple transcript variants encoding a single isoform. [provided by RefSeq, Jul 2008]. " ], [ "Q9BYJ4-1", "NP_001003827.1", "tripartite motif-containing protein 34 isoform 1", "488", "The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, B-box type 1 and B-box type 2 domain, and a coiled-coil region. Expression of this gene is up-regulated by interferon. This gene is mapped to chromosome 11p15, where it resides within a TRIM gene cluster. Alternative splicing results in multiple transcript variants. A read-through transcript from the upstream TRIM6 gene has also been observed, which results in a fusion product from these neighboring family members. [provided by RefSeq, Oct 2010]. " ], [ "Q8IVS2-1", "NP_055322.1", "malonyl-CoA-acyl carrier protein transacylase, mitochondrial isoform b precursor", "180", "The protein encoded by this gene is found exclusively in the mitochondrion, where it catalyzes the transfer of a malonyl group from malonyl-CoA to the mitochondrial acyl carrier protein. The encoded protein may be part of a fatty acid synthase complex that is more like the type II prokaryotic and plastid complexes rather than the type I human cytosolic complex. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2012]. " ], [ "Q8N720-1", "NP_001009958.1", "zinc finger protein 655 isoform c", "110", "This gene encodes a zinc finger protein. The zinc finger proteins are involved in DNA binding and protein-protein interactions. Multiple alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]. " ], [ "Q9BXW7-1", "NP_060299.4", "haloacid dehalogenase-like hydrolase domain-containing 5 isoform 1", "393", "" ], [ "Q7L4S7-1", "NP_001009584.1", "protein ARMCX6", "300", "" ], [ "Q8TBZ5-1", "NP_001127912.1", "zinc finger protein 502", "544", "" ], [ "Q9UJ78-4", "NP_001034738.1", "zinc finger MYM-type protein 5 isoform 2", "208", "" ], [ "Q6P387-1", "NP_001094343.1", "uncharacterized protein C16orf46 isoform 1", "388", "" ], [ "Q9BVG8-3", "NP_001123571.1", "kinesin-like protein KIFC3 isoform 3", "687", "This gene encodes a member of the kinesin-14 family of microtubule motors. Members of this family play a role in the formation, maintenance and remodeling of the bipolar mitotic spindle. The protein encoded by this gene has cytoplasmic functions in the interphase cells. It may also be involved in the final stages of cytokinesis. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]. " ], [ "Q96HH4-1", "NP_001135782.1", "transmembrane protein 169", "297", "" ], [ "Q6NS38-1", "NP_001001655.1", "DNA oxidative demethylase ALKBH2 isoform 1", "261", "The Escherichia coli AlkB protein protects against the cytotoxicity of methylating agents by repair of the specific DNA lesions generated in single-stranded DNA. ALKBH2 and ALKBH3 (MIM 610603) are E. coli AlkB homologs that catalyze the removal of 1-methyladenine and 3-methylcytosine (Duncan et al., 2002 [PubMed 12486230]).[supplied by OMIM, Mar 2008]. " ], [ "Q9NVR7-1", "NP_001127887.1", "TBCC domain-containing protein 1 isoform a", "557", "" ], [ "Q8N8F7-1", "NP_001127940.1", "leucine-rich single-pass membrane protein 1", "131", "" ], [ "Q9BRV3-1", "NP_001116309.1", "sugar transporter SWEET1 isoform b", "166", "" ], [ "Q96RT8-1", "NP_001096080.1", "gamma-tubulin complex component 5 isoform b", "1024", "" ], [ "P51522-1", "NP_001099019.1", "zinc finger protein 83", "516", "" ], [ "Q8NE31-1", "NP_001001971.1", "protein FAM13C isoform 2", "487", "" ], [ "Q96PV4-1", "NP_001096620.1", "paraneoplastic antigen-like protein 5", "448", "This gene encodes a member of the paraneoplastic Ma antigen protein family. These proteins have been implicated in the development of paraneoplastic disorders resulting from an immune response directed against them. Paraneoplastic disorders are the result of an abnormal immune response to a tumor. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Oct 2011]. " ], [ "Q8TBC5-1", "NP_001139014.1", "zinc finger and SCAN domain-containing protein 18 isoform 1", "566", "" ], [ "Q86V59-1", "NP_001096619.1", "paraneoplastic antigen-like protein 8A isoform b", "378", "" ], [ "Q9BVX2-1", "NP_001137313.1", "transmembrane protein 106C isoform b", "231", "" ], [ "Q8NDC4-1", "NP_001092301.1", "MORN repeat-containing protein 4", "146", "" ], [ "Q4LDR2-1", "NP_001041717.1", "cortexin-3", "81", "" ], [ "Q9NV79-1", "NP_001098395.1", "protein-L-isoaspartate O-methyltransferase domain-containing protein 2 isoform 2", "334", "" ], [ "A6PVL3-1", "NP_001091080.1", "kinocilin isoform 2", "101", "" ], [ "Q8NHS4-1", "NP_001129070.1", "clathrin heavy chain linker domain-containing protein 1 isoform 2", "464", "" ], [ "Q9Y577-1", "NP_001020111.1", "E3 ubiquitin-protein ligase TRIM17 isoform 1", "477", "The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The protein localizes to cytoplasmic bodies. The protein is expressed almost exclusively in the testis, but its function is unknown. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]. " ], [ "Q8N7R7-1", "NP_001135772.1", "cyclin-Y-like protein 1 isoform 1", "308", "" ], [ "Q9UIL4-1", "NP_005346.3", "kinesin-like protein KIF25 isoform 2", "332", "The protein encoded by this gene is a member of the kinesin-like protein family. Protein family members are microtubule-dependent molecular motors that transport organelles within cells and move chromosomes during cell division. However, the particular function of this gene product has not yet been determined. Two alternatively spliced transcript variants which encode products have been described. Other splice variants have been found that lack exon 2 and the initiation codon for translation. [provided by RefSeq, Jul 2008]. " ], [ "Q5VWK0-1", "NP_001137459.1", "neuroblastoma breakpoint family member 6 isoform 1", "667", "This gene is a member of the neuroblastoma breakpoint family (NBPF) which consists of dozens of recently duplicated genes primarily located in segmental duplications on human chromosome 1. This gene family has experienced its greatest expansion within the human lineage and has expanded, to a lesser extent, among primates in general. Members of this gene family are characterized by tandemly repeated copies of DUF1220 protein domains. Gene copy number variations in the human chromosomal region 1q21.1, where most DUF1220 domains are located, have been implicated in a number of developmental and neurogenetic diseases such as microcephaly, macrocephaly, autism, schizophrenia, cognitive disability, congenital heart disease, neuroblastoma, and congenital kidney and urinary tract anomalies. Altered expression of some gene family members is associated with several types of cancer. This gene family contains numerous pseudogenes. Alternative splicing of this gene results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Mar 2013]. " ], [ "Q9H0I3-1", "NP_001135774.1", "coiled-coil domain-containing protein 113 isoform 2", "323", "" ], [ "Q8N7B9-1", "NP_001138405.1", "EF-hand calcium-binding domain-containing protein 3 isoform a", "490", "" ], [ "Q9NXK6-1", "NP_001098024.1", "membrane progestin receptor gamma", "330", "" ], [ "Q9BSK1-1", "NP_001129062.1", "zinc finger protein 577 isoform b", "426", "" ], [ "Q6ZRZ4-1", "NP_001001938.1", "uncharacterized protein C9orf47 isoform 1 precursor", "202", "" ], [ "Q9H6B9-1", "NP_001136358.1", "epoxide hydrolase 3", "360", "" ], [ "Q8NEM1-1", "NP_001123494.1", "zinc finger protein 680 isoform 2", "123", "" ], [ "Q3YBM2-1", "NP_001094781.1", "transmembrane protein 176B isoform a", "270", "" ], [ "P41247-1", "NP_001135861.1", "patatin-like phospholipase domain-containing protein 4 isoform 1 precursor", "253", "This gene encodes a member of the patatin-like family of phospholipases. The encoded enzyme has both triacylglycerol lipase and transacylase activities and may be involved in adipocyte triglyceride homeostasis. Alternate splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome Y. [provided by RefSeq, Feb 2010]. " ], [ "Q8WW43-1", "NP_001139118.1", "gamma-secretase subunit APH-1B isoform 2", "216", "This gene encodes a multi-pass transmembrane protein that is a functional component of the gamma-secretase complex, which also contains presenilin and nicastrin. This protein represents a stabilizing cofactor for the presenilin holoprotein in the complex. The gamma-secretase complex catalyzes the cleavage of integral proteins such as notch receptors and beta-amyloid precursor protein. [provided by RefSeq, Sep 2011]. " ], [ "Q9H069-1", "NP_001123562.1", "dynein regulatory complex subunit 3 isoform a", "523", "" ], [ "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 - 1.5.36\n\nCreated on\n - 2019-01-23T17:21:05.888176\n\nModified on\n - 2020-04-10T11:25:40.102630\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. 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/ln2wwwdata/source/refseq_protein_all_9606.gpff\n Name: human_protein_info_refseq.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/human_protein_info_refseq.csv\n Output Subdomain\n Name: human_protein_info_refseq.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/human_protein_info_refseq.csv\n Name: human_protein_info_refseq.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/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: \"11675\"\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: \"18347\"\n Name: \"p_refseq_ac_best_match\"\n Description: \"Best match NCBI RefSeq protein accession to UniProtKB canonical accession\"\n Unique Values: \"18347\"\n Name: \"refseq_protein_name\"\n Description: \"Name of the protein in NCBI RefSeq database\"\n Unique Values: \"18346\"\n Name: \"refseq_protein_length\"\n Description: \"Length of the protein in NCBI RefSeq database\"\n Unique Values: \"2013\"", "downloadurl": "/ln2data/releases/data/v-1.5.36/reviewed/human_protein_info_refseq.csv" }