Tag: RefSeq

KEGG T07682: 118706260

Entry 118725205         ncRNA     T07682                                  Name (RefSeq) U1 spliceosomal RNA   KO K14276   U1 spliceosomal RNA Organism pkl  Pipistrellus kuhlii (Kuhl’s pipistrelle) Pathway pkl03040   Spliceosome Brite KEGG Orthology (KO) [BR:pkl00001] 09120 Genetic Information Processing  09121 Transcription   03040 Spliceosome    118725205 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03041 Spliceosome [BR:pkl03041]    118725205  09184 RNA family   03100 Non-coding RNAs [BR:pkl03100]    118725205Spliceosome [BR:pkl03041] Splicing related RNAs  118725205Non-coding RNAs [BR:pkl03100] Small non-coding…

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KEGG T01015: 4329963

Entry 4332822           CDS       T01015                                  Name (RefSeq) LOW QUALITY PROTEIN: nuclear cap-binding protein subunit 1-like   KO K12882   nuclear cap-binding protein subunit 1 Organism osa  Oryza sativa japonica (Japanese rice) (RefSeq) Pathway osa03013   Nucleocytoplasmic transport osa03015   mRNA surveillance pathway osa03040   Spliceosome Brite KEGG Orthology (KO) [BR:osa00001] 09120 Genetic Information Processing  09121 Transcription   03040 Spliceosome    4332822  09122 Translation   03013 Nucleocytoplasmic transport    4332822   03015 mRNA…

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KEGG T01710: 100306272

Entry 100782702         CDS       T01710                                  Symbol COX2 Name (RefSeq) cytochrome c oxidase subunit 2, mitochondrial   KO K02261   cytochrome c oxidase subunit 2 Organism gmx  Glycine max (soybean) Pathway gmx00190   Oxidative phosphorylation gmx01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:gmx00001] 09100 Metabolism  09102 Energy metabolism   00190 Oxidative phosphorylation    100782702 (COX2) 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03029 Mitochondrial biogenesis…

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Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals

The specific environmental/history/collection context The Huseby Klev materials were unearthed and collected by archaeologists (including two of the co-authors of this article) during the excavation of this coastal hunter-fisher-gatherer site in the 90s50. The material assemblage was rich and well preserved: human bones, animal bones, plant remains and pieces of…

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Finding EntreZ IDs for refseq IDs

Finding EntreZ IDs for refseq IDs 1 Hi all, I have a list of bacterial RefSeq IDs corresponding to protein sequences (e.g., WP_007430823.1, WP_019686959.1, etc.). I need to retrieve the corresponding EntreZ IDs for these RefSeq IDs, in order to cotinue the RNA-seq downstream analysis (GO enrichment analysis ). Here’s…

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IKK gamma (IKBKG) Human shRNA Plasmid Kit (Locus ID 8517)

Product Data Locus ID 8517 Synonyms AMCBX1; EDAID1; FIP-3; FIP3; Fip3p; IKK-gamma; IKKAP1; IKKG; IMD33; IP; IP1; IP2; IPD2; NEMO; ZC2HC9 Vector pGFP-C-shLenti E. coli Selection Chloramphenicol (34 ug/ml) Mammalian Cell Selection Puromycin Format Lentiviral plasmids Kit Components IKBKG – Human, 4 unique 29mer shRNA constructs in lentiviral GFP vector(Gene…

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ZCWCC1 (MORC2) Human shRNA Lentiviral Particle (Locus)

Product Data Locus ID 22880 Synonyms CMT2Z; DIGFAN; ZCW3; ZCWCC1 Vector pGFP-C-shLenti Format Lentiviral particles RefSeq NM_001303256, NM_001303257, NM_014941, NM_014941.1, NM_014941.2, NM_014941.3, NM_001303257.1, NM_001303257.2, NM_001303256.1, NM_001303256.2, BC019257, BC136782, BC141657, BM683680, NM_001303256.3 UniProt ID Q9Y6X9 Summary This gene encodes a member of the Microrchidia (MORC) protein superfamily. The encoded protein is…

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FRK Human shRNA Lentiviral Particle (Locus ID 2444) Clinisciences

Product Data Locus ID 2444 Synonyms GTK; PTK5; RAK Vector pGFP-C-shLenti Format Lentiviral particles RefSeq NM_002031, NM_002031.1, NM_002031.2, BC012916, BC012916.1, NM_002031.3 UniProt ID P42685 Summary The protein encoded by this gene belongs to the TYR family of protein kinases. This tyrosine kinase is a nuclear protein and may function during…

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Analysis of sepsis combined with pulmonary infection by mNGS

Introduction Sepsis is one of the major diseases that poses a serious threat to human health, and its incidence and in-hospital mortality rates remain high despite the continuous updating of sepsis guidelines.1 Its main clinical manifestations are elevated body temperature, chills, and rapid heart rate, and it is most common…

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Human CD26 (DPP4) activation kit by CRISPRa Clinisciences

Kit Components GA101256G1, CD26 gRNA vector 1 in pCas-Guide-GFP-CRISPRa, Target Sequence: CGACGTCATTTTTAGCTAAG GA101256G2, CD26 gRNA vector 2 in pCas-Guide-GFP-CRISPRa, Target Sequence: GAGCCGTGGGGGAGGGGAAA GA101256G3, CD26 gRNA vector 3 in pCas-Guide-GFP-CRISPRa, Target Sequence: AACCTCACGTGGACAGGCGA 1 CRISPRa-Enhancer vector, SKU GE100056 1 CRISPRa scramble vector, SKU GE100077 Disclaimer These products are manufactured and supplied…

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DADA2 formatted 16S rRNA gene sequences for both bacteria & archaea

Description This version is to stay up to date with the improvements and increase in 16S rRNA gene sequences (SSU) added to the GTDB release 214.1.  Please read this post for the stats on the updates. gtdb.ecogenomic.org/stats/r214 . There has been no change to the RDP-RefSeq reference database If anyone…

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Stk3 Mouse shRNA Plasmid (Locus ID 56274) Clinisciences

Product Data Locus ID 56274 Synonyms 0610042I06Rik; mess1; MST; Mst2; Mst3; Ste20 Vector pGFP-C-shLenti E. coli Selection Chloramphenicol (34 ug/ml) Mammalian Cell Selection Puromycin Format Lentiviral plasmids Kit Components Stk3 – Mouse, 4 unique 29mer shRNA constructs in lentiviral GFP vector(Gene ID = 56274). 5µg purified plasmid DNA per construct29-mer…

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Human TIA1 activation kit by CRISPRa Clinisciences

Product Data Format 3 gRNAs (5ug each), 1 scramble ctrl (10ug) and 1 enhancer vector (10ug) Symbol TIA1 Locus ID 7072 Kit Components GA104875G1, TIA1 gRNA vector 1 in pCas-Guide-GFP-CRISPRa GA104875G2, TIA1 gRNA vector 2 in pCas-Guide-GFP-CRISPRa GA104875G3, TIA1 gRNA vector 3 in pCas-Guide-GFP-CRISPRa 1 CRISPRa-Enhancer vector, SKU GE100056 1…

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Is it possible to obtain all bacterial assemblies from RefSeq and GenBank that contain a specific gene?

Is it possible to obtain all bacterial assemblies from RefSeq and GenBank that contain a specific gene? 0 Hello, I am trying to do some analysis on bacterial assemblies containing a particular AMR gene. I tried searching through NCBI genbank, refseq and it does not give me all the assemblies….

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Wheat Sequencing Consortium Awarded NSF Grant to Mine Wheat Diversity for Food Security

Newswise — The International Wheat Genome Sequencing Consortium (IWGSC) is starting a two-year project, with funding from the U.S. National Science Foundation (NSF), to mine an untapped genetic resource for wheat improvement by sequencing the genomes of ancient varieties representing the worldwide diversity of bread wheat. In this project –…

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Filter reference/subject sequences based on mapping – usegalaxy.eu support

vebaev December 12, 2023, 3:39pm 1 Hi all, I’m trying to map some reads against some refseq sequences (many, not a genome). Is there a tool I can use to filter and get which refseq seq have for example at least 100 mapped reads, or by some covarage? jennaj December…

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Methylation Analysis Tutorial in R_part1

The code and approaches that I share here are those I am using to analyze TCGA methylation data. At the bottom of the page, you can find references used to make this tutorial. If you are coming from a computer background, please bear with a geneticist who tried to code…

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how to merge human reference genome and GTF file with a custom sequence.

Hello Biostars, I am looking for some guidance on how to merge some files for my rna-bulk sequencing analysis. Let me start by describing the problem: I recieved an mRNA sequence of 4775 characters which I would like to merge with the human reference genome that I download from NCBI…

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20-OR | FGFR2 FISH Probe, Dye Color: Orange Biotrend

Gene Summary The protein encoded by this gene is a member of the fibroblast growth factor receptor family, where amino acid sequence is highly conserved between members and throughout evolution. FGFR family members differ from one another in their ligand affinities and tissue distribution. A full-length representative protein consists of…

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Human hg38 chr6:31,165,200-31,165,800 UCSC Genome Browser v457

     Custom Tracks ac4C-RIP-seq peaks, hESC CTL-1hidedensesquishpackfull ac4C-RIP-seq peaks, hESC CTL-2hidedensesquishpackfull ac4C-RIP-seq peaks, hESC NAT10-KD-1hidedensesquishpackfull ac4C-RIP-seq peaks, hESC NAT10-KD-2hidedensesquishpackfull    Mapping and Sequencing Base Positionhidedensefull p14 Fix Patcheshidedensesquishpackfull p14 Alt Haplotypeshidedensesquishpackfull Assemblyhidedensesquishpackfull Centromereshidedensesquishpackfull Chromosome Bandhidedensesquishpackfull Clone Endshidedensesquishpackfull Exome Probesetshidedensesquishpackfull FISH Cloneshidedensesquishpackfull Gaphidedensesquishpackfull GC Percenthidedensefull GRC Contigshidedensefull GRC Incidenthidedensesquishpackfull Hg19…

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Issues with Chromosome Encoding and VCF Annotation in dbSNP Alpha Release

Body: Hello, Biostars Community, I am working on creating a custom database of variants using the VCF from the latest dbSNP alpha release available at ftp.ncbi.nih.gov/snp/population_frequency/latest_release/. I have encountered a couple of issues that I’m hoping someone might help me resolve. Firstly, the chromosome encoding uses RefSeq IDs (e.g., NC_000007.12)…

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Acd Rat shRNA Plasmid (Locus ID 307798) Clinisciences

Product Data Locus ID 307798 Synonyms MGC116400 Vector pRS E. coli Selection Ampicillin Mammalian Cell Selection Puromycin Format Retroviral plasmids Kit Components Acd – Rat, 4 unique 29mer shRNA constructs in retroviral untagged vector(Gene ID = 307798). 5µg purified plasmid DNA per construct29-mer scrambled shRNA cassette in pRS Vector, TR30012,…

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A genome assembly for Orinus kokonorica provides insights into the origin, adaptive evolution and further diversification of two closely related grass genera

Jiao, Y. N. et al. Ancestral polyploidy in seed plants and angiosperms. Nature 473, 97–100 (2011). Article  PubMed  Google Scholar  Levin, D. A. Polyploidy and novelty in flowering plants. Am. Nat. 122, 1–25 (1983). Article  Google Scholar  Soltis, P. S. & Soltis, D. E. Ancient WGD events as drivers of…

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Dryad | Data — Progressive Cactus alignment of 298 drosophilid species

Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. Whole-genome sequence alignments link evolution at the nucleotide level across species and are a critical but computationally intensive step for…

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Alfalfa vein mottling virus, a novel potyvirid infecting Medicago sativa L. | Virology Journal

Plant material Five alfalfa plants (stems and leaves) were sampled from each of the four different fields, 10–15 acres in size, located in Yuma Country, Arizona, USA. Geographic coordinates of the alfalfa fields and the adjacent crops are shown in Table 1. Table 1 Geographic locations of alfalfa fields Total…

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r-bioc-phyloseq 1.22.3-1

/usr/ root:root 0o755 /usr/lib/ root:root 0o755 /usr/lib/R/ root:root 0o755 /usr/lib/R/site-library/ root:root 0o755 /usr/lib/R/site-library/phyloseq/ root:root 0o755 /usr/lib/R/site-library/phyloseq/CITATION text/plain root:root 0o644 606 bytes /usr/lib/R/site-library/phyloseq/data/ root:root 0o755 /usr/lib/R/site-library/phyloseq/data/datalist text/plain root:root 0o644 44 bytes /usr/lib/R/site-library/phyloseq/data/enterotype.RData application/x-xz root:root 0o644 190.7 KB /usr/lib/R/site-library/phyloseq/data/esophagus.RData application/x-xz root:root 0o644 1.8 KB /usr/lib/R/site-library/phyloseq/data/GlobalPatterns.RData application/x-xz root:root 0o644 425.4 KB /usr/lib/R/site-library/phyloseq/data/soilrep.RData application/x-xz root:root 0o644 104.9 KB /usr/lib/R/site-library/phyloseq/DESCRIPTION text/plain…

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Summary of Pseudomonas borbori DSM 17834, version 27.1

Summary of Pseudomonas borbori DSM 17834, version 27.1 Tier 3 Uncurated Database Database Authors: Pallavi Subhraveti1, Quang Ong1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1 1SRI International Summary: This Pathway/Genome Database (PGDB) was generated on 27-Feb-2018 from the annotated genome of Pseudomonas borbori DSM 17834, as obtained from…

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KEGG T01005: 473325

Entry 473325            CDS       T01005                                  Symbol RNASE2 Name (RefSeq) non-secretory ribonuclease precursor   KO K01168   pancreatic ribonuclease [EC:4.6.1.18] Organism ptr  Pan troglodytes (chimpanzee) Brite KEGG Orthology (KO) [BR:ptr00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03019 Messenger RNA biogenesis [BR:ptr03019]    473325 (RNASE2)   04131 Membrane trafficking [BR:ptr04131]    473325 (RNASE2)Enzymes [BR:ptr01000] 4. Lyases  4.6  Phosphorus-oxygen lyases   4.6.1  Phosphorus-oxygen lyases (only sub-subclass identified to date)    4.6.1.18  pancreatic ribonuclease     473325 (RNASE2)Messenger…

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Where do these snpeff annotation come from?

Where do these snpeff annotation come from? 0 I am annotating a VCF with annotation from snpeff, which I want to use eventually to parse for predicted loss of function variants I want to understand the annotation better and document how they are happening. I run this command: snpEff “hg38″…

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KEGG T01007: 415125

Entry 415125            CDS       T01007                                  Symbol FGFR2 Name (RefSeq) fibroblast growth factor receptor 2 precursor   KO K05093   fibroblast growth factor receptor 2 [EC:2.7.10.1] Organism cfa  Canis lupus familiaris (dog) Pathway cfa01521   EGFR tyrosine kinase inhibitor resistance cfa04010   MAPK signaling pathway cfa04014   Ras signaling pathway cfa04015   Rap1 signaling pathway cfa04020   Calcium signaling pathway cfa04144   Endocytosis…

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KEGG T02994: 18601618

Entry 18601618          CDS       T02994                                  Name (RefSeq) alpha-glucan phosphorylase 1   KO K00688   glycogen phosphorylase [EC:2.4.1.1] Organism tcc  Theobroma cacao (cacao) Pathway tcc00500   Starch and sucrose metabolism tcc01100   Metabolic pathways tcc01110   Biosynthesis of secondary metabolites Brite KEGG Orthology (KO) [BR:tcc00001] 09100 Metabolism  09101 Carbohydrate metabolism   00500 Starch and sucrose metabolism    18601618Enzymes [BR:tcc01000] 2. Transferases  2.4  Glycosyltransferases   2.4.1  Hexosyltransferases    2.4.1.1  glycogen phosphorylase     18601618 BRITE hierarchy SSDB OrthologParalogGene clusterGFIT…

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OAS2 Human shRNA Plasmid Kit (Locus ID 4939) Clinisciences

Product Data Locus ID 4939 Vector pRS E. coli Selection Ampicillin Mammalian Cell Selection Puromycin Format Retroviral plasmids Kit Components OAS2 – Human, 4 unique 29mer shRNA constructs in retroviral untagged vector(Gene ID = 4939). 5µg purified plasmid DNA per construct29-mer scrambled shRNA cassette in pRS Vector, TR30012, included for…

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Index of /~vgn/oldbioinformatics/vgn/2_entrez/2e_sequence-databases/nucleotides/refseq

Name Last modified Size Description Parent Directory   –   FINDER.DAT 2006-05-09 12:31 920   Icon_ 2006-02-18 12:54 0   RESOURCE.FRK/ 2006-03-29 10:12 –   RefSeq.GIF 2006-03-21 18:31 56K   Spacer.GIF 2006-03-22 08:27 878   refseq.htm 2006-03-23 11:07 6.8K   spacer-flint.GIF 2006-03-22 08:27 1.1K   spacer-shale.GIF 2006-03-22 08:27 902  …

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KEGG T02920: 102247935

Entry 102247935         CDS       T02920                                  Symbol TRMT44 Name (RefSeq) tRNA methyltransferase 44 homolog (S. cerevisiae)   KO K15447   tRNASer (uridine44-2′-O)-methyltransferase [EC:2.1.1.211] Organism myb  Myotis brandtii (Brandt’s bat) Brite KEGG Orthology (KO) [BR:myb00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03016 Transfer RNA biogenesis [BR:myb03016]    102247935 (TRMT44)Enzymes [BR:myb01000] 2. Transferases  2.1  Transferring one-carbon groups   2.1.1  Methyltransferases    2.1.1.211  tRNASer (uridine44-2′-O)-methyltransferase     102247935 (TRMT44)Transfer RNA biogenesis [BR:myb03016] Eukaryotic type  tRNA modification…

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KEGG T01001: 1474

Entry 1474              CDS       T01001                                  Symbol CST6, ECTD15 Name (RefSeq) cystatin E/M   KO K13902   cystatin-M Organism hsa  Homo sapiens (human) Disease H00651   Hypohidrotic ectodermal dysplasia Brite KEGG Orthology (KO) [BR:hsa00001] 09180 Brite Hierarchies  09181 Protein families: metabolism   01002 Peptidases and inhibitors [BR:hsa01002]    1474 (CST6)Peptidases and inhibitors [BR:hsa01002] Peptidase inhibitors  Family I25: cystatin family   1474 (CST6) BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif…

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KEGG T01001: 637

Entry 637               CDS       T01001                                  Symbol BID, FP497 Name (RefSeq) BH3 interacting domain death agonist   KO K04726   BH3 interacting domain death agonist Organism hsa  Homo sapiens (human) Pathway hsa01524   Platinum drug resistance hsa04071   Sphingolipid signaling pathway hsa04115   p53 signaling pathway hsa04210   Apoptosis hsa04215   Apoptosis – multiple species hsa04217   Necroptosis hsa04650   Natural killer cell mediated…

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NFIB Human shRNA Plasmid Kit (Locus ID 4781) Clinisciences

Product Data Locus ID 4781 Synonyms CTF; HMGIC/NFIB; MACID; NF-I/B; NF1-B; NFI-B; NFI-RED; NFIB2; NFIB3 Vector pGFP-V-RS E. coli Selection Kanamycin Mammalian Cell Selection Puromycin Format Retroviral plasmids Kit Components NFIB – Human, 4 unique 29mer shRNA constructs in retroviral GFP vector(Gene ID = 4781). 5µg purified plasmid DNA per…

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Gene of choice – RefSeq Accession: NM_ cDNA NM_ ACATTTGCTT CTGACACAAC TGTGTTCACT AGCAACCTCA

Gene of choice: HBB (hemoglobin subunit beta) located in chromosome11:5,225,464 – 5,227,071 which contains 1,608bp. RefSeq Accession: NM_00518 cDNA NM_000518 ACATTTGCTT CTGACACAAC TGTGTTCACT AGCAACCTCA AACAGACACC 50 ATGGTGCATC TGACTCCTGA GGAGAAGTCT GCCGTTACTG CCCTGTGGGG 100 CAAGGTGAAC GTGGATGAAG TTGGTGGTGA GGCCCTGGGC AGGCTGCTGG 150 TGGTCTACCC TTGGACCCAG AGGTTCTTTG AGTCCTTTGG GGATCTGTCC 200 ACTCCTGATG CTGTTATGGG CAACCCTAAG GTGAAGGCTC ATGGCAAGAA 250…

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GYPB Human shRNA Plasmid Kit (Locus ID 2994) Clinisciences

Product Data Locus ID 2994 Synonyms CD235b; GPB; GYP; GYPA; MNS; PAS-3; SS Vector pGFP-C-shLenti E. coli Selection Chloramphenicol (34 ug/ml) Mammalian Cell Selection Puromycin Format Lentiviral plasmids Kit Components GYPB – Human, 4 unique 29mer shRNA constructs in lentiviral GFP vector(Gene ID = 2994). 5µg purified plasmid DNA per…

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what is the RefSeq? | 3 Answers from Research papers

whole genome sequencing of ASFV 5 answers What are the challenges and opportunities of data storytelling? 5 answers what methods exist for genotyping non model species? 5 answers RNA expression data ConsensusClusterPlus other similar tools? 5 answers What are the gaps in tuber crops genomic studies? 5 answers Have quantitative…

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AK2 Human shRNA Plasmid Kit (Locus ID 204) Clinisciences

Product Data Locus ID 204 Synonyms ADK2 Vector pGFP-C-shLenti E. coli Selection Chloramphenicol (34 ug/ml) Mammalian Cell Selection Puromycin Format Lentiviral plasmids Kit Components AK2 – Human, 4 unique 29mer shRNA constructs in lentiviral GFP vector(Gene ID = 204). 5µg purified plasmid DNA per construct29-mer scrambled shRNA cassette in pGFP-C-shLenti…

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Improving Species Level-taxonomic Assignment from 16S rRNA Sequencing Technologies

Affiliations Expand Affiliations 1 Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L’Hospitalet del Llobregat, Barcelona, Catalonia, Spain. 2 ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Catalonia, Spain. 3 Department of Clinical Sciences, Faculty of Medicine and Health Sciences and Universitat de Barcelona Institute…

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did pilon improve my genome?

did pilon improve my genome? 0 my doubt is if my sequence has actually improved? refseq is the reference sequence. polished is the output from pilon and contigs.fasta is my file generated from spades. pls help I used the command Java -Xmx2048m -jar pilon-1.24.jar –genome refseq.fasta –frags sorted bam.bam –output…

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Metagenome profiling and containment estimation through abundance-corrected k-mer sketching with sylph

Profiling metagenomes against databases allows for the detection and quantification of microbes, even at low abundances where assembly is not possible. We introduce sylph, a metagenome profiler that estimates metagenome-genome average nucleotide identity (ANI) through zero-inflated Poisson k-mer statistics, enabling ANI-based taxa detection. Sylph is the most accurate method on…

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EMDB < EMD-14025

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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The Biostar Herald for Monday, November 20, 2023

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…

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EMDB < EMD-16930

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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snRNA-seq of mouse brain cortex – Project

 Home Project CNP0003558   Source:  CNGB Project  ( ID CNP0003558 ) Project name: – Description: – Data type : – Sample scope: – Relevance: – Submitter: –    Organization: – Related RefSeq Project: – Accession in other database: – Literature(s): – Release date: – Updated: – DOI: – Statistic: Assembly: – Sample: –…

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11-100test | EpCAM antibody [VU-1D9] (PerCP-Cy5.5) Clinisciences

Application Note *Optimal dilutions/concentrations should be determined by the researcher. Application Recommended Dilution FACS 4 μl reagent / 100 μl of whole blood or 10⁶ cells in a suspension Not tested in other applications. Calculated MW 35 kDa. ( Note ) Product Note This antibody recognizes an epitope within EGF-like…

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SIGIRR Human shRNA Lentiviral Particle (Locus ID 59307)

Product Data Locus ID 59307 Synonyms IL-1R8; TIR8 Vector pGFP-C-shLenti Format Lentiviral particles RefSeq NM_001135053, NM_001135054, NM_021805, NM_021805.1, NM_021805.2, NM_001135053.1, NM_001135054.1, BC003591, BC003591.1, BC025953, BC106007, NM_001135054.2, NM_001135053.2 UniProt ID Q6IA17 Summary Acts as a negative regulator of the Toll-like and IL-1R receptor signaling pathways. Attenuates the recruitment of receptor-proximal signaling…

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IL6 Human shRNA Plasmid Kit (Locus ID 3569) Clinisciences

Product Data Locus ID 3569 Synonyms BSF-2; BSF2; CDF; HGF; HSF; IFN-beta-2; IFNB2; IL-6 Vector pRS E. coli Selection Ampicillin Mammalian Cell Selection Puromycin Format Retroviral plasmids Kit Components IL6 – Human, 4 unique 29mer shRNA constructs in retroviral untagged vector(Gene ID = 3569). 5µg purified plasmid DNA per construct29-mer…

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KEGG T06063: 106511269

Entry 106522761         CDS       T06063                                  Symbol pak1 Name (RefSeq) serine/threonine-protein kinase PAK 1   KO K04409   p21-activated kinase 1 [EC:2.7.11.1] Organism alim  Austrofundulus limnaeus (annual killifish) Pathway alim04010   MAPK signaling pathway alim04012   ErbB signaling pathway alim04510   Focal adhesion alim04625   C-type lectin receptor signaling pathway alim04810   Regulation of actin cytoskeleton alim05132   Salmonella infection Brite KEGG Orthology…

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KEGG T01028: 706234

Entry 706234            CDS       T01028                                  Symbol TRAP1 Name (RefSeq) heat shock protein 75 kDa, mitochondrial   KO K09488   TNF receptor-associated protein 1 Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc05012   Parkinson disease mcc05022   Pathways of neurodegeneration – multiple diseases Brite KEGG Orthology (KO) [BR:mcc00001] 09160 Human Diseases  09164 Neurodegenerative disease   05012 Parkinson disease    706234 (TRAP1)   05022 Pathways of neurodegeneration –…

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CD96 Human shRNA Lentiviral Particle (Locus ID 10225)

Product Data Locus ID 10225 Synonyms TACTILE Vector pGFP-C-shLenti Format Lentiviral particles RefSeq NM_001318889, NM_005816, NM_198196, NR_134917, NM_198196.1, NM_198196.2, NM_005816.1, NM_005816.2, NM_005816.3, NM_005816.4, BC020749, BC027914, BM561433, NM_005816.5 UniProt ID P40200 Summary The protein encoded by this gene belongs to the immunoglobulin superfamily. It is a type I membrane protein. The…

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KEGG T03271: 103675060

Entry 103675060         CDS       T03271                                  Symbol APPL1 Name (RefSeq) DCC-interacting protein 13-alpha   KO K08733   DCC-interacting protein 13 alpha Organism umr  Ursus maritimus (polar bear) Pathway umr04211   Longevity regulating pathway umr05200   Pathways in cancer umr05210   Colorectal cancer Brite KEGG Orthology (KO) [BR:umr00001] 09150 Organismal Systems  09149 Aging   04211 Longevity regulating pathway    103675060 (APPL1) 09160 Human Diseases  09161 Cancer: overview   05200 Pathways in…

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AMH Human shRNA Plasmid Kit (Locus ID 268) Clinisciences

Product Data Locus ID 268 Synonyms MIF; MIS Vector pRS E. coli Selection Ampicillin Mammalian Cell Selection Puromycin Format Retroviral plasmids Kit Components AMH – Human, 4 unique 29mer shRNA constructs in retroviral untagged vector(Gene ID = 268). 5µg purified plasmid DNA per construct29-mer scrambled shRNA cassette in pRS Vector,…

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Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years

Egan, E. S., Fogel, M. A. & Waldor, M. K. Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes. Mol. Microbiol. 56, 1129–1138 (2005). Article  CAS  PubMed  Google Scholar  Harrison, P. W., Lower, R. P., Kim, N. K. & Young, J. P. Introducing the bacterial ‘chromid’: not a…

Continue Reading Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years

KEGG T01001: 257194

Entry 257194            CDS       T01001                                  Symbol NEGR1, DMML2433, IGLON4, KILON, Ntra Name (RefSeq) neuronal growth regulator 1   KO K06775   neuronal growth regulator 1 Organism hsa  Homo sapiens (human) Pathway hsa04514   Cell adhesion molecules Brite KEGG Orthology (KO) [BR:hsa00001] 09130 Environmental Information Processing  09133 Signaling molecules and interaction   04514 Cell adhesion molecules    257194 (NEGR1) 09180 Brite Hierarchies  09183 Protein families: signaling…

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IGF1 Receptor (IGF1R) Human shRNA Plasmid Kit (Locus ID)

Product Data Locus ID 3480 Synonyms CD221; IGFIR; IGFR; JTK13 Vector pRS E. coli Selection Ampicillin Mammalian Cell Selection Puromycin Format Retroviral plasmids Kit Components IGF1R – Human, 4 unique 29mer shRNA constructs in retroviral untagged vector(Gene ID = 3480). 5µg purified plasmid DNA per construct29-mer scrambled shRNA cassette in…

Continue Reading IGF1 Receptor (IGF1R) Human shRNA Plasmid Kit (Locus ID)

KEGG T08541: 104528229

Entry 104528229         CDS       T08541                                  Symbol SLC15A4 Name (RefSeq) solute carrier family 15 member 4   KO K14638   solute carrier family 15 (peptide/histidine transporter), member 3/4 Organism acar  Antrostomus carolinensis (chuck-will’s-widow) Brite KEGG Orthology (KO) [BR:acar00001] 09180 Brite Hierarchies  09183 Protein families: signaling and cellular processes   02000 Transporters [BR:acar02000]    104528229 (SLC15A4)Transporters [BR:acar02000] Solute carrier family (SLC)  SLC15: Proton oligopeptide cotransporter   104528229 (SLC15A4)…

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KEGG T01011: 100038077

Entry 100038077         CDS       T01011                                  Symbol nkx2-2 Name (RefSeq) homeobox protein Nkx-2.2 isoform X1   KO K08029   homeobox protein Nkx-2.2 Organism xtr  Xenopus tropicalis (tropical clawed frog) Brite KEGG Orthology (KO) [BR:xtr00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   03000 Transcription factors [BR:xtr03000]    100038077 (nkx2-2)Transcription factors [BR:xtr03000] Eukaryotic type  Helix-turn-helix   Homeo domain ANTP: NKL    100038077 (nkx2-2) BRITE hierarchy SSDB OrthologParalogGene clusterGFIT…

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Advillin (AVIL) Human shRNA Plasmid Kit (Locus ID 10677)

Product Data Locus ID 10677 Synonyms ADVIL; DOC6; NPHS21; p92 Vector pGFP-C-shLenti E. coli Selection Chloramphenicol (34 ug/ml) Mammalian Cell Selection Puromycin Format Lentiviral plasmids Kit Components AVIL – Human, 4 unique 29mer shRNA constructs in lentiviral GFP vector(Gene ID = 10677). 5µg purified plasmid DNA per construct29-mer scrambled shRNA…

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KEGG T09424: 118385109

Entry 118385109         CDS       T09424                                  Name (RefSeq) adenylosuccinate synthetase isozyme 2-like   KO K01939   adenylosuccinate synthase [EC:6.3.4.4] Organism oke  Oncorhynchus keta (chum salmon) Pathway oke00230   Purine metabolism oke00250   Alanine, aspartate and glutamate metabolism oke01100   Metabolic pathways oke01232   Nucleotide metabolism oke01240   Biosynthesis of cofactors Module oke_M00049   Adenine ribonucleotide biosynthesis, IMP => ADP,ATP Brite KEGG Orthology (KO)…

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KEGG T08782: 127423656

Entry 127423656         CDS       T08782                                  Name (RefSeq) heparan sulfate glucosamine 3-O-sulfotransferase 3B1-like   KO K07809   [heparan sulfate]-glucosamine 3-sulfotransferase 3 [EC:2.8.2.30] Organism masi  Myxocyprinus asiaticus (Chinese sucker) Pathway masi00534   Glycosaminoglycan biosynthesis – heparan sulfate / heparin Brite KEGG Orthology (KO) [BR:masi00001] 09100 Metabolism  09107 Glycan biosynthesis and metabolism   00534 Glycosaminoglycan biosynthesis – heparan sulfate / heparin    127423656 09180 Brite Hierarchies  09181 Protein…

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RefSeq: NC_003424 CDS #248

RefSeq: NC_003424 CDS #248 >NC_003424 (refseq) complement(join(604496..604959,605015..605355, /translatio MSSSSKDSSFQVETPVQNILETSTNSELQDQVSSPYEPDYNSPVKQAAASISALQTQDDT LFNNVDERTLENKDGNKSDDANFDQVSGIPSGSLEIPILNSATSNIRLTPSDTYNNIPVS DTNNEEISKNIYGAPILESTSSDFQSKDSLSTTQPSVSGGNGSTSQSPPSLDVEQNKPFS ISNEPVEQETENSSTKDLQVYDFQTASEHLPEQSLQNTTYYDPSKTYSSVNFEEIEYGKS HEKLDLPYRTTDFIPYSKDLSTSPEAHRTSIYSYSANLPNYYNEHNELHEHHNPQTPSSP ESAYSPENLQLNHEAQNVEYLGNNAAEKSLQMNLEDEQRFQQFLKDEESIMSNWYPGQFP SASRLFLGHLNTKSLSKRNLWKVFKIYGPLAQIVLKANYGFVQFFTNEDCARALNAEQGN FVRGQKLHLEISKIQKKYQNQIENMKKGSHVTKSNQYSEMIGNLPYPTSSRKRTRSPLMS KGKSYDRKGSISMSKNFSPDCEILVTEDCPKEFVWGVEKVFQERRLNIHTTCLYRDSNLQ VIIKSCIINSVKSIILINAGLAHLGKVSVQVFKDGSSDSEVRCDEYAAVDVMVAASIVHH AKTSLMHSAASSTPSYNGERIVPDVPSPCISTNPNLPALVGSLDSVNLHHLLGFIQNTYS TTSYIPTRVSFNPNDTGGSFGTITSQSQFVVNEMPKNYARDNYEALHSQESRQRSSVAGN KQLQKILEQLAELKQPDF BLAST Read more here: Source link

Continue Reading RefSeq: NC_003424 CDS #248

RefSeq: NC_010943 CDS #580

RefSeq: NC_010943 CDS #580 >NC_010943 (refseq) 628606..629976 /translation= MPIHSSVLELIGQTPIVKAQRLDTGVCELYLKLESANPGGSIKDRIGLSMIEAAEQRGDL KPGATLVEGTAGNTGLGLALVAQQKGYKLILVVPDKMSREKIFNLKAMGAEVRLTRSDVA KGHPEYYQDLAKTIAEQTPGAYFINQFGNPDNPAAHEFGTGPEILEQMGGDLDAIVFGCG SSGTMTGLSRAFAKLSPKTELVLADPVGSILAEYINDGVLNDKSGSWLVEGIGEDFLPSI SDFSRVKKAYAISDAESFHTARELLGKEGILGGSSTGTLLAAALKYCKEQTTPKKVLVLV CDTGNKYLSKMYNDYWMLDNGFLERPQHGDLRDLILRPYGQRDTVVIGPNDLLTTAYQRM KLYDVSQLPVMDGDQLVGIVDESDVLLHVYGDEARFRDTVATAMVSKLDRLDVKSPIEAL LPVFDRGQVAIVMDGNAFLGLITRIDLLNYLRRRVQ BLAST Read more here: Source link

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RefSeq: NC_001134 CDS #316

RefSeq: NC_001134 CDS #316 >NC_001134 (refseq) 625772..628309 /translation= MSAALPSIQLPVDYNNLFNEITDFLVTFKQDTLSSDATRNENEDENLDAENIEQHLLEKG PKYMAMLQKVANRELNSVIIDLDDILQYQNEKFLQGTQADDLVSAIQQNANHFTELFCRA IDNNMPLPTKEIDYKDDVLDVILNQRRLRNERMLSDRTNEIRSENLMDTTMDPPSSMNDA LREVVEDETELFPPNLTRRYFLYFKPLSQNCARRYRKKAISSKPLSVRQIKGDFLGQLIT VRGIITRVSDVKPAVEVIAYTCDQCGYEVFQEVNSRTFTPLSECTSEECSQNQTKGQLFM STRASKFSAFQECKIQELSQQVPVGHIPRSLNIHVNGTLVRSLSPGDIVDVTGIFLPAPY TGFKALKAGLLTETYLEAQFVRQHKKKFASFSLTSDVEERVMELITSGDVYNRLAKSIAP EIYGNLDVKKALLLLLVGGVDKRVGDGMKIRGDINVCLMGDPGVAKSQLLKAICKISPRG VYTTGKGSSGVGLTAAVMKDPVTDEMILEGGALVLADNGICCIDEFDKMDESDRTAIHEV MEQQTISISKAGINTTLNARTSILAAANPLYGRYNPRLSPLDNINLPAALLSRFDILFLM LDIPSRDDDEKLAEHVTYVHMHNKQPDLDFTPVEPSKMREYIAYAKTKRPVMSEAVNDYV VQAYIRLRQDSKREMDSKFSFGQATPRTLLGIIRLSQALAKLRLADMVDIDDVEEALRLV RVSKESLYQETNKSKEDESPTTKIFTIIKKMLQETGKNTLSYENIVKTVRLRGFTMLQLS NCIQEYSYLNVWHLINEGNTLKFVDDGTMDTDQEDSLVSTPKLAPQTTASANVSAQDSDI DLQDA BLAST Read more here: Source link

Continue Reading RefSeq: NC_001134 CDS #316

A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources

40,039 MAGs reconstructed from large-scale genome-resolved metagenomics To reconstruct previously unexplored bacterial and archaeal genomes, we performed a large-scale single-sample metagenomic assembly on 3304 soil metagenomes across the globe (Fig. 1a), including 363 metagenomes from the in-house dataset and 2941 from publicly available metagenomes. The soil samples were mainly collected from…

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Recovery of microbial DNA by agar-containing solution from extremely low-biomass specimens including skin

Ethical considerations This study complies with relevant institutional, national, and international guidelines and legislation. The Ethics Committee at the RIKEN Center for Integrative Medical Sciences (H30-4) approved this study, and written informed consent was obtained from all volunteers who provided specimens. Sampling solutions The AgST solution was prepared as follows:…

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Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance

Sample collection and spiking Chicken fecal samples were collected and processed as follows: one spoonful of fecal material (≈ 1 g) was collected and stored in a DNA/RNA Shield™ Fecal Collection Tube R1101 containing 9 ml of DNA/RNA-shield (Zymo Research, Irvine, CA, USA), according to the manufacturer’s instructions. The sample was mixed…

Continue Reading Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance

STAFF SCIENTIST 1 -Deputy Program Head, Sequence Enhancements, Tools, and Delivery (SeqPlus) Program job with National Library of Medicine, National Center for Biotechnology Information

The National Library of Medicine (NLM), National Center for Biotechnology Information (NCBI),  Information Engineering Branch (IEB) is recruiting for a Staff Scientist 1 to support the Sequence  Enhancements, Tools, and Delivery (SeqPlus) Program, which includes eukaryotic, prokaryotic, and viral Reference Sequence (RefSeq) databases, the Basic Local Alignment Search Tool (BLAST), the Conserved…

Continue Reading STAFF SCIENTIST 1 -Deputy Program Head, Sequence Enhancements, Tools, and Delivery (SeqPlus) Program job with National Library of Medicine, National Center for Biotechnology Information

siRNA, Anti-Human LARP4B, 2′-OMe (SIRGT36755WQ-2OMe)

Online Inquiry For Research Use Only. Do NOT use in humans or animals. For Research Use Only. Do NOT use in humans or animals. The product SIRGT36755WQ-2OMe is a type of small interfering RNA (siRNA) that targets LARP4B gene and regulates the expression of gene. The siRNA interferes with the…

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siRNA, Anti-Human WIPF1, LNA (SIRGT24895WQ-LNA)

Online Inquiry For Research Use Only. Do NOT use in humans or animals. For Research Use Only. Do NOT use in humans or animals. The product SIRGT24895WQ-LNA is a type of small interfering RNA (siRNA) that targets WIPF1 gene and regulates the expression of gene. The siRNA interferes with the…

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Job Opening – Bioinformatics Intern- Summer 2024 – Rockville, MD

In partnership with a major Life Science organization we are seeking candidates for a summer Biological Data Analysis Internship based out of Rockville, MD. This is a 10 week Summer internship for 2024. Expected start date is June 3rd through August 9th, 2024. This is a 40 hour/week; 100% remote…

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KEGG T01028: 701915

Entry 701915            CDS       T01028                                  Symbol KRT25 Name (RefSeq) keratin, type I cytoskeletal 25   KO K07604   type I keratin, acidic Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc04915   Estrogen signaling pathway mcc05150   Staphylococcus aureus infection Brite KEGG Orthology (KO) [BR:mcc00001] 09150 Organismal Systems  09152 Endocrine system   04915 Estrogen signaling pathway    701915 (KRT25) 09160 Human Diseases  09171 Infectious disease: bacterial   05150 Staphylococcus…

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Zebrafish danRer11 chr6:43,426,661-43,433,266 UCSC Genome Browser v456

     DANIO-CODE Track Hub 3P-seq trackshidedensesquishpackfull CAGE-seq trackshidedensesquishpackfull ChIP-seq trackshidedensesquishpackfull RNA-seq trackshidedensefull Cell Typeshidedensesquishpackfull Consensus promotershidedensesquishpackfull Conservation and CRISPR targetshideshow COPEs and pooled DOPEshideshow Enhancer validationhideshow HiC trackshidedensefull Stages_Typeshidedensesquishpackfull    Mapping and Sequencing Base Positionhidedensefull Assemblyhidedensesquishpackfull Gaphidedensesquishpackfull GC Percenthidedensefull GRC Incidenthidedensesquishpackfull INSDChidedensesquishpackfull RefSeq Acchidedensesquishpackfull Restr Enzymeshidedensesquishpackfull Short Matchhidedensesquishpackfull   …

Continue Reading Zebrafish danRer11 chr6:43,426,661-43,433,266 UCSC Genome Browser v456

KEGG T01028: 698365

Entry 698365            CDS       T01028                                  Symbol AMACR Name (RefSeq) alpha-methylacyl-CoA racemase   KO K01796   alpha-methylacyl-CoA racemase [EC:5.1.99.4] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc00120   Primary bile acid biosynthesis mcc01100   Metabolic pathways mcc04146   Peroxisome Module mcc_M00104   Bile acid biosynthesis, cholesterol => cholate/chenodeoxycholate Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism  09103 Lipid metabolism   00120 Primary bile acid biosynthesis    698365 (AMACR) 09140…

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EMDB < Search results

Field: Choose…EMDB IDTitleAuthorORCIDEM methodCurrent statusDeposition dateRelease dateDeposition siteLast processing siteFitted modelsRaw dataResolutionResolution methodSoftwareLigand nameComplex nameDomain nameDrug nameGO term nameInterPro term nameChEBI term nameExternal reference Publication titlePublication yearJournalPublication author Sample typeSample nameOrganismOrganism (NCBI code)StrainOrganTissueCellOrganelleCellular LocationE.C. numberMolecular Weight methodMolecular Weight (Da)Recombinant ExpressionRecombinant organismRecombinant organism (NCBI code)Recombinant strainRecombinant expression cellRecombinant expression plasmidDNA/RNA classificationDNA/RNA…

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RVFScan predicts virulence factor genes and hypervirulence of the clinical metagenome | Briefings in Bioinformatics

Abstract Bacterial infections often involve virulence factors that play a crucial role in the pathogenicity of bacteria. Accurate detection of virulence factor genes (VFGs) is essential for precise treatment and prognostic management of hypervirulent bacterial infections. However, there is a lack of rapid and accurate methods for VFG identification from…

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CHRNA2 Human shRNA Plasmid Kit (Locus ID 1135) Quimigen

Product Data Locus ID 1135 Vector pRS E. coli Selection Ampicillin Mammalian Cell Selection Puromycin Format Retroviral plasmids Kit Components CHRNA2 – Human, 4 unique 29mer shRNA constructs in retroviral untagged vector(Gene ID = 1135). 5µg purified plasmid DNA per construct29-mer scrambled shRNA cassette in pRS Vector, TR30012, included for…

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KEGG T01028: 703937

Entry 703937            CDS       T01028                                  Symbol PTPRG Name (RefSeq) receptor-type tyrosine-protein phosphatase gamma isoform X2   KO K16667   receptor-type tyrosine-protein phosphatase gamma [EC:3.1.3.48] Organism mcc  Macaca mulatta (rhesus monkey) Brite KEGG Orthology (KO) [BR:mcc00001] 09180 Brite Hierarchies  09181 Protein families: metabolism   01009 Protein phosphatases and associated proteins [BR:mcc01009]    703937 (PTPRG)Enzymes [BR:mcc01000] 3. Hydrolases  3.1  Acting on ester bonds   3.1.3  Phosphoric-monoester hydrolases    3.1.3.48  protein-tyrosine-phosphatase     703937 (PTPRG)Protein phosphatases and…

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KEGG T07278: 119316072

Entry 119322531         CDS       T07278                                  Name (RefSeq) porphobilinogen deaminase, chloroplastic-like   KO K01749   hydroxymethylbilane synthase [EC:2.5.1.61] Organism tdc  Triticum dicoccoides (wild emmer wheat) Pathway tdc00860   Porphyrin metabolism tdc01100   Metabolic pathways tdc01110   Biosynthesis of secondary metabolites tdc01240   Biosynthesis of cofactors Module tdc_M00121   Heme biosynthesis, plants and bacteria, glutamate => heme Brite KEGG Orthology (KO) [BR:tdc00001] 09100 Metabolism  09108…

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Characterization of the microbiome and volatile compounds in anal gland secretions from domestic cats (Felis catus) using metagenomics and metabolomics

Albone, E. S. Mammalian semiochemistry. The investigation of chemical signals between mammals. 2–5 (1984). Wyatt, T. D. Pheromones and Animal Behaviour: Communication by Smell and Taste (Cambridge University Press, 2003). Book  Google Scholar  Doty, R. L. Odor-guided behavior in mammals. Experientia 42, 257–271 (1986). Article  CAS  PubMed  Google Scholar  Brennan,…

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siRNA, Anti-Human ADCY5, 2′-MOE (SIRGT03069WQ-2MOE)

Online Inquiry For Research Use Only. Do NOT use in humans or animals. For Research Use Only. Do NOT use in humans or animals. The product SIRGT03069WQ-2MOE is a type of small interfering RNA (siRNA) that targets ADCY5 gene and regulates the expression of gene. The siRNA interferes with the…

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Now Available! Compare NCBI RefSeq and UniProt Datasets

Do you need to compare and combine data based on NCBI RefSeq and UniProt datasets, and aren’t sure which proteins are comparable? For many years, NCBI Gene has provided information about the relationships between RefSeq and UniProt accessions courtesy of data imported from UniProt, but the tremendous growth of both…

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KEGG T01028: 704242

Entry 704242            CDS       T01028                                  Symbol CYP39A1 Name (RefSeq) 24-hydroxycholesterol 7-alpha-hydroxylase   KO K07439   24-hydroxycholesterol 7alpha-hydroxylase [EC:1.14.14.26] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc00120   Primary bile acid biosynthesis Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism  09103 Lipid metabolism   00120 Primary bile acid biosynthesis    704242 (CYP39A1) 09180 Brite Hierarchies  09181 Protein families: metabolism   00199 Cytochrome P450 [BR:mcc00199]    704242 (CYP39A1)Enzymes [BR:mcc01000] 1. Oxidoreductases  1.14  Acting on paired…

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UniProt: A0A8U0V2F9_MUSPF

ID A0A8U0V2F9_MUSPF Unreviewed; 413 AA. AC A0A8U0V2F9; DT 12-OCT-2022, integrated into UniProtKB/TrEMBL. DT 12-OCT-2022, sequence version 1. DT 03-MAY-2023, entry version 4. DE SubName: Full=Protein C-ets-1 isoform X5 {ECO:0000313|RefSeq:XP_044936298.1}; GN Name=ETS1 {ECO:0000313|RefSeq:XP_044936298.1}; OS Mustela putorius furo (European domestic ferret) (Mustela furo). OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC…

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siRNA, Anti-Human CAD (SIRGT00532WQ) – Creative Biolabs

Online Inquiry For Research Use Only. Do NOT use in humans or animals. For Research Use Only. Do NOT use in humans or animals. The product SIRGT00532WQ is a type of small interfering RNA (siRNA) that targets CAD gene and regulates the expression of gene. The siRNA interferes with the…

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KEGG T01028: 694719

Entry 694719            CDS       T01028                                  Symbol RPL23 Name (RefSeq) 60S ribosomal protein L23   KO K02894   large subunit ribosomal protein L23e Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc03010   Ribosome mcc05171   Coronavirus disease – COVID-19 Brite KEGG Orthology (KO) [BR:mcc00001] 09120 Genetic Information Processing  09122 Translation   03010 Ribosome    694719 (RPL23) 09160 Human Diseases  09172 Infectious disease: viral   05171 Coronavirus disease – COVID-19    694719…

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KEGG T08540: 104459063

Entry 104463828         CDS       T08540                                  Symbol ACOX3 Name (RefSeq) peroxisomal acyl-coenzyme A oxidase 3   KO K00232   acyl-CoA oxidase [EC:1.3.3.6] Organism pguu  Pterocles gutturalis (yellow-throated sandgrouse) Pathway pguu00071   Fatty acid degradation pguu00410   beta-Alanine metabolism pguu00592   alpha-Linolenic acid metabolism pguu00640   Propanoate metabolism pguu01040   Biosynthesis of unsaturated fatty acids pguu01100   Metabolic pathways pguu01200   Carbon metabolism pguu01212   Fatty…

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In VEP annotation, how is the codon field interpreted?

In VEP annotation, how is the codon field interpreted? 0 After annotating with VEP a VCF file, we obtain different fields. One of them is called Codons which represents the affected codon in the transcript of the gene. Below is a screenshot of Insertions from a sample: HGVSp_Short RefSeq Codons…

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KEGG T01028: 704366

Entry 704366            CDS       T01028                                  Symbol ZDHHC15 Name (RefSeq) palmitoyltransferase ZDHHC15   KO K20028   palmitoyltransferase ZDHHC2/15/20 [EC:2.3.1.225] Organism mcc  Macaca mulatta (rhesus monkey) Brite KEGG Orthology (KO) [BR:mcc00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   04131 Membrane trafficking [BR:mcc04131]    704366 (ZDHHC15)Enzymes [BR:mcc01000] 2. Transferases  2.3  Acyltransferases   2.3.1  Transferring groups other than aminoacyl groups    2.3.1.225  protein S-acyltransferase     704366 (ZDHHC15)Membrane trafficking [BR:mcc04131] SNARE  SNARE associated proteins   Palmitoyltransferases    704366 (ZDHHC15) BRITE hierarchy…

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KEGG T01028: 695442

Entry 695442            CDS       T01028                                  Symbol RPLP1 Name (RefSeq) 60S acidic ribosomal protein P1   KO K02942   large subunit ribosomal protein LP1 Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc03010   Ribosome mcc05171   Coronavirus disease – COVID-19 Brite KEGG Orthology (KO) [BR:mcc00001] 09120 Genetic Information Processing  09122 Translation   03010 Ribosome    695442 (RPLP1) 09160 Human Diseases  09172 Infectious disease: viral   05171 Coronavirus disease –…

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KEGG T01028: 717682

Entry 717682            CDS       T01028                                  Symbol SEPTIN2 Name (RefSeq) septin-2 isoform X1   KO K16942   septin 2 Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc05100   Bacterial invasion of epithelial cells Brite KEGG Orthology (KO) [BR:mcc00001] 09160 Human Diseases  09171 Infectious disease: bacterial   05100 Bacterial invasion of epithelial cells    717682 (SEPTIN2) 09180 Brite Hierarchies  09182 Protein families: genetic information processing   04131 Membrane trafficking…

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KEGG T01028: 699325

Entry 699325            CDS       T01028                                  Symbol OSBP Name (RefSeq) oxysterol-binding protein 1   KO K20456   oxysterol-binding protein 1 Organism mcc  Macaca mulatta (rhesus monkey) Brite KEGG Orthology (KO) [BR:mcc00001] 09180 Brite Hierarchies  09182 Protein families: genetic information processing   04131 Membrane trafficking [BR:mcc04131]    699325 (OSBP)Membrane trafficking [BR:mcc04131] Endoplasmic reticulum (ER) – Golgi transport  Others   Oxysterol-binding proteins    699325 (OSBP) BRITE hierarchy SSDB OrthologParalogGene clusterGFIT Motif…

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KEGG T04128: 106346836

Entry 111199314         CDS       T04128                                  Name (RefSeq) GDP-L-fucose synthase 1 isoform X2   KO K02377   GDP-L-fucose synthase [EC:1.1.1.271] Organism bna  Brassica napus (rape) Pathway bna00051   Fructose and mannose metabolism bna00520   Amino sugar and nucleotide sugar metabolism bna01100   Metabolic pathways bna01250   Biosynthesis of nucleotide sugars Brite KEGG Orthology (KO) [BR:bna00001] 09100 Metabolism  09101 Carbohydrate metabolism   00051 Fructose and mannose…

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Fibronectin (FN1) Human shRNA Plasmid Kit (Locus ID 2335)

Product Data Locus ID 2335 Synonyms CIG; ED-B; FINC; FN; FNZ; GFND; GFND2; LETS; MSF; SMDCF Vector pGFP-V-RS E. coli Selection Kanamycin Mammalian Cell Selection Puromycin Format Retroviral plasmids Kit Components FN1 – Human, 4 unique 29mer shRNA constructs in retroviral GFP vector(Gene ID = 2335). 5µg purified plasmid DNA…

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KEGG T01028: 706713

Entry 706713            CDS       T01028                                  Symbol HNMT Name (RefSeq) histamine N-methyltransferase   KO K00546   histamine N-methyltransferase [EC:2.1.1.8] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc00340   Histidine metabolism mcc01100   Metabolic pathways Brite KEGG Orthology (KO) [BR:mcc00001] 09100 Metabolism  09105 Amino acid metabolism   00340 Histidine metabolism    706713 (HNMT) 09180 Brite Hierarchies  09183 Protein families: signaling and cellular processes   04147 Exosome [BR:mcc04147]    706713 (HNMT)Enzymes [BR:mcc01000] 2. Transferases  2.1  Transferring…

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KEGG T01028: 694392

Entry 694392            CDS       T01028                                  Symbol WEE2 Name (RefSeq) wee1-like protein kinase 2   KO K06632   wee1-like protein kinase [EC:2.7.11.1] Organism mcc  Macaca mulatta (rhesus monkey) Pathway mcc04110   Cell cycle mcc05170   Human immunodeficiency virus 1 infection Brite KEGG Orthology (KO) [BR:mcc00001] 09140 Cellular Processes  09143 Cell growth and death   04110 Cell cycle    694392 (WEE2) 09160 Human Diseases  09172 Infectious disease: viral   05170…

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KEGG T02386: 101070831

Entry 101070831         CDS       T02386                                  Symbol cldn3d Name (RefSeq) claudin-4   KO K06087   claudin Organism tru  Takifugu rubripes (torafugu) Pathway tru04514   Cell adhesion molecules tru04530   Tight junction Brite KEGG Orthology (KO) [BR:tru00001] 09130 Environmental Information Processing  09133 Signaling molecules and interaction   04514 Cell adhesion molecules    101070831 (cldn3d) 09140 Cellular Processes  09144 Cellular community – eukaryotes   04530 Tight junction    101070831 (cldn3d) 09180 Brite Hierarchies  09183 Protein…

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