SequencesExonsGenesMRNAGenomicExonSequenceGenomePrimersINTRONSUpstreamTransgeneHuman transcriptomeTranscriptomeTATAPromoterProteinSNPsClustersEukaryotesMachado-JosephRNAsProteinsTissuesClinicalYeastRegulatory regionsVariantsGenomesSitesResiduesBiochemistryCDNAH3K9me3DistinctInsertionNovoFeaturesJournal
Sequences19
- The transcript from this gene contains four Alu sequences flanked by direct repeats in the 3' untranslated region. (wikipedia.org)
- TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. (lookformedical.com)
- The region of DNA which borders the 3' end of a transcription unit and where a variety of regulatory sequences are located. (lookformedical.com)
- BLAST-able datasets include Cucumis sativus genomic DNA, splice-aligned transcripts and proteins, gene models, and other aligned sequences. (plantgdb.org)
- The genes are flanked on either side by highly conserved transcription start and stop signals and have intergenic sequences varying in length from 9 to 42 nt. (umd.edu)
- The availability of multiple PAS in the same 3' regulatory region enables the inclusion or exclusion of 3' untranslated region (3'UTR) sequences, resulting in transcripts that may differ in particularities involving post-transcriptional processes such as stability, transport and translation ( Mayr, 2016 ), and even protein localization ( Berkovits and Mayr, 2015 ). (frontiersin.org)
- The non-coding regions downstream of coding sequences (CDS) is usually termed terminators. (frontiersin.org)
- In the 5'-flanking region of exon 2, several consensus sequences were found, such as a TATA-like sequence and negative regulatory element box-1, -2 and -3. (elsevierpure.com)
- these sequences were referred to as telomeres [ 3-5 ]. (actanaturae.ru)
- In a structural gene, the transcribed region contains the coding sequences that dictate the amino acid sequence of a polypeptide chain. (basicmedicalkey.com)
- Exons, which contain the coding sequences for the proteins, are separated in pre-mRNA by introns , regions that have no coding function. (basicmedicalkey.com)
- Strikingly, small RNAs of both polarities are generated from the entire transgene and flanking genomic sequences â€" not only from the transposon fragment. (refine.bio)
- In two of the transgenes studied, the cDNA of (hPC) was inserted at the translational start site of a 7.8 kbp mouse WAP genomic DNA Eco RI fragment containing 2.6 kbp of 5' flanking, 3.9 kbp WAP coding (exons and introns), and 1.3 kbp 3' untranslated region (UTR) and flanking sequences (designated WAPPC1 and WAPPC2). (vt.edu)
- A third transgene consisted of only the 2.6 kbp of WAP 5' UTR and flanking DNA, 1.4 kbp hPC cDNA, and 1.3 kbp of 3' WAP UTR and flanking DNA with no linker sequences (designated WAPPC3). (vt.edu)
- Flanking regions contain conserved sequences essential for gene expression. (mhmedical.com)
- Primary transcript is a large mRNA precursor, with both intron and exon sequences, which is extensively processed in the nucleus to yield the final mRNA. (mhmedical.com)
- This machinery recognizes pre-mRNA sequences at several motifs - the 5′ and 3′ splice sites, the branch point, and polypyrimidine tracts - positioned at exon-intron boundaries [ 4 ]. (biomedcentral.com)
- The extragenic sequences at the extreme 3′ (leader) and 5′ (trailer) ends of the genomes are conserved. (ictv.global)
- Those sites contain the highly conserved pentamer 3′-UAAUU-5′ Most genes are separated by non-conserved intergenic sequences, but some genes overlap. (ictv.global)
Exons4
- Search for any CsGDBgene or aligned sequence by ID or keyword , and download complete sequence or flanking 5' or 3' regions, exons, or introns (FASTA format). (plantgdb.org)
- This test provides full coverage of all coding exons of the CLDN16 gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. (preventiongenetics.com)
- Coding exons and flanking regions were screened by polymerase chain reaction (PCR) amplification and sequenced. (uwc.ac.za)
- The coding exons for CRYAA showed two sequence variants: S134W and K166N in exon 3. (uwc.ac.za)
Genes6
- 2017). Promoter Variation and Expression Levels of Inflammatory Genes IL1A, IL1B, IL6 and TNF in Blood of Spinocerebellar Ataxia Type 3 (SCA3) Patients . (up.pt)
- Transposition of this element into coding and regulatory regions of genes is responsible for many heritable diseases. (lookformedical.com)
- The ~1.5 Mb candidate region was shown to contain five protein-coding genes. (biomedcentral.com)
- We also identified several genes that do not appear to be protein coding, and generated 17 kb of novel transcript sequence data from re-sequencing 97 EST clones. (biomedcentral.com)
- The candidate interval was shown to exhibit an extraordinary level of alternate splicing - 19 transcripts were identified for the 5 protein coding genes, but it appears that a significant portion (14/19) of these alternate transcripts did not have an open reading frame, hence their functional role is questionable. (biomedcentral.com)
- Genes are flanked by conserved transcriptional initiation and termination (polyadenylation) sites. (ictv.global)
MRNA9
- Using in planta nucleotide-resolution mRNA structurome probing, we discovered that this stress-induced switch in translation is mediated by highly structured regions detected downstream of uAUGs in TE-up transcripts. (biorxiv.org)
- The preinitiation complex then scans along the 5' leader sequence of the mRNA to initiate translation at a start codon 1 - 3 . (biorxiv.org)
- The 3' regulatory regions have a great diversity of cis -regulatory elements directly involved in polyadenylation, stability, transport and mRNA translation, essential to achieve the desired levels of gene expression. (frontiersin.org)
- Polyadenylation is essential for the stability of the transcript, preventing the mRNA from being the target of posttranscriptional gene silencing (PTGS) via RNA-dependent RNA polymerase 6 (RDR6) in plants ( Luo and Chen, 2007 ). (frontiersin.org)
- Polyadenylation of eukaryotic transcripts is usually restricted to mRNA, providing transcripts with stability from degradation by nucleases. (syr.edu)
- S1 nuclease mapping was used to identify three major mRNA transcripts with different 5' termini. (unipr.it)
- In bacteria , a single RNA polymerase produces the primary transcript precursors for all three major classes of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). (basicmedicalkey.com)
- The precursors of mRNA (called pre-mRNA ) have a guanosine "cap" added at the 5′-end and a poly(A) "tail" at the 3′-end. (basicmedicalkey.com)
- Production of α 2 mRNA exceeds that of α 1 , by factor of 1.5 to 3. (mhmedical.com)
Genomic6
- For any specified genomic region , download genomic DNA (FASTA format), all aligned/computed transcripts or proteins (FASTA format), or all genome annotations (GenBank, GFF3 or EMBL format). (plantgdb.org)
- Sequence analysis tools accessed from the Genome Context View menu use the current genomic region as input. (plantgdb.org)
- Spliced alignment of user-specified transcript datasets to genomic DNA from any region in CsGDB. (plantgdb.org)
- We find 116 887 and 137 557 nucleosome-depleted regions (NDRs) in human and mouse FGCs, covering a large set of germline-specific and highly dynamic regulatory genomic elements, such as enhancers. (nature.com)
- However, it has been proven that more than 62% of genomic DNA serves as a template for transcription, which indicates that there are abundant non-coding RNAs (ncRNAs) in human transcriptome [ 2 , 3 ]. (ijbs.com)
- Genomic RNA is not polyadenylated at the 3′ end and there is no evidence for a 5′-terminal cap structure or a covalently-linked protein. (ictv.global)
Exon3
- The 5'-flanking region of exon 1 had features characteristic of a housekeeping gene: it was GC-rich, lacked TATA boxes and CAAT boxes in the standard positions, and contained potential binding sites for the transcription factor SP1. (elsevierpure.com)
- Analysis of PP2Cβ transcripts by reverse transcriptase-PCR showed that exon-1 transcripts were expressed ubiquitously in all of the tissues examined, whereas exon-2 transcripts were predominantly expressed in the testis, intestine and liver. (elsevierpure.com)
- Euchromatic breakpoint of In(2)A4 inversion was localized at 105 bp region (chr2L:21182214-21182318) of the second exon of the Mcm10 gene, the heterochromatic breakpoint is located at the block of dodecasatellite in 2L pericentromeric heterochromatin. (refine.bio)
Sequence7
- 2012). Sequence analysis of 5′ regulatory regions of the Machado-Joseph disease gene (ATXN3) . (up.pt)
- [ 14 ] A region known as the reactive center loop (RCL) protrudes above the core of the serpin molecule and has a sequence of amino acids that is complementary to binding sites in the active sites of the target proteases. (medscape.com)
- Analysis using multiple sequence alignments revealed four potential polyadenylation sites including three internal regions and the 3′ end of the rRNA. (syr.edu)
- The nucleotide sequence of the yeast gene TRP5 and its 5' and 3' flanking regions was determined. (unipr.it)
- A portion of the connecting region of yeast tryptophan synthase exhibits nucleotide sequence similarity to the 3' terminus of E. coli trpC and the trpC-trpB intercistronic region. (unipr.it)
- Ap-V1 differs from a human strain ( Ap-ha ) by a 2-bp substitution in the 16S rRNA sequence ( 3 ) and appears to be restricted to ruminant species ( 2 , 4 ). (cdc.gov)
- more 2021-3-26 · The National Library of Medicine (NLM), on the NIH campus in Bethesda, Maryland, is the world's largest biomedical library and the developer of electronic information services that delivers data to millions of scientists, health professionals … Efficient cleavage requires at least two copies of the NgoMIV recognition sequence. (netlify.app)
Genome5
- The length of the human genome is about 3 billion base pairs. (lookformedical.com)
- The genome contains a 55 nt leader region at 3' end. (umd.edu)
- Pospiviroidae's type species, potato spindle tuber viroid (PSTVd), has a rod-like secondary structure ∼360-nt-long genome that can be functionally and structurally divided into five domains: (i) terminal left, (ii) pathogenicity (P), (iii) central (C) containing the conserved central region, (iv) variable (v) and (5) terminal right (TR) (5). (degruyter.com)
- A 5' flanking region of TRP5 was shown by DNA/DNA hybridization to be present in multiple copies in the yeast genome. (unipr.it)
- Both crRNA-tracrRNA duplexes and sgRNAs can be used to target SpCas9 for multiplexed genome editing in eukaryotic cells 1 , 3 . (cdc.gov)
Primers3
- Further analysis using a polyadenylation test, re-sequencing, and gene-specific PCR using primers flanking the presumed poly (A) sites confirmed the presence of polyadenylated rRNA in this parasite. (syr.edu)
- We used oligonucleotide primers AB1207 (5′-GGGAGTGCTCTGGTTAGATTTAGG-3′) and AB1221 (5′-ATAGAACAAGAGCAGGGAGAAGAC-3′) or AB1207 and AB1058 (5′-GAACCATCCCCTTAAAATACTTTC-3′) to amplify the msp2/p44 gene, the upstream gene p44ESup1, and the intergenic region between them. (cdc.gov)
- T he MnSOD, CAT, and GAPDH transcripts wer e amplified using the following primers ( Bostwick et al. (netlify.app)
INTRONS2
- The parts of a transcript of a split GENE remaining after the INTRONS are removed. (lookformedical.com)
- Thus, results from the combination in WAPPC3 of intact 5' and 3' WAP UTR with the cDNA of hPC suggests that introns are not necessary to enable high level expression in the mammary gland when using WAP regulatory elements. (vt.edu)
Upstream3
- To identify common features shared by transcripts with stress-upregulated translation efficiency (TE-up), we first performed high-resolution ribosome-sequencing in Arabidopsis during pattern-triggered immunity and found that TE-up transcripts are enriched with upstream open reading frames (uORFs). (biorxiv.org)
- The expression site encoding MSP2/P44 is composed of the MSP2/P44 coding region itself, including a central hypervariable region, an intergenic region containing binding sites for a regulatory transcription factor ApxR, and an upstream gene known either as p44ESup1 or omp-1n ( 9 , 10 ). (cdc.gov)
- Further analyses revealed that proband's duplicated β-globin gene cluster (∼650 kb) encompassing HBB A does not include the immediate upstream locus control region (LCR) or 3′ DNase I hypersensitivity (HS) element. (kcl.ac.uk)
Transgene1
- We show that transgene-derived hsp70 piRNAs stimulate in trans cleavage of cognate endogenous transcripts with subsequent processing of the non-homologous parts of these transcripts into piRNAs. (refine.bio)
Human transcriptome1
- Sequential assembly of the human spliceosome on RNA transcripts regulates splicing across the human transcriptome. (biomedcentral.com)
Transcriptome1
- Through APA, a single gene containing multiple PAS can generate a considerable number of transcript isoforms, thereby producing a highly diversified transcriptome ( Tian and Manley, 2013 ). (frontiersin.org)
TATA1
- Importantly, the CD5 5'-flanking region contains TATA and CAAT boxes, and recognition sites for Ikaros in the B cells, but not in T cells. (biomedcentral.com)
Promoter3
- These elements may be found in both promoter and enhancer regions. (lookformedical.com)
- We further showed that under oxidative stress conditions, H3K4me3 and H3K9me3 spread to the promoter region of Jheh1 gene. (nature.com)
- A gene also includes regions of DNA that regulate production of the encoded product, such as a promoter region. (basicmedicalkey.com)
Protein3
- To survive stress, eukaryotes selectively translate stress-related transcripts while inhibiting growth-associated protein production. (biorxiv.org)
- Relative specific transcript and protein levels in the transgenic animals studied suggest that the rates of translation initiation may be different for the mRNAs of each of the transgenes studied. (vt.edu)
- Non-protein coding transcript. (h-invitational.jp)
SNPs1
- 2012). Transcript Diversity of Machado-Joseph Disease Gene (ATXN3) Is Not Directly Determined by SNPs in Exonic or Flanking Intronic Regions . (up.pt)
Clusters2
- piRNAs are processed from the transcripts encoded by specialized heterochromatic clusters enriched in damaged copies of transposons. (refine.bio)
- We show that such transgenes, being inserted in unique euchromatic regions which normally do not produce small RNAs, become de novo bidirectional piRNA clusters that silence I-element activity in the germline. (refine.bio)
Eukaryotes1
- Recently polyadenylated transcripts have also been discovered in rRNA in some eukaryotes including humans and yeast. (syr.edu)
Machado-Joseph1
- 2010). Increased transcript diversity: Novel splicing variants of Machado-Joseph Disease gene (ATXN3) . (up.pt)
RNAs2
- The primary transcripts are modified and trimmed to produce the mature RNAs. (basicmedicalkey.com)
- Unlike linear RNAs, circRNAs form covalent-closed continuous loops without 5' to 3' polarities and poly (A) tails. (ijbs.com)
Proteins2
- The serpin family of proteins have a highly conserved molecular structure, with 3 beta-sheets and 9 alpha-helices. (medscape.com)
- In addition, after transcription, a wide array of RNA-binding proteins interacts with cis -acting elements located mainly in the 3' untranslated region, determining the fate of mRNAs in eukaryotic cells. (frontiersin.org)
Tissues1
- The minuscule amount of transcripts from microdissected tissues, which can be single cells, needs to be amplified to be detected by microarray or RNA-seq. (github.io)
Clinical1
- However, the disease was named after Jean-Alfred Fournier, a Parisian venereologist, on the basis of a transcript from an 1883 clinical lecture in which Fournier presented a case of perineal gangrene in an otherwise healthy young man, adding this to a compiled series of 4 additional cases. (medscape.com)
Yeast1
- The two segments are joined by a connecting region of 28 residues in the yeast enzyme which is not homologous to either the alpha or beta chains of the bacterial enzyme. (unipr.it)
Regulatory regions2
- Although a small number of 3' regulatory regions have been identified and validated so far, many studies have shown that plant 3' regulatory regions have a higher potential to regulate gene expression in plants compared to widely used 3' regulatory regions, such as NOS and OCS from Agrobacterium tumefaciens and 35S from cauliflower mosaic virus. (frontiersin.org)
- In this review, we discuss the role of 3' regulatory regions in gene expression, and the superior potential that plant 3' regulatory regions have compared to NOS, OCS and 35S 3' regulatory regions. (frontiersin.org)
Variants1
- 2012). Glucocerebrosidase gene variants in parkinsonian patients with Machado Joseph/spinocerebellar ataxia 3 . (up.pt)
Genomes2
- The limitations of current methods are particularly evident in the vast noncoding regions of eukaryotic genomes, which, despite important recent progress 3 - 6 , remain poorly annotated and understood. (biorxiv.org)
- Filovirus genomes are characterized by the gene order: 3′-NP-VP35-VP40-GP-VP30-VP24-L-5′ (Figure 2). (ictv.global)
Sites3
- In this patient, the observed transcription from the duplicated, distally displaced HBB A cluster demonstrates that the loss of LCR and flanking 3′HS sites do not lead to complete silencing of HBB transcription. (kcl.ac.uk)
- One critical step involves recruitment of the pre-assembled U4/U6.U5 tri-snRNP to Complex A, which engages 5′ and 3′ splice sites, to form the pre-catalytic Complex B. Complex B then undergoes profound structural and conformational changes that lead to catalytic activation and conversion to Complex B act , which initiates catalysis and nucleates the formation of Complex C, which completes the splicing reaction [ 3 , 4 ]. (biomedcentral.com)
- We generated a set of sgRNAs targeting multiple sites within the human EMX1 and PVALB loci with different tracrRNA 3′ truncations ( Fig. 1a ). (cdc.gov)
Residues1
- Plasma antithrombin is comprised of 432 amino acids, 6 of which are cysteine residues that form 3 intramolecular disulfide bonds. (medscape.com)
Biochemistry2
- European Journal of Biochemistry , 263 (3), 736-745. (elsevierpure.com)
- Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics , 4 (3), 179-186. (syr.edu)
CDNA1
- Using the RACE technique, the 5' region of CD5 cDNA was amplified through an adaptor-ligated 5' primer coupled with a 3' end-specific primer. (biomedcentral.com)
H3K9me31
- Chromatin immunoprecipitation analysis shows that in ovaries the trimethylated histone 3 lysine 9 (H3K9me3) mark associates with transgenes producing piRNAs. (refine.bio)
Distinct1
- Subsequent analysis by transient transfection assay with a reporter gene showed that these regions act as distinct promoters. (elsevierpure.com)
Insertion1
- Analysis of mRNAs transcribed from the P gene showed that 35% of the transcripts were edited by insertion of one non-templated G residue at an editing site leading to production of V mRNAs. (umd.edu)
Novo1
- At least in plants, DNA regions that become de novo methylated can be defined by homologous RNA molecules in a process termed RNA-directed DNA methylation (RdDM). (degruyter.com)
Features1
- Are there common features in transcripts that are responsible for stress-induced translation? (biorxiv.org)
Journal1
- Journal of Molecular Neuroscience, 49 (3), 539 - 543. (up.pt)