Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Data of 10 SSR markers for genomes of homo sapiens and monkeys.

ABSTRACT: In this data, we present 10 Simple Sequence Repeat(SSR) markers TAGA, TCAT, GAAT, AGAT, AGAA, GATA, TATC, CTTT, TCTG and TCTA which are extracted from the genomes of homo sapiens and monkeys using string matching mechanism [1]. All loci showed 4 Base Pair(bp) in allele size, indicating that there are some polymorphisms between individuals correlating to the number of SSR repeats that maybe useful for the detection of similarity among the genotypes. Collectively, these data show that the SSR extraction is a valuable method to illustrate genetic variation of genomes.

SUBMITTER: Reddy KKVVVS

PROVIDER: S-EPMC5407499 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Data of 10 SSR markers for genomes of homo sapiens and monkeys.

Reddy K K V V V S KKVVVS Raju S Viswanadha SV Someswara Rao Chinta C

Data in brief 20170413

In this data, we present 10 Simple Sequence Repeat(SSR) markers TAGA, TCAT, GAAT, AGAT, AGAA, GATA, TATC, CTTT, TCTG and TCTA which are extracted from the genomes of homo sapiens and monkeys using string matching mechanism [1]. All loci showed 4 Base Pair(bp) in allele size, indicating that there are some polymorphisms between individuals correlating to the number of SSR repeats that maybe useful for the detection of similarity among the genotypes. Collectively, these data show that the SSR extr ...[more]

PMID: 28480320

Similar Datasets

Structure of filamin A immunoglobulin-like repeat 10 from Homo sapiens.

Project description:Filamin A (FlnA) plays a critical role in cytoskeletal organization, cell motility and cellular signaling. FlnA utilizes different binding sites on a series of 24 immunoglobulin-like domains (Ig repeats) to interact with diverse cytosolic proteins and with cytoplasmic portions of membrane proteins. Mutations in a specific domain, Ig10 (FlnA-Ig10), are correlated with two severe forms of the otopalatodigital syndrome spectrum disorders Melnick-Needles syndrome and frontometaphyseal dysplasia. The crystal structure of FlnA-Ig10 determined at 2.44?Å resolution provides insight into the perturbations caused by these mutations.

| S-EPMC3151117 | biostudies-literature

How tufted capuchin monkeys (Sapajus spp.) and humans (Homo sapiens) handle a jointed tool.

Project description:The embodied theory of tooling predicts that when using a grasped object as a tool, individuals accommodate their actions to manage the altered degrees of freedom in the body-plus-object system. We tested predictions from this theory by studying how 3 tufted capuchin monkeys (Sapajus spp.) and 6 humans (Homo sapiens) used a hoe to retrieve a token. The hoe's handle was rigid, had 2 segments with 1 planar joint, or had 3 segments with 2 (orthogonal) planar joints. When jointed, rotating the handle could render it rigid. The monkeys used more actions to retrieve the token when the handle had 1 joint than when it had no joints or 2 joints. They did not use exploratory actions frequently nor in a directed manner in any condition. Although they sometimes rotated the handle of the hoe, they did not make it rigid. In a follow-up study, we explored whether humans would rotate the handle to use a 2-jointed hoe in a conventional manner, as predicted both by the embodied theory and theories of functional fixedness in humans. Two people rotated the handle to use the hoe conventionally, but 4 people did not; instead, they used the hoe as it was presented, as did the monkeys. These results confirm some predictions but also highlight shortcomings of the embodied theory with respect to specifying the consequences of adding multiple degrees of freedom. The study of species' perceptual sensitivity to jointed object's inertial properties could help to refine the embodied theory of tooling. (PsycInfo Database Record (c) 2021 APA, all rights reserved).

| S-EPMC8632068 | biostudies-literature

Launch! Self-agency as a discriminative cue for humans (Homo sapiens) and monkeys (Macaca Mulatta).

Project description:Self-agency is a crucial aspect of self-awareness. It is underresearched given the phenomenon's subjectivity and difficulty of study. It is particularly underresearched comparatively, given that animals cannot receive agency instructions or make agency declarations. Accordingly, we developed a distinctively new self-agency paradigm. Humans and rhesus macaques learned event categories differentiated by whether the participant's volitional response controlled a screen launch. They learned by trial and error after minimal instructions with no agency orientation (humans) or no instructions (monkeys). After learning, humans' verbalized category descriptions were coded for self-agency attributions. Across three experiments, humans' agency attributions qualitatively improved discrimination performance-participants not invoking self-agency rarely exceeded chance performance. It also produced a diagnostic latency profile: classification accuracy depended heavily on the temporal relationship between the button-press and the launch, but only for those invoking agency. In our last experiment, monkeys performed the launch task. Their performance and latency profiles mirrored that of humans. Thus, self-agency can be self-discovered as a frame organizing discrimination. And it may be used as a discrimination cue by some nonhuman animals as well. (PsycInfo Database Record (c) 2021 APA, all rights reserved).

| S-EPMC8277898 | biostudies-literature

Khoe-San Genomes Reveal Unique Variation and Confirm the Deepest Population Divergence in Homo sapiens.

Project description:The southern African indigenous Khoe-San populations harbor the most divergent lineages of all living peoples. Exploring their genomes is key to understanding deep human history. We sequenced 25 full genomes from five Khoe-San populations, revealing many novel variants, that 25% of variants are unique to the Khoe-San, and that the Khoe-San group harbors the greatest level of diversity across the globe. In line with previous studies, we found several gene regions with extreme values in genome-wide scans for selection, potentially caused by natural selection in the lineage leading to Homo sapiens and more recent in time. These gene regions included immunity-, sperm-, brain-, diet-, and muscle-related genes. When accounting for recent admixture, all Khoe-San groups display genetic diversity approaching the levels in other African groups and a reduction in effective population size starting around 100,000 years ago. Hence, all human groups show a reduction in effective population size commencing around the time of the Out-of-Africa migrations, which coincides with changes in the paleoclimate records, changes that potentially impacted all humans at the time.

| S-EPMC7530619 | biostudies-literature

Crystal structure of Homo sapiens kynureninase.

Project description:Kynureninase is a member of a large family of catalytically diverse but structurally homologous pyridoxal 5'-phosphate (PLP) dependent enzymes known as the aspartate aminotransferase superfamily or alpha-family. The Homo sapiens and other eukaryotic constitutive kynureninases preferentially catalyze the hydrolytic cleavage of 3-hydroxy-l-kynurenine to produce 3-hydroxyanthranilate and l-alanine, while l-kynurenine is the substrate of many prokaryotic inducible kynureninases. The human enzyme was cloned with an N-terminal hexahistidine tag, expressed, and purified from a bacterial expression system using Ni metal ion affinity chromatography. Kinetic characterization of the recombinant enzyme reveals classic Michaelis-Menten behavior, with a Km of 28.3 +/- 1.9 microM and a specific activity of 1.75 micromol min-1 mg-1 for 3-hydroxy-dl-kynurenine. Crystals of recombinant kynureninase that diffracted to 2.0 A were obtained, and the atomic structure of the PLP-bound holoenzyme was determined by molecular replacement using the Pseudomonas fluorescens kynureninase structure (PDB entry 1qz9) as the phasing model. A structural superposition with the P. fluorescens kynureninase revealed that these two structures resemble the "open" and "closed" conformations of aspartate aminotransferase. The comparison illustrates the dynamic nature of these proteins' small domains and reveals a role for Arg-434 similar to its role in other AAT alpha-family members. Docking of 3-hydroxy-l-kynurenine into the human kynureninase active site suggests that Asn-333 and His-102 are involved in substrate binding and molecular discrimination between inducible and constitutive kynureninase substrates.

| S-EPMC2531291 | biostudies-literature

Homo sapiens whole blood.

Project description:RNA extracted at 240min. Samples are rRNA depleted. Expression measurement of Homo sapiens genes.

2019-07-31 | GSE114179 | GEO

Method for identification of 10 SSR markers from monkey genomes and its statistical inference with One & Two-way ANOVA.

Project description:DNA tracts that include simple sequence repeats (SSRs), sometimes known as genetic "stutters), are composed of a few to many tandem repetitions of a short base-pair motif. These sequences frequently mutate, changing the amount of repetitions. SSRs are frequently found in promoters, untranslated regions, and even coding sequences, therefore these alterations can significantly affect practically every aspect of gene activity. SSR alleles can also contribute to normal diversity in brain and behavioural features. Mutational expansion of certain triplet repeats is the cause of a number of inherited neurodegenerative diseases. Due to its importance in genetic research, in this paper we explored Ten SSR markers TAGA, TCAT, GAAT, AGAT, AGAA, GATA, TATC, CTTT, TCTG and TCTA that are identified from the genomes of Eleven distinct monkeys: A.Nancymaae, C.C.Imitator, C.Atys, M.Leucophaeus, P.Paniscus, R.Bieti, R.Roxellana, S.Boliviensis, T.Syrichta, C.A.Palliatus and M.Nemestrina using pattern matching mechanism. We identified 4bp SSR from eleven monkey dataset's Unchr chromosome mainly in this paper. The proposed approach finds the exact place/location of the SSR's and number of times that it appears in the given genome sequence. The identified patterns are analyzed with One-way and Two-way ANOVA that gives better analysis which is useful for genomic studies. Also, this 4bp Ten SSR markers data is a valuable to illustrate genetic variation of genomic study.•The great specificity of data sets produced from monkey genomes with pattern matching has been demonstrated.•These findings show that SSR identification could be a useful tool for determining genome similarity and comparability.•Researchers can use the raw sequencing data to conduct additional bioinformatics analysis.

| S-EPMC9474309 | biostudies-literature

The evolution of Homo sapiens denisova and Homo sapiens neanderthalensis miRNA targeting genes in the prenatal and postnatal brain.

Project description:As the evolution of miRNA genes has been found to be one of the important factors in formation of the modern type of man, we performed a comparative analysis of the evolution of miRNA genes in two archaic hominines, Homo sapiens neanderthalensis and Homo sapiens denisova, and elucidated the expression of their target mRNAs in bain.A comparative analysis of the genomes of primates, including species in the genus Homo, identified a group of miRNA genes having fixed substitutions with important implications for the evolution of Homo sapiens neanderthalensis and Homo sapiens denisova. The mRNAs targeted by miRNAs with mutations specific for Homo sapiens denisova exhibited enhanced expression during postnatal brain development in modern humans. By contrast, the expression of mRNAs targeted by miRNAs bearing variations specific for Homo sapiens neanderthalensis was shown to be enhanced in prenatal brain development.Our results highlight the importance of changes in miRNA gene sequences in the course of Homo sapiens denisova and Homo sapiens neanderthalensis evolution. The genetic alterations of miRNAs regulating the spatiotemporal expression of multiple genes in the prenatal and postnatal brain may contribute to the progressive evolution of brain function, which is consistent with the observations of fine technical and typological properties of tools and decorative items reported from archaeological Denisovan sites. The data also suggest that differential spatial-temporal regulation of gene products promoted by the subspecies-specific mutations in the miRNA genes might have occurred in the brains of Homo sapiens denisova and Homo sapiens neanderthalensis, potentially contributing to the cultural differences between these two archaic hominines.

| S-EPMC4686780 | biostudies-literature

Selection of Phototransduction Genes in Homo sapiens.

Project description:PurposeWe investigated the evidence of recent positive selection in the human phototransduction system at single nucleotide polymorphism (SNP) and gene level.MethodsSNP genotyping data from the International HapMap Project for European, Eastern Asian, and African populations was used to discover differences in haplotype length and allele frequency between these populations. Numeric selection metrics were computed for each SNP and aggregated into gene-level metrics to measure evidence of recent positive selection. The level of recent positive selection in phototransduction genes was evaluated and compared to a set of genes shown previously to be under recent selection, and a set of highly conserved genes as positive and negative controls, respectively.ResultsSix of 20 phototransduction genes evaluated had gene-level selection metrics above the 90th percentile: RGS9, GNB1, RHO, PDE6G, GNAT1, and SLC24A1. The selection signal across these genes was found to be of similar magnitude to the positive control genes and much greater than the negative control genes.ConclusionsThere is evidence for selective pressure in the genes involved in retinal phototransduction, and traces of this selective pressure can be demonstrated using SNP-level and gene-level metrics of allelic variation. We hypothesize that the selective pressure on these genes was related to their role in low light vision and retinal adaptation to ambient light changes. Uncovering the underlying genetics of evolutionary adaptations in phototransduction not only allows greater understanding of vision and visual diseases, but also the development of patient-specific diagnostic and intervention strategies.

| S-EPMC3743458 | biostudies-literature

Do you see what I see? A comparative investigation of the Delboeuf illusion in humans (Homo sapiens), rhesus monkeys (Macaca mulatta), and capuchin monkeys (Cebus apella).

Project description:Studying visual illusions is critical to understanding typical visual perception. We investigated whether rhesus monkeys (Macaca mulatta) and capuchin monkeys (Cebus apella) perceived the Delboeuf illusion in a similar manner as human adults (Homo sapiens). To test this, in Experiment 1, we presented monkeys and humans with a relative discrimination task that required subjects to choose the larger of 2 central dots that were sometimes encircled by concentric rings. As predicted, humans demonstrated evidence of the Delboeuf illusion, overestimating central dots when small rings surrounded them and underestimating the size of central dots when large rings surrounded them. However, monkeys did not show evidence of the illusion. To rule out an alternate explanation, in Experiment 2, we presented all species with an absolute classification task that required them to classify a central dot as "small" or "large." We presented a range of ring sizes to determine whether the Delboeuf illusion would occur for any dot-to-ring ratios. Here, we found evidence of the Delboeuf illusion in all 3 species. Humans and monkeys underestimated central dot size to a progressively greater degree with progressively larger rings. The Delboeuf illusion now has been extended to include capuchin monkeys and rhesus monkeys, and through such comparative investigations we can better evaluate hypotheses regarding illusion perception among nonhuman animals.

| S-EPMC4594174 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data