SSRD: Simple Sequence Repeats Database of the Human Genome

Simple sequence repeats are predominantly found in most organisms. They play a major role in studies of genetic diversity, and are useful as diagnostic markers for many diseases. The simple sequence repeats database (SSRD) for the human genome was created for easy access to such repeats, for analysis, and to be used to understand their biological significance. The data includes the abundance and distribution of SSRs in the coding and non-coding regions of the genome, as well as their association with the UTRs of genes. The exact locations of repeats with respect to genomic regions (such as UTRs, exons, introns or intergenic regions) and their association with STS markers are also highlighted. The resource will facilitate repeat sequence analysis in the human genome and the understanding of the functional and evolutionary significance of simple sequence repeats. SSRD is available through two websites, http://www.ccmb.res.in/ssr and http://www.ingenovis.com/ssr.

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A comprehensive microsatellite landscape of human Y-DNA at kilobase resolution

BMC Genomics ◽

10.1186/s12864-021-07389-5 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Douyue Li ◽

Saichao Pan ◽

Hongxi Zhang ◽

Yongzhuo Fu ◽

Zhuli Peng ◽

...

Keyword(s):

Simple Sequence Repeats ◽

Biological Significance ◽

Differential Method ◽

High Density ◽

The Other ◽

Distribution Law ◽

Base Pairs ◽

Density Peaks ◽

Intergenic Regions ◽

Simple Sequence

Abstract Background Though interest in human simple sequence repeats (SSRs) is increasing, little is known about the exact distributional features of numerous SSRs in human Y-DNA at chromosomal level. Herein, totally 540 maps were established, which could clearly display SSR landscape in every bin of 1 k base pairs (Kbp) along the sequenced part of human reference Y-DNA (NC_000024.10), by our developed differential method for improving the existing method to reveal SSR distributional characteristics in large genomic sequences. Results The maps show that SSRs accumulate significantly with forming density peaks in at least 2040 bins of 1 Kbp, which involve different coding, noncoding and intergenic regions of the Y-DNA, and 10 especially high density peaks were reported to associate with biological significances, suggesting that the other hundreds of especially high density peaks might also be biologically significant and worth further analyzing. In contrast, the maps also show that SSRs are extremely sparse in at least 207 bins of 1 Kbp, including many noncoding and intergenic regions of the Y-DNA, which is inconsistent with the widely accepted view that SSRs are mostly rich in these regions, and these sparse distributions are possibly due to powerfully regional selection. Additionally, many regions harbor SSR clusters with same or similar motif in the Y-DNA. Conclusions These 540 maps may provide the important information of clearly position-related SSR distributional features along the human reference Y-DNA for better understanding the genome structures of the Y-DNA. This study may contribute to further exploring the biological significance and distribution law of the huge numbers of SSRs in human Y-DNA.

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Distribution patterns and variation analysis of simple sequence repeats in different genomic regions of bovid genomes

Scientific Reports ◽

10.1038/s41598-018-32286-5 ◽

2018 ◽

Vol 8 (1) ◽

Cited By ~ 9

Author(s):

Wen-Hua Qi ◽

Xue-Mei Jiang ◽

Chao-Chao Yan ◽

Wan-Qing Zhang ◽

Guo-Sheng Xiao ◽

...

Keyword(s):

Simple Sequence Repeats ◽

Distribution Patterns ◽

Variation Analysis ◽

Genomic Regions ◽

Simple Sequence

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Simple sequence repeats in organellar genomes of rice: frequency and distribution in genic and intergenic regions

Bioinformatics ◽

10.1093/bioinformatics/btl547 ◽

2006 ◽

Vol 23 (1) ◽

pp. 1-4 ◽

Cited By ~ 52

Author(s):

Passoupathy Rajendrakumar ◽

Akshaya Kumar Biswal ◽

Sena M. Balachandran ◽

Kommoju Srinivasarao ◽

Raman M. Sundaram

Keyword(s):

Simple Sequence Repeats ◽

Organellar Genomes ◽

Intergenic Regions ◽

Simple Sequence

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Distinct patterns of simple sequence repeats and GC distribution in intragenic and intergenic regions of primate genomes

Aging ◽

10.18632/aging.101025 ◽

2016 ◽

Vol 8 (11) ◽

pp. 2635-2654 ◽

Cited By ~ 10

Author(s):

Wen-Hua Qi ◽

Chao-chao Yan ◽

Wu-Jiao Li ◽

Xue-Mei Jiang ◽

Guang-Zhou Li ◽

...

Keyword(s):

Simple Sequence Repeats ◽

Intergenic Regions ◽

Simple Sequence

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The biological significance of variation in satellite DNA and heterochromatin in newts of the genus Triturus : an evolutionary perspective

Philosophical Transactions of the Royal Society of London Series B Biological Sciences ◽

10.1098/rstb.1986.0005 ◽

1986 ◽

Vol 312 (1154) ◽

pp. 243-259 ◽

Cited By ~ 57

Keyword(s):

Cell Cycle ◽

Satellite Dna ◽

Biological Significance ◽

Evolutionary Significance ◽

Sequence Structure ◽

Cell Cycle Time ◽

Satellite Dnas ◽

Evolutionary Changes ◽

Available Information ◽

Simple Sequence

The functional and evolutionary significance of highly repetitive, simple sequence (satellite) DNA is analysed by examining available information on the patterns of variation of heterochromatin and cloned satellites among newts (family Salamandridae), and particularly species of the European genus Triturus . This information is used to develop a model linking evolutionary changes in satellite DNAs and chromosome structure. In this model, satellites accumulate initially in large tandem blocks around centromeres of some or all of the chromosomes, mainly by repeated chromosomal exchanges in these regions. Centromeric blocks later become broken up and dispersed by small, random chromosome rearrangements in these regions. They are dispersed first to pericentric locations and then gradually more distally into the chromosome arms and telomeres. Dispersal of a particular satellite is accompanied by changes in sequence structure (for example, base substitutions, deletions, etc.) and a corresponding decrease in its detectability at either the molecular or cytological level. On the basis of this model, observed satellites in newt species may be classified as ‘old ’, ‘young’, or of ‘intermediate’ phylogenetic age. The functions and effects of satellite DNA and heterochromatin at the cellular and organismal levels are also discussed. It is suggested that satellite DNA may have an impact on cell proliferation through the effect of late-replicating satellite-rich heterochromatin on the duration of S-phase of the cell cycle. It is argued that even small alterations in cell cycle time due to changes in heterochromatin am ount may have magnified effects on organismal growth that may be of adaptive significance.

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Exon and intron sharing in opposite direction-an undocumented phenomenon in human genome-between Pou5f1 and Tcf19 genes

BMC Genomics ◽

10.1186/s12864-021-08039-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Majid Mehravar ◽

Fatemeh Ghaemimanesh ◽

Ensieh M. Poursani

Keyword(s):

Human Genome ◽

Splice Variants ◽

Biological Significance ◽

In Silico Analysis ◽

Overlapping Genes ◽

Overlapping Gene ◽

Domains Of Life ◽

New Form ◽

Genomic Regions ◽

Expressed Sequence

Abstract Background Overlapping genes share same genomic regions in parallel (sense) or anti-parallel (anti-sense) orientations. These gene pairs seem to occur in all domains of life and are best known from viruses. However, the advantage and biological significance of overlapping genes is still unclear. Expressed sequence tags (ESTs) analysis enabled us to uncover an overlapping gene pair in the human genome. Results By using in silico analysis of previous experimental documentations, we reveal a new form of overlapping genes in the human genome, in which two genes found on opposite strands (Pou5f1 and Tcf19), share two exons and one intron enclosed, at the same positions, between OCT4B3 and TCF19-D splice variants. Conclusions This new form of overlapping gene expands our previous perception of splicing events and may shed more light on the complexity of gene regulation in higher organisms. Additional such genes might be detected by ESTs analysis also of other organisms.

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