NDLI: Evolution and functional classification of vertebrate gene deserts.

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Evolution and functional classification of vertebrate gene deserts.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Ovcharenko, Ivan Loots, Gabriela G. Nobrega, Marcelo A. Hardison, Ross C. Miller, Webb Stubbs, Lisa
Description	Country affiliation: United States Author Affiliation: Ovcharenko I ( Energy, Environment, Biology, and Institutional Computing, Lawrence Livermore National Laboratory, Livermore, California 94550, USA. ovcharenko1@llnl.gov)
Abstract	Large tracts of the human genome, known as gene deserts, are devoid of protein-coding genes. Dichotomy in their level of conservation with chicken separates these regions into two distinct categories, stable and variable. The separation is not caused by differences in rates of neutral evolution but instead appears to be related to different biological functions of stable and variable gene deserts in the human genome. Gene Ontology categories of the adjacent genes are strongly biased toward transcriptional regulation and development for the stable gene deserts, and toward distinctively different functions for the variable gene deserts. Stable gene deserts resist chromosomal rearrangements and appear to harbor multiple distant regulatory elements physically linked to their neighboring genes, with the linearity of conservation invariant throughout vertebrate evolution.
File Format	HTM / HTML
ISSN	10889051
e-ISSN	15495469
Journal	Genome Research
Issue Number	1
Volume Number	15
Language	English
Publisher	Cold Spring Harbor Laboratory Press
Publisher Date	2005-01-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Discipline Genetics Discipline Genomics Evolution, Molecular Genes Physiology Animals Genetics Conserved Sequence Dna Sequence, Unstable Gene Amplification Genes, Essential Genome Genome, Human Mice Short Interspersed Nucleotide Elements Untranslated Regions Comparative Study Research Support, U.s. Gov't, Non-p.h.s. Research Support, U.s. Gov't, P.h.s.
Content Type	Text
Resource Type	Article
Subject	Genetics Genetics (clinical)

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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V-SINEs: a new superfamily of vertebrate SINEs that are widespread in vertebrate genomes and retain a strongly conserved segment within each repetitive unit.

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.

Retroelement distributions in the human genome: variations associated with age and proximity to genes.

High concentrations of long interspersed nuclear element sequence distinguish monoallelically expressed genes.

Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes.

Mammalian non-LTR retrotransposons: for better or worse, in sickness and in health.

Short interspersed transposable elements (SINEs) are excluded from imprinted regions in the human genome.

ATLAS: a system to selectively identify human-specific L1 insertions.

Sequence features in regions of weak and strong linkage disequilibrium.

Evolution and functional classification of vertebrate gene deserts.

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V-SINEs: a new superfamily of vertebrate SINEs that are widespread in vertebrate genomes and retain a strongly conserved segment within each repetitive unit.

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.

Retroelement distributions in the human genome: variations associated with age and proximity to genes.

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