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Multi-species Conserved Sequences

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...

Conservation of Protein Domains

Conservation of Protein Domains

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

Conserved Binding Sites

Conserved Binding Sites

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...

Cis-regulatory Sequences

Cis-regulatory Sequences

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Related Experiment Video

Updated: Apr 27, 2026

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

UCbase 2.0: ultraconserved sequences database (2014 update).

Vincenzo Lomonaco¹, Riccardo Martoglia¹, Federica Mandreoli¹

¹Computer Engineering Department, University of Modena, Via Campi 213/b, 44100, Modena, Department of Statistical Sciences, University of Bologna, Via Belle Arti 41, 40126, Bologna, Italy, Department of Genetics, Environment and Evolution, Genetics Institute, University College London, London, WC1E 6BT, UK and Department of Life Sciences, Center for Genome Research, University of Modena and Reggio Emilia, Via G. Campi 287, 41100, Modena, Italy.

Database : the Journal of Biological Databases and Curation

|June 22, 2014

Summary

This summary is machine-generated.

UCbase 2.0 enhances ultraconserved sequence (UCR) analysis with updated human genome data and interactive visualization tools. This web resource aids research into UCRs

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An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

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The ITS2 Database

The ITS2 Database

Published on: March 12, 2012

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Last Updated: Apr 27, 2026

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation

Published on: February 10, 2023

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

The ITS2 Database

The ITS2 Database

Published on: March 12, 2012

Area of Science:

Genomics
Bioinformatics

Background:

Ultraconserved regions (UCRs) are highly identical sequences (>200 bases) across human, mouse, and rat genomes.
UCRs are frequently implicated in cancer and differential gene expression in human malignancies.

Purpose of the Study:

To present UCbase 2.0, an updated and expanded web tool for analyzing ultraconserved sequences (UCRs).
To provide enhanced features for UCR analysis, including updated genome annotation and interactive visualization.

Main Methods:

UCbase 2.0 integrates the human genome annotation (hg19) and the Systematized Nomenclature of Medicine classification for disorder-chromosomal coordinates.
The platform includes a query tool for Single Nucleotide Polymorphisms (SNPs) and a MySQL interface for direct database interrogation.
A graph visualization interface linked to the UCSC genome browser facilitates interactive interpretation of UCR chromosomal positions.

Main Results:

UCbase 2.0 offers an updated and extended analysis platform for ultraconserved sequences.
New features include integrated disorder-chromosomal mapping, SNP querying, and direct database access.
Enhanced interactive visualization aids in understanding UCR genomic positioning.

Conclusions:

UCbase 2.0 is a valuable, platform-independent web resource for researchers studying ultraconserved sequences.
The tool's advanced features facilitate deeper insights into the role of UCRs in genomics and disease.