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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 analyses the...

Cis-regulatory Sequences

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

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 DNA...

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 analyses the...

General Transcription Factors

General Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...

Cis-regulatory Sequences

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

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Related Experiment Video

Updated: Jul 16, 2026

Dissection of Hippocampal Dentate Gyrus from Adult Mouse

Dissection of Hippocampal Dentate Gyrus from Adult Mouse

Published on: November 18, 2009

The mammalian FEN-1 locus: structure and conserved sequence features.

Z E Karanjawala¹, X Shi, C L Hsieh

¹Norris Comprehensive Cancer Center, Department of Pathology, University of Southern California School of Medicine, Los Angeles 90089, USA.

Microbial & Comparative Genomics

|March 17, 2001

Summary

Flap endonuclease 1 (FEN-1) is crucial for DNA replication and repair. Researchers compared the murine and human FEN-1 gene loci, finding conserved sequences that may regulate transcription.

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Last Updated: Jul 16, 2026

Dissection of Hippocampal Dentate Gyrus from Adult Mouse

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Published on: November 18, 2009

An Integrated Approach for Microprotein Identification and Sequence Analysis

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Published on: July 12, 2022

Fluorescence-Based Detection of FEN1 Nuclease Activity and Screening of Small-Molecule Inhibitors

Fluorescence-Based Detection of FEN1 Nuclease Activity and Screening of Small-Molecule Inhibitors

Published on: June 27, 2025

Area of Science:

Molecular Biology
Genetics
Biochemistry

Background:

Flap endonuclease 1 (FEN-1) is a vital enzyme in eukaryotes, essential for DNA replication by cleaving 5' DNA flaps between Okazaki fragments.
FEN-1 also plays critical roles in base excision repair and nonhomologous DNA end joining across eukaryotic organisms, from yeast to humans.

Purpose of the Study:

To elucidate the genomic structure of the murine Flap endonuclease 1 (FEN-1) locus.
To compare the murine FEN-1 locus with its human counterpart.
To identify conserved sequence elements and investigate their potential regulatory functions.

Main Methods:

Comparative genomic analysis of murine and human FEN-1 loci.
Sequence analysis of the 5' and 3' untranslated regions (UTRs) and upstream regulatory regions.
Identification of nucleotide sequence homology between species.

Main Results:

The murine and human FEN-1 genes share a single exon coding region.
Both loci exhibit transcriptional initiation within a CpG island.
Significant nucleotide sequence homology (30-230 bp) was observed in the 5'UTR, 3'UTR, and immediately upstream of the 5'UTR.

Conclusions:

Conserved sequence blocks in the FEN-1 locus suggest potential roles in transcriptional regulation.
These conserved regions might indicate the presence of an overlapping gene with opposing transcriptional orientation.
Further studies are warranted to determine the precise function of these conserved elements in FEN-1 gene regulation.