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Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

Gene Families

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Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...

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Related Experiment Video

Updated: May 12, 2026

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis

Published on: November 11, 2014

Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs.

Norihiro Maeda¹, Takeya Kasukawa, Rieko Oyama

¹Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, Wako, Japan. rgscerg@gsc.riken.jp

|May 10, 2006

Summary

This summary is machine-generated.

The FANTOM3 project significantly expanded the mouse transcriptome catalog by annotating over 100,000 full-length enriched cDNAs. This effort provides the most extensive coverage of the mouse proteome to date, advancing our understanding of gene expression.

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Last Updated: May 12, 2026

Identification of Key Factors Regulating Self-renewal and Differentiation in EML Hematopoietic Precursor Cells by RNA-sequencing Analysis

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Published on: November 11, 2014

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Published on: March 29, 2019

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Published on: August 15, 2019

Area of Science:

Transcriptomics
Genomics
Bioinformatics

Background:

The FANTOM consortium aims to comprehensively map mammalian transcriptomes.
Previous FANTOM2 dataset identified 60,770 full-length enriched cDNAs.
FANTOM2 revealed only partial coverage of the estimated mouse protein-coding genes.

Purpose of the Study:

To create a complete catalog of mouse genes.
To identify and functionally annotate all full-length enriched cDNAs.
To improve the accuracy and efficiency of transcriptome annotation.

Main Methods:

Continued cloning and sequencing of full-length enriched cDNAs.
Enhanced automated annotation pipeline with new prediction programs.
Developed a web-based interface for simplified manual curation and expert review.

Main Results:

Annotated a total of 102,801 full-length enriched mouse cDNAs.
Functionally annotated 56,722 transcripts as protein-coding, achieving extensive mouse proteome coverage.
Increased the count of distinct non-protein-coding transcripts to 34,030.

Conclusions:

The FANTOM3 annotation system enhances comprehensive characterization of the mouse transcriptome.
The developed annotation pipeline can be applied to transcriptomes of other species.
FANTOM3 provides the most extensive full-length cDNA coverage of the mouse proteome currently available.