Alternative Poly(A) Sites database

Abbreviation:APASdb

General Information

APASdb can visualize the precise map and usage quantification of different APA isoforms for all genes. The datasets are deeply profiled by the sequencing alternative polyadenylation sites (SAPAS) method capable of high-throughput sequencing 3'-ends of polyadenylated transcripts. Thus, APASdb details all the heterogeneous cleavage sites downstream of poly(A) signals, and maintains near complete coverage for APA sites. Furthermore, APASdb provides the quantification of a given APA variant among transcripts with different APA sites by computing their corresponding normalized-reads. In addition, APASdb supports URL-based retrieval, browsing and display of exon-intron structure, poly(A) signals, poly(A) sites location and usage reads, and 3'-untranslated regions (3'-UTRs). Currently, APASdb involves APA in various biological processes and diseases in human, mouse and zebrafish.

Homepage http://mosas.sysu.edu.cn/utr

Developed in China

Created in 2014

Taxonomic range

Scope and data types

Regulation of gene expression

Untranslated region (UTR)

How to cite this record FAIRsharing.org: APASdb; Alternative Poly(A) Sites database; DOI: https://doi.org/10.25504/FAIRsharing.zvh04m; Last edited: Feb. 22, 2018, 2:58 p.m.; Last accessed: Nov 13 2018 5 p.m.

Record updated: Nov. 18, 2016, 4:29 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.zvh04m' by 'The FAIRsharing Team' at 16:29, 18 Nov 2016 (approved):

	'description' has been modified:
		Before: a web-accessible database, named APASdb (http://mosas.sysu.edu.cn/utr), which can visualize the precise map and usage quantification of different APA isoforms for all genes. The datasets are deeply profiled by the sequencing alternative polyadenylation sites (SAPAS) method capable of high-throughput sequencing 3'-ends of polyadenylated transcripts. Thus, APASdb details all the heterogeneous cleavage sites downstream of poly(A) signals, and maintains near complete coverage for APA sites, much better than the previous databases using conventional methods. Furthermore, APASdb provides the quantification of a given APA variant among transcripts with different APA sites by computing their corresponding normalized-reads, making our database more useful. In addition, APASdb supports URL-based retrieval, browsing and display of exon-intron structure, poly(A) signals, poly(A) sites location and usage reads, and 3'-untranslated regions (3'-UTRs). Currently, APASdb involves APA in various biological processes and diseases in human, mouse and zebrafish.
		After:  APASdb can visualize the precise map and usage quantification of different APA isoforms for all genes. The datasets are deeply profiled by the sequencing alternative polyadenylation sites (SAPAS) method capable of high-throughput sequencing 3'-ends of polyadenylated transcripts. Thus, APASdb details all the heterogeneous cleavage sites downstream of poly(A) signals, and maintains near complete coverage for APA sites. Furthermore, APASdb provides the quantification of a given APA variant among transcripts with different APA sites by computing their corresponding normalized-reads. In addition, APASdb supports URL-based retrieval, browsing and display of exon-intron structure, poly(A) signals, poly(A) sites location and usage reads, and 3'-untranslated regions (3'-UTRs). Currently, APASdb involves APA in various biological processes and diseases in human, mouse and zebrafish. Domain list has changed:  Previous values: DNA sequence data|process|http://purl.obolibrary.org/obo/OBI_0000626 Life Science|domain| Polyadenylation site|| Transcription regulation|| New values:  DNA sequence data|process|http://purl.obolibrary.org/obo/OBI_0000626 Life Science|domain| Polyadenylation site|| Transcription regulation|| UTRs||

Edits to 'https://fairsharing.org/FAIRsharing.zvh04m' by 'The FAIRsharing Team' at 09:31, 06 Oct 2016 (approved):

	'contactName' has been modified:
		Before:
			Leiming YOU
		After:
			Leiming You
			Domain list has changed: 
			Previous values:
			DNA sequence data|process|http://purl.obolibrary.org/obo/OBI_0000626
			Polyadenylation site||
			Transcription regulation||
			New values: 
			DNA sequence data|process|http://purl.obolibrary.org/obo/OBI_0000626
			Polyadenylation site||
			Transcription regulation||
			Life Science|domain|
			Tools have changed: 
			Previous values:
			Search
			Browse
			Blast
			New values: 
			Blast
			Data processes have changed: 
			Previous values:
			Download
			New values: 
			Download
			search
			browse
			Organisations have changed: 
			Previous values:
			Beijing University of Chinese Medicine
			New values: 
			Beijing University of Chinese Medicine|China
			Grants have changed: 
			Previous values:
			New values: 
			2013CB917800 
			2013CB835304
			2011CB946101
		Added:
		Removed:

Support

General

contact form	http://mosas.sysu.edu.cn/utr/mail.php
help	http://mosas.sysu.edu.cn/utr/APASdbs_hel ...

Additional Information

Contact

Leiming You

Tools

Blast

http://mosas.sysu.edu.cn/utr/blast.php

Access / Retrieve Data

Conditions of Use

Data Access

Download	http://mosas.sysu.edu.cn/utr/download_datasets.php
search	http://mosas.sysu.edu.cn/utr/search_APASdb.php
browse	http://mosas.sysu.edu.cn/utr/gbrowse.php

Publications

APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals.

You L, Wu J, Feng Y, Fu Y, Guo Y, Long L, Zhang H, Luan Y, Tian P, Chen L, Huang G, Huang S, Li Y, Li J, Chen C, Zhang Y, Chen S, Xu A
Nucleic Acid Research 2014

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

FASTA Sequence Format

Related Databases

No related databases defined

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is in need of a maintainer. If you login, you'll be able to claim this record.

Funds

National Basic Research Program of China, Beijing, China (Government body)

Maintains

Beijing University of Chinese Medicine, China

Grant Number(s)

2011CB946101 (National Basic Research Program of China, Beijing, China)
2013CB835304 (National Basic Research Program of China, Beijing, China)
2013CB917800 (National Basic Research Program of China, Beijing, China)

Alternative Poly(A) Sites database

We need your help!

Developed by

Contact Us

About FAIRsharing