Searching APA Sites, APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals

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Analysis of genomic poly(A) sites

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[1]. For APASdbs, a genome-wide database describing alternative poly(A) sites and detailing the heterogeneous cleavage sites dwonstream each poly(A) signal in various biological conditions and deseases. It supports query by using a ID (currently Ensembl or UCSC ID only), gene name, symbols or description variable in publications and databases. Searching examples: cxcl12a, cxcl, chemokine, also ENSDARG00000037116 (Ensembl id only for Danio rerio), uc009dsc.2, uc003qht.2 (UCSC id only for Mus musculus and Homo sapiens).

[2]. For Transcripts, that annotates and stores transcript sequences, querying by using a ID, gene name, symbols or description. Example: ssr4, ssr, TLR, caspase, also Bb_073760F are available for v7h2, but v15h11 and v18h27 currently only surport id query.

[3]. For Proteins, it saves proteins sequences to supports Blast, providing query by protein ID in databases, For example Bb_073760F.

[4]. For ESTs, it stores Expressed sequence tags to supports Blast, but also provides obtaining sequences by EST-ID in databases, For example est_xb_1526.

[5]. For Genomes, it collects genome sequences and also supports Blast, querying by using a chr ID in publication and databases such as Sc0000024 (only for lancelet), chr1, chr22 and so on.

[6]. For ncRNAs, that collects ncRNAs such as tRNA, snRNA, rRNA, miRNA and so on. It provides Blast and querying by Ensembl Transcript or Gene ID. For example, ENSDART00000128920.

[7]. For miRNAs, it stores miRNAs sequences and supply Blast and searching by miRBase ID and Name, like bfl-miR-2058, dre-miR-430a and MIMAT0001423.

Searching APA sites in 3'UTR of a interesting gene

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Lancelet
Branchiostoma belcheri

Database: for

Dataset description: Detailed description on the searching dataset can be referred by unfolding more description in the dataset-list page 'APAS Search'.
Tips for searching: search using a ID (currently Ensembl or UCSC ID only), gene name, symbols or description variable in publications and databases.
Searching examples: cxcl12a, cxcl, chemokine, also ENSDARG00000037116 (Ensembl id only for Danio rerio), uc009dsc.2, uc003qht.2 (UCSC id only for Mus musculus and Homo sapiens).

1.

Poly(A)-site map

Poly(A)-site usage

Heterogeneous cleavage-site selection

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Pooled

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Normal intestine

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V.anguillarum-infected intestine

Gene id:	Bb_231830F
Gene name:	TLR15
Chromosome:	Sc0000319(+)
Gene locus:	Sc0000319:69316-70083
Gene description:	Toll-like receptor 15
Notes:

Transcript id:	Bb_231830F
Transcript name:	TLR15
Transcript locus:	Sc0000319(+):69316-70083

Start codon:	69316
Stop codon:	70081
Alternative polyA sites:	Mapped to the searched transcript, containing the 5' and 3' flanking region of 1kb.
Alternative polyA sites:	70344
polyA signals:	AATACA

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Tips for marking poly(A) sites in the corresponding genome sequence:

All the heterogeneous cleavage sites clustered to a poly(A) site, are underlined and highlighted in light red, and their upstream poly(A) signals if exists, are highlighted in light green. Especially, the most-frequently used cleavage site defined as the reference poly(A) site in a cluster, is specially highlighted in dark red and underlined in bold. Also, the searched transcript locus is indicated, including the marked exons (light grey background with a brown font), introns and UTRs (light grey background with a green font).

> Bb_231830F; TLR15, Toll-like receptor 15

Sc0000319:(+)

TLR15

Transcript

69316

Transcript

69316

Codon

70081

Transcript

70083

1(100%)

signal:AATACA

pA:70344

Start

Start

StopCodon

End

in down_1kb

PolyA sites and polyA signals mapped to the searched transcript, including the 5' and 3' flanking region of 1kb

0

Normal intestine

1

V.anguillarum-infected intestine

PolyA sites produced by APA in Vibrio anguillarum-infected intestine and normal control. Vibrio anguillarum (V.anguillarum), a severe pathogen of marine fish. Mean reads: 1.

Citation:
(Leiming You, et al. Nucleic Acids Res. 2015, 43: D59-D67) APASdb: a database describing alternative poly(A) sites and selection of heterogeneous cleavage sites downstream of poly(A) signals.

Jan 11, 2021. Last updated

Copyright© Laboratory of Molecular Medicine, Sun Yat-Sen University, High Education Mega Center, Guangzhou 510006 China.