Help: Tutorial 3 -- ATTED-II

last update; Jun. 25. 2019

Tutorial 3:
Regulatory estimation of a gene, At5g62490 (ABA-responsive protein)

Search At5g62490 using search box next to the title logo.

Click the AGI code in resulting table to jump to the locus page.

Locus page provides following information.

Coexpressed gene network

The coexpressed gene list indicates that this gene is coexpressed with genes for "late embryogenesis".

Expression patterns

This gene is up-regulated by osmotic and salt stresses as well as ABA treatment. Drastic expression during embryogenesis is also shown, suggesting that this gene may function for embryogenesis.

Predicted cis elements

Cis elements are predicted at 60-62bp and 101-103bp upstream from TSS. Although 6 predicted heptamers are provided, they are grouped into 2 cis elements for position, GACACGTGT and CCACGTGGC, sharing CACGTG core.

In the cis element page, users can obtain following information.

Public annotation of this cis element

This predicted heptamer corresponds to the reported cis elements named ABRE or G-box.

Posision specificity of this cis element

This element prefers the position from 50 to 100bp upstream of TSS, indicating that this ABRE-like element found in At5g62490 appears at the most appropriate position (60-62bp upstream from TSS).

Samples to activate this cis element

The graph for cis element specificity of experimental condition shows that genes containing this cis element in their promoters prefer to be up-regulated responding to ABA treatment and osmotic and salt stresses.
This pattern is consistent with expression pattern of At5g62490, supporting the possibility that this gene is regulated through this cis element.

Candidates of transcription factors to bind this cis element

In these genes, RD26 and G-box binding factor 3 (GBF3) are good candidates because these genes expresses at embryogenesis and up-regulated by ABA treatment and osmotic and salt stresses according to expression pattern in each locus page. Actually, RD26 is known to function for ABA-dependent stress signaling and its homologous transcription factors recognize CACG core. GBF3 is known to bind G-box sequence for ABA signaling.
Cis element pages for the second group of heptamers found in the locus page contain almost identical information except for the position preference, which is the best at 100bp, indicating the second cis element also appears at the most appropriate position (101-103bp).

In summary, information in ATTED-II suggests a following regulatory scheme;

Osmotic or salt stresses stimulate ABA signaling.
ABA signal up-regulates At5g62490 together with co-expressed genes for late embryogenesis through two ABREs and such transcription factors like RD26 and GBF3.