Identification of RCC1 Gene Family

The hidden Markov model (HMM) profile of the RCC1 gene family (PF00415) in PFAM (http://pfam.xfam.org/) was downloaded and used to identify the RCC1 genes in the local protein database of bread wheat, emmer wheat (Triticum dicoccoides, 2n = 4x = 28, AABB) and Aegilops tauschii (2n = 2x = 14, DD) (downloaded from Ensembl Plants, http://plants.ensembl.org/index.html) with the hmmsearch tool of HMMER3.1 software (HMMER 3.1; http://hmmer.org/). To avoid missing RCC1 family members, an aligned file of a high-quality protein set (E value < 1 × 10⁻²⁰) in MEGA X software (Kumar et al., 2018 (link)
) was used to reconstruct the new HMM profile, which was used as the query to search all the RCC1 members (E value < 0.01) in all bread wheat, emmer wheat, and Aegilops tauschii proteins, respectively. All the detected protein sequences were submitted to the PFAM (http://pfam.xfam.org/), SMART domain search (http://smart.embl.de/smart/batch.pl) (Letunic et al., 2021 (link)
), and NCBI Batch CD-search database (https://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi) to confirm the structural integrity of the RCC1 domain (Marchler-Bauer et al., 2005 (link)
). The non-redundant, verified genes encoding proteins with RCC1 domains were assigned as members of the RCC1 gene family.

Free full text: Click here

An X., Zhao S., Luo X., Chen C., Liu T., Li W., Zou L, & Sun C. (2023). Genome-wide identification and expression analysis of the regulator of chromosome condensation 1 gene family in wheat (Triticum aestivum L.). Frontiers in Plant Science, 14, 1124905.

Publication 2023

Aegilops Bread Family members Gene Gene profile Plants Protein sequences Proteins Proteins domains Set protein Triticum Wheat

Corresponding Organization :

Other organizations : ZheJiang Academy of Agricultural Sciences, Cotton Research Institute

Top 5 similar protocols

Variable analysis

independent variables

Use of the hidden Markov model (HMM) profile of the RCC1 gene family (PF00415) in PFAM to identify the RCC1 genes in the local protein database of bread wheat, emmer wheat (Triticum dicoccoides, 2n = 4x = 28, AABB) and Aegilops tauschii (2n = 2x = 14, DD)

dependent variables

Identification of RCC1 genes in the local protein database of bread wheat, emmer wheat (Triticum dicoccoides, 2n = 4x = 28, AABB) and Aegilops tauschii (2n = 2x = 14, DD)

control variables

Use of a high-quality protein set (E value < 1 × 10^-20) to reconstruct the new HMM profile, which was used as the query to search all the RCC1 members (E value < 0.01) in all bread wheat, emmer wheat, and Aegilops tauschii proteins, respectively
Submission of all the detected protein sequences to the PFAM, SMART domain search, and NCBI Batch CD-search database to confirm the structural integrity of the RCC1 domain

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!