DOI: 10.5281/zenodo.18467066
title: Supplementary materials of Identifying genes with conserved splicing structure and orthologous isoforms in human, mouse and dog

description: ## Authors:Nicolas Guillaudeux, Catherine Belleannée, Samuel Blanquart

## Files contained

This repository contains all the additional documents of the article and in particular the described database[^fn1].

### Information of the 2,167 gene triplet orthologs across human, mouse and dog

- `Additional_file_9.gtf` --- Gene information in human with predicted transcripts for the 2,167 gene set in gtf format.

- `Additional_file_10.gtf` --- Gene information in mouse with predicted transcripts for the 2,167 gene set in gtf format.

- `Additional_file_11.gtf` --- Gene information in dog with predicted transcripts for the 2,167 gene set in gtf format.

### Information of the 253 gene triplets that have a conserved gene structure and transcriptome across human, mouse and dog

- `Additional_file_8.gtf` --- Gene Ontology information for the 253 gene set. (1)

- `Additional_file_1.gtf` --- Full gene information in human with known and predicted transcripts for the 253 gene set in gtf format. (1)

- `Additional_file_2.gtf` --- Full gene information in mouse with known and predicted transcripts for the 253 gene set in gtf format. (1)

- `Additional_file_3.gtf` --- Full gene information in dog with known and predicted transcripts for the 253 gene set in gtf format. (1)

- `Additional_file_4.csv` --- List of the 879 orthologous CDS groups with their transcript identifiers. This file is an Excel spreadsheet with, for each orthologous CDS group, its transcript identifiers in the three species. (1)

- `Additional_file_5.csv` --- Size of each CDS orthology group concerning the 118 gene set (alternative UTRs). This file is an Excel spreadsheet with, for each orthologous gene triplet and each CDS orthology group, the number of transcripts encoding a same CDS per species. (1)

- `Additional_file_6.csv` --- List of the 1,029 predicted transcripts and their associated evidence found in external databases for the 253 gene triplet set. The additional file is an Excel spreadsheet with, for each predicted transcript, its evidence tag. (1)

### Information on the evaluation of existing evidence for predicted transcripts at the 253 orthologous gene triplets.

- `Additional_file_14.bed`: Specific exon junctions found in human, for the 253 gene set, with our prediction and not known in Ensembl release 90 in bed format.

- `Additional_file_15.bed`: Specific exon junctions found in mouse, for the 253 gene set, with our prediction and not known in Ensembl release 90 in bed format.

- `Additional_file_16.bed`: Specific exon junctions found in dog, for the 253 gene set, with our prediction and not known in Ensembl release 90 in bed format.

- `Additional_file_17.csv`: Number of reads aligned with specific exon junction in each human tissue sample tested. This file is an Excel spreadsheet with, for each specific exon junction, its number of reads alignes per tissue.

- `Additional_file_18.csv`: Number of reads aligned with specific exon junction in each mouse tissue sample tested. This file is an Excel spreadsheet with, for each specific exon junction, its number of reads alignes per tissue.

- `Additional_file_19.csv`: Number of reads aligned with specific exon junction in each dog tissue sample tested. This file is an Excel spreadsheet with, for each specific exon junction, its number of reads alignes per tissue.

### Information of the database **transcript_ortho**

- `Additional_file_7.pdf` --- Relational diagram of the Transcript_ortho SQL database. (1)

- `Additional_file_12.sql.gz` --- Dump of the **transcript_ortho** database. The database describes all the data for the 253 gene triplet set.

- `Additional_file_13.md` --- Readme of the database **transcript_ortho**. This file describes how to install and to query the database with example of applications.

 

*All files with (1) in description are attached to the article published by BMC Genomics.*

# Reference

[^fn1]: Guillaudeux et al. Identifying genes with conserved splicing structure and orthologous isoforms in human, mouse and dog; 

https://doi.org/10.1186/s12864-022-08429-4