Gencode, TSS for known genes.

Description

Starting positions of Gencode vM35 transcript entries. This collection is restricted to protein-coding genes. Note that the genomic coordinates referred to as TSS are not true transcription start sites confirmed with a reliable mRNA 5'end sequencing techonology such as CAGE. They are just the starting positions of cDNA clones containing the full coding region of a gene.

Source

Raw data was downloaded from: https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M35/gencode.vM35.annotation.gff3.gz
Input file format: GFF3
Download date: 03-08-2024

Samples

From M. musculus (June 2020 GRCm39/mm39).

Genome Annotation:

	Filename	Description	Feature	GEO-ID
1	gencode.vM35.mm39.sga	TSS from Gencode vM35	TSS	-

Notes on samples:

The SGA file of this series includes in the sixth field a transcript Id of the form ENSEMBLE-ID..gene-name, e.g. ENSMUST00000159265..Xkr4.

Technical Notes

The starting positions of Gencode transcripts were extracted and reformatted with a custom shell script available from: https://epd.expasy.org/ftp/mga/mm39/gencode/scripts/

References

Frankish A, Carbonell-Sala S, Diekhans M, Jungreis I, Loveland JE et al. GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Res. 2023 Jan 6;51(D1):D942-D949. doi: 10.1093/nar/gkac1071. 36420896

Last update: 4 Aug 2024

Page made by Philipp Bucher