REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
transcripts and structural annotations of human	Frankish et al. (2021)	https://www.gencodegenes.org/human/release_37.html
transcripts of Arabidopsis thaliana	Arabidopsis Genome Initiative et al. (2000)	https://bar.utoronto.ca/thalemine/dataCategories.do
structural annotations of Arabidopsis thaliana	Cheng et al. (2017)	https://bar.utoronto.ca/thalemine/dataCategories.do
transcripts and structural annotations of rice	Kawahara et al. (2013)	http://rice.uga.edu/downloads_gad.shtml
Iso-Seq data of Amborella	Sharon et al. (2013)	https://www.ncbi.nlm.nih.gov/bioproject/PRJNA374048
genome sequence of Amborella	Amborella Genome Project et al. (2013)	https://www.ncbi.nlm.nih.gov/genome/12031?genome_assembly_id=225336
AStrap transcripts dataset	Ji et al. (2019)	https://github.com/BMILAB/AStrap
Software and algorithms
PacBio’s SMRT analysis	Liu et al. (2017)	https://www.pacb.com/products-and-services/analytical-software/smrt-analysis/
BLASTN	Altschul et al. (1990)	https://blast.ncbi.nlm.nih.gov/Blast.cgi
SUPPA2	Trincado et al. (2018)	https://github.com/comprna/SUPPA
PASA	Campbell et al. (2006)	https://github.com/PASApipeline/PASApipeline
Python	Python Software Foundation	https://www.python.org
Tensorflow	Abadi et al. (2016)	https://tensorflow.google.cn
AStrap	Ji et al. (2019)	https://github.com/BMILAB/AStrap
Isosplitter	Wang et al. (2021)	https://github.com/Hengfu-Yin/IsoSplitter
DeepASmRNA	This study	https://github.com/CMB-BNU/DeepASmRNA or http://cmb.bnu.edu.cn/DeepASmRNA/index.php/download