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Table 4 The number of genes and transcripts on the primary chromosomes (excluding alternative scaffolds) of GRCh38 in the CHESS 3, RefSeq v110, and GENCODE v41 catalogs

From: CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure

 

CHESS

RefSeq

GENCODE

Gene type

 Protein-coding genes

19,839

19,884

19,419

 lncRNA genes

17,623

17,793

18,041

 microRNA

1914

1914

1879

Transcript type

 Protein-coding transcript

99,202

129,740

169,195a

 lncRNA transcript

34,708

29,048

53,216

 pseudogene

16,572

15,357

20,234

 tRNA

453

453

535

 snoRNA

1195

1195

942

 snRNA

153

153

1901

 rRNA

40

40

47

 VDJ segments

565

565

200

 Other

213

12,493

3822

Total transcripts

158,377

191,917

251,236

  1. lncRNA long noncoding RNA gene, snoRNA small nucleolar RNA, snRNA small nuclear RNA, rRNA ribosomal RNA, tRNA transfer RNA
  2. aProtein-coding transcripts for GENCODE include all transcripts for genes with the biotype protein_coding, including those with tags such as “retained_intron,” “mRNA_start_NF,” “nonsense_mediated_decay,” and others