Table 1.

Classes of Genes Defined in Sequence Ontology and Corresponding Class Descriptors in Unique Gene Identifiers

Class of gene	Sequence ontology ID	Sequence ontology definition	Class descriptor
Protein-coding gene	SO:0001217	A gene that codes for a protein	CG
Ribosomal RNA gene	SO:0001637	A gene that encodes a ribosomal RNA	rRNA
Transfer RNA gene	SO:0001272	A gene that encodes a transfer RNA	tRNA
Non-coding RNA gene			ncRNA
Long non-coding RNA gene	SO:0001877	A non-coding RNA over 200 nucleotides in length.	IncRNA
Long intergenic non-coding RNA gene	SO:0001463	A multiexonic non-coding RNA transcribed by RNA polymerase II.	lincRNA
Small nuclear RNA gene	SO:0001268	A gene that encodes a small nuclear RNA	snRNA
Small nucleolar RNA gene	SO:0001267	A gene that encodes a small nucleolar RNA	snoRNA
Micro RNA gene	SO:0001265	A gene that encodes a microRNA	mi RNA
piwi-associated RNA gene	SO:0001035	A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements.	piRNA
Enhancer RNA	SO:0001870	A short ncRNA that is transcribed from an enhancer. May have a regulatory function.	eRNA
Mitochondrial gene	SO:0000088	A gene located in mitochondrial sequence	mt
Pseudogene	SO:0000336	A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their “normal” paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its “normal” paralog).	ps