Ultraconserved regions (UCRs) are DNA segments greater than 200 nucleotides in length with 100% sequence identity between humans, rats and mice (Bejerano et al., 2004). 481 UCRs have been described. Of these, 111 (known as "exonic" UCRs) coincide with human protein-coding genes, while 256 UCRs (termed "non-exonic") do not appear to be transcribed at all. It is not yet clear whether any of the remaining 114 "possibly exonic" UCRs are transcribed. Bejerano, et al. (2004) determined that, of the non-exonic UCRs, 100 (39%) occur within the introns of known genes, while the remaining 156 are intergenic. Non-exonic UCRs are usually located near transcription factor and developmental regulatory genes. However, the exonic and possibly exonic elements display no such localization bias (Bejerano et al., 2004). The transcribed UCRs, known as T-UCRs, comprise a special class of UCRs that generate a set of long non-coding RNAs (LncRNAs).

 

Since currently available UCR annotations are based on an earlier build of the human genome (hg17; Bejerano et al., 2004), we re-annotated all UCRs using the more recent hg19 build. The UCRs were then re-organized into three different categories (exonic, intronic and intergenic) by matching the location of each with RefSeq genes (Figure 1). The new categories provide more thorough annotation for each UCR. In addition, the association between UCRs and cancer-associated genomic regions (CAGRs) are defined. Examples of the detailed annotations of the UCRs are presented in Table 2.

Figure 1. Re-annotation of UCRs. Representation of the different UCR classes according to their genomic location with respect to protein-coding genes. An example of each class is shown.

 

The updated annotation of 481 UCRs (hg19)						The annotation of 481 UCRs by Bejerano (hg17)
UCR name	UCR length	UCR coordinates (HG19)	UCR type	Host gene of the UCR	CAGR or FRA type	UCR type (possibly exonic, exonic, non-exonic)	Host gene of UCR
uc.1	207	chr1:10597697-10597903	intronic	PEX14	LOH,	possibly exonic	PEX14
uc.2	207	chr1:10732543-10732749	intronic	CASZ1	LOH,	non-exonic	FLJ20321
uc.13	237	chr1:36359190-36359426	exonic	EIF2C1		exonic	EIF2C1
uc.28	355	chr1:70696713-70697067	exonic	SFRS11, SRSF11	FRA<2Mb	exonic	SFRS11
uc.62	234	chr2:60780682-60780915	exonic	BCL11A	AMPLIF	exonic	BCL11A
uc.193	319	chr6:86321686-86322004	exonic	SYNCRIP	LOH	exonic	SYNCRIP
uc.368	228	chr14:34068576-34068803	intronic	NPAS3	LOH, AMPLIF	non-exonic	NPAS3
uc.369	213	chr14:34122617-34122829	intronic	NPAS3	LOH, AMPLIF	non-exonic	NPAS3

 

Bejerano, G., Pheasant, M., Makunin, I., Stephen, S., Kent, W.J., Mattick, J.S., and Haussler, D. (2004). Ultraconserved elements in the human genome. Science 304, 1321-1325.