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T-UCR Research

The Updated Annotation of the 481 UCRs

 

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.

T-UCR_annotation-1

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.

Example of re-annotated UCRs

 

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



Related Services
T-UCR Array Service
LncRNA Array Service
LncRNA qPCR Service

 

References:

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.

 

 

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