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Table 1 Vertebrate HCNE terminology disambiguation

From: Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes

Abbreviation

Term

Early reference

Definition

UCR

Ultraconserved region

[26]

≥200 bp 100% conserved between human and mouse

  

[5]

Nontranscribed, ≥50 bp ≥95% conserved between human and mouse, and at least partially aligned to fugu

UCE

Ultraconserved element

[89]

≥100 bp 100% conserved between human and mouse

CNS

Conserved noncoding sequence

[90]

Nongenic, human:mouse, >100 bp and with ≥70% identity

CNE

Conserved noncoding element

[6]

Nontranscribed, >100 bp human:fugu alignments with MegaBlast

HCNR

Highly conserved noncoding region

[7]

Visual inspection of mouse: Xenopus:zebrafish alignments

  

[91]

Same as [5]

HCNE

Highly conserved noncoding element

[28]

Windows ≥50 bp that do not overlap coding regions and for which the probability of being under purifying selection, given the conservation score, is ≥95%

CNC

Conserved noncoding region (?)

[38]

 

CNG

Conserved nongenic sequence

[92]

Nontranscribed, human:mouse BLAST with an e-value < 10-20 and similarity ≥98%

HCE

Highly conserved element

[46]

UCE from Bejerano et al. [26] + UCR from Sandelin et al. [5] + UCR from Sandelin et al. [5] + CNE from Woolfe et al. [6]