Description of sequence changes: 
examples RNA-level

Last modified March 30, 2016

Since references to WWW-sites are not yet acknowledged as citations, please mention den Dunnen JT and Antonarakis SE (2000). Hum.Mutat. 15:7-12 when referring to these pages.



Within this page examples will be given for the description of sequence variations which are unique for RNA. For other examples go to those describing changes in DNA. Examples for protein level are given at the protein page. All examples are described relative to a Reference Sequence, here a coding DNA sequence.

Reference sequence RNA-level

Part of gene nucleotide numbering
Reference Sequence 
nucleotide numbering
coding DNA
Reference Sequence
 nucleotide numbering
Reference Sequence
5' gene flanking region 1 to 270 (-300 to -31)  -
exon 1 5' UTR 271 to 300 -30 to -1  -
coding region 301 to 312 1 to 12 1 to 4
intron 1 313 to 412 12+1 ... 12+50,
13-50 ... 13-1
exon 2 413 to 488 13 to 88 5 to 29 (30)
intron 2 489 to 689 88+1 ... 88+100,
89-100 ... 89-1 
exon 3 689 to 723 89 to 123 30 to 41
intron 3 contains rare alternatively spliced exon from 800 to 859 (coding DNA 123+77 to 123+136) 724 to 1023 123+1 ... 123+150,
124-150 ... 124-1 
exon 4 1024 to 1200 124 to 300 42 to 100
intron 4 1201 to 1600 300+1 ... 300+200,
301-200 ... 301-1 
exon 5 coding region 1601 to 1630 301 to 330 101 to 109
3' UTR, containing a (CA)7-stretch from nts 1700 to 1713 (coding DNA *71 to *83); poly-A addition site at 1825 (coding DNA *195) 1631 to 1850 *1 to *220 -
3' gene flanking region 1851 to 2000 (*221 to *370)

Reference sequence of imaginary gene used for the exaples given on this page. Nucleotide +1 in the coding DNA reference sequence is the A of the ATG translation initiation codon. Abbreviations used: nt = nucleotide, nts = nucleotides, UTR = untranslated region of the mRNA. For a picture of part of this hypothetical sequence see Figure.


It should be noted that the descriptions at RNA level, like those at protein level, are often deduced and not based on experimental evidence. Publications describing changes at RNA level should make it clear whether experimental proof was available or not. In fact, changes at RNA level should not be provided unless RNA was actually analysed, i.e. experimental proof is available. When changes are reported for which experimental proof is not available one should consider to list them between brackets.

Sequence changes at RNA level are basically described like those at the DNA level, with a few modifications;

RNA processing / initiation

Several changes at DNA level can influence the amount of RNA transcribed (e.g. changes altering the promoter sequence) or RNA processing (e.g. transcription initiation site, polyA-addition signal, polyA-addition site; for changes affecting RNA splicing see below). Unless experimental proof is available, the effect on RNA level should be reported as "?" (i.e. unknown or not analysed).  However, for many changes an effect on RNA will be very likely (e.g. when the respective sites are directly changed). In such cases, although RNA has not been analysed, one is tempted to list these changes and indicate the deduced effect. Suggested descriptions are (see Recommendations);


changes affecting splicing result on RNA-level either in a deletion (shift of a splice site to within an exon or skipping of a complete exon) or an insertion (shift of a splice site to within an intron or inclusion of an intronic sequence as a new exon). Such changes can be described following the rules to describe deletions and insertions (see DNA level). However, some additional changes might occur.

One change, more RNA molecules

When a change affects RNA-processing, yielding two or more transcripts, these are described between square brackets, separated by a  ","-character (see Recommendations

Large deletions

Large deletions involving the promoter region of the gene or the gene's 3'-end usually have an unpredictable effect on transcript level. In general, when the promoter is deleted no transcript will be produced (change described as "r.0"), unless another promoter is activated. The latter frequently occurs when a deletion fuses two genes which are directed in the same transcriptional orientation. When a deletion removes the gene's 3'-end, the transcript usually finds a new 3'-terminal exon. In addition to the changes which will affect the content of the transcript (sequences transcribed), most large deletions will also affect the transcript levels.

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