life cycle; these sequences occupy only a small fraction of the genome (<2%). noncoding dna is made up of all of those sequences (approx. 98% of the genome) that are not used to encode proteins. some noncoding dna contains genes for rna molecules with important biological functions (noncoding rna, for example ribosomal rna and transfer rna). the exploration of the function and evolutionary origin of noncoding dna is an important goal of contemporary genome research, including the encode (encyclopedia of dna elements) project, which aims to survey the entire human genome, using a variety of experimental tools whose results are indicative of molecular activity. it is however disputed whether molecular activity (transcription of dna into rna) alone implies that the rna produced has a meaningful biological function, since experiments have shown that random nonfunctional dna will also reproducibly recruit transcription factors resulting in transcription into nonfunctional rna. there is no consensus on what constitutes a "functional" element in the genome since geneticists, evolutionary biologists, and molecular biologists employ different definitions and methods. due to the ambiguity in the terminology, different schools of thought have emerged. in evolutionary definitions, "functional" dna, whether it is coding or non-coding, contributes to the fitness of the organism, and therefore is maintained by negative evolutionary pressure whereas "non-functional" dna has no benefit to the organism and therefore is under neutral selective pressure. this type of dna has been described as junk dna in genetic definitions, "functional" dna is related to how dna segments manifest by phenotype and "nonfunctional" is related to loss-of-function effects on the organism. in biochemical definitions, "functional" dna relates to dna sequences that specify molecular products (e.g. noncoding rnas) and biochemical activities with mechanistic roles in gene or genome regulation (i.e. dna sequences that impact cellular level activity such as cell type, condition, and molecular processes). there is no consensus in the literature on the amount of functional dna since, depending on how "function" is understood, ranges have been estimated from up to 90% of the human genome is likely nonfunctional dna (junk dna) to up to 80% of the genome is likely functional. it is also possible that junk dna may acquire a function in the future and therefore may play a role in evolution, but this is likely to occur only very rarely. finally dna that is deliterious to the organism and is under negative selective pressure is called garbage dna. because non-coding dna greatly outnumbers coding dna, the concept of the sequenced genome has become a more focused analytical concept than the classical concept of the dna-coding gene. coding sequences (protein-coding genes) human genes categorized by function of the transcribed proteins, given both as number of encoding genes and percentage of all genes protein-coding sequences represent the most widely studied and best understood component of the human genome. these sequences ultimately lead to the production of all human proteins, although several biological processes (e.g. dna rearrangements and alternative pre-mrna splicing) can lead to the production of many more unique proteins than the number of protein-coding genes. the complete modular protein-coding capacity of the genome is contained within the exome, and consists of dna sequences encoded by exons that can be translated into proteins. because of its biological importance, and the fact that it constitutes less than 2% of the genome, sequencing of the exome was the first major milepost of the human genome project. number of protein-coding genes. about 20,000 human proteins have been annotated in databases such as uniprot. historically, estimates for the number of protein genes have varied widely, ranging up to 2,000,000 in the late 1960s, but several researchers pointed out in the early 1970s that the estimated mutational load from deleterious mutations placed an upper limit of approximately 40,000 for the total number of functional loci (this includes protein-coding and functional non-coding genes). the number of human protein-coding genes is not significantly larger than that of many less complex organisms, such as the roundworm and the fruit fly. this difference may result from the extensive use of alternative pre-mrna splicing in humans, which provides the ability to build a very large number of modular proteins through the selective incorporation of exons. protein-coding capacity per chromosome. protein-coding genes are distributed unevenly across the chromosomes, ranging from a few dozen to more than 2000, with an especially high gene density within chromosomes 1, 11, and 19. each chromosome contains various gene-rich and gene-poor regions, which may be correlated with chromosome bands and gc-content. the significance of these nonrandom patterns of gene density is not well understood. size of protein-coding genes. the size of protein-coding genes within the human genome shows enormous variability. for example, the gene for histone h1a (hist1hia) is relatively small and simple, lacking introns and encoding an 781 nucleotide-long mrna that produces a 215 amino acid protein from its 648 nucleotide open reading frame. dystrophin (dmd) was the largest protein-coding gene in the 2001 human reference genome, spanning a total of 2.2 million nucleotides, while more recent systematic meta-analysis of updated human genome data identified an even larger protein-coding gene, rbfox1 (rna binding protein, fox-1 homolog 1), spanning a total of 2.47 million nucleotides. titin (ttn) has the longest coding sequence (114,414 nucleotides), the largest number of exons (363), and the longest single exon (17,106 nucleotides). as estimated based on a curated set of protein-coding genes over the whole genome, the median size is 26,288 nucleotides (mean = 66,577), the median exon size, 133 nucleotides (mean = 309), the median number of exons, 8 (mean = 11), and the median encoded protein is 425 amino acids (mean = 553) in length. examples of human protein-coding genes proteinchromgenelengthexonsexon lengthintron lengthalt splicing breast cancer type 2 susceptibility protein13brca283,7362711,38672,350yes cystic fibrosis transmembrane conductance regulator7cftr202,881274,440198,441yes cytochrome bmtmtcyb1,14011,1400no dystrophinxdmd2,220,3817910,5002,209,881yes glyceraldehyde-3-phosphate dehydrogenase12gapdh4,44491,4253,019yes hemoglobin beta subunit11hbb1,6053626979no histone h1a6hist1h1a78117810no titin2ttn281,434364104,301177,133yes noncoding dna (ncdna) noncoding dna is defined as all of the dna sequences within a genome that are not found within protein-coding exons, and so are never represented within the amino acid sequence of expressed proteins. by this definition, more than 98% of the human genomes is composed of ncdna. numerous classes of noncoding dna have been identified, including genes for noncoding rna (e.g. trna and rrna), pseudogenes, introns, untranslated regions of mrna, regulatory dna sequences, repetitive dna sequences, and sequences related to mobile genetic elements. numerous sequences that are included within genes are also defined as noncoding dna. these include genes for noncoding rna (e.g. trna, rrna), and untranslated components of protein-coding genes (e.g. introns, and 5' and 3' untranslated regions of mrna). protein-coding sequences (specifically, coding exons) constitute less than 1.5% of the human genome. in addition, about 26% of the human genome is introns. aside from genes (exons and introns) and known regulatory sequences (8–20%), the human genome contains regions of noncoding dna. the exact amount of noncoding dna that plays a role in cell physiology has been hotly debated. recent analysis by the encode project indicates that 80% of the entire human genome is either transcribed, binds to regulatory proteins, or is associated with some other biochemical activity. it however remains controversial whether all of this biochemical activity contributes to cell physiology, or whether a substantial portion of this is the result of transcriptional and biochemical noise, which must be actively filtered out by the organism. excluding protein-coding sequences, introns, and regulatory regions, much of the non-coding dna is composed of: many dna sequences that do not play a role in gene expression have important biological functions. comparative genomics studies indicate that about 5% of the genome contains sequences of noncoding dna that are highly conserved, sometimes on time-scales representing hundreds of millions of years, implying that these noncoding regions are under strong evolutionary pressure and purifying selection. many of these sequences regulate the structure of chromosomes by limiting the regions of heterochromatin formation and regulating structural features of the chromosomes, such as the telomeres and centromeres. other noncoding regions serve as origins of dna replication. finally several regions are transcribed into functional noncoding rna that regulate the expression of protein-coding genes (for example), mrna translation and stability (see mirna), chromatin structure (including histone modifications, for example), dna methylation (for example), dna recombination (for example), and cross-regulate other noncoding rnas (for example). it is also likely that many transcribed noncoding regions do not serve any role and that this transcription is the product of non-specific rna polymerase activity. pseudogenes pseudogenes are inactive copies of protein-coding genes, often generated by gene duplication, that have become nonfunctional through the accumulation of inactivating mutations. the number of pseudogenes in the human genome is on the order of 13,000, and in some chromosomes is nearly the same as the number of functional protein-coding genes. gene duplication is a major mechanism through which new genetic material is generated during molecular evolution. for example, the olfactory receptor gene family is one of the best-documented examples of pseudogenes in the human genome. more than 60 percent of the genes in this family are non-functional pseudogenes in humans. by comparison, only 20 percent of genes in the mouse olfactory receptor gene family are pseudogenes. research suggests that this is a species-specific characteristic, as the most closely related primates all have proportionally fewer pseudogenes. this genetic discovery helps to explain the less acute sense of smell in humans relative to other mammals. genes for noncoding rna (ncrna) noncoding rna molecules play many essential roles in cells, especially in the many reactions of protein synthesis and rna processing. noncoding rna include trna, ribosomal rna, microrna, snrna and other non-coding rna genes including about 60,000 long non-coding rnas (lncrnas). although the number of reported lncrna genes continues to rise and the exact number in the human genome is yet to be defined, many of them are argued to be non-functional. many ncrnas are critical elements in gene regulation and expression. noncoding rna also contributes to epigenetics, transcription, rna splicing, and the translational machinery. the role of rna in genetic regulation and disease offers a new potential level of unexplored genomic complexity. introns and untranslated regions of mrna in addition to the ncrna molecules that are encoded by discrete genes, the initial transcripts of protein coding genes usually contain extensive noncoding sequences, in the form of introns, 5'-untranslated regions (5'-utr), and 3'-untranslated regions (3'-utr). within most protein-coding genes of the human genome, the length of intron sequences is 10- to 100-times the length of exon sequences. regulatory dna sequences the human genome has many different regulatory sequences which are crucial to controlling gene expression. conservative estimates indicate that these sequences make up 8% of the genome, however extrapolations from the encode project give that 20-40% of the genome is gene regulatory sequence. some types of non-coding dna are genetic "switches" that do not encode proteins, but do regulate when and where genes are expressed (called enhancers). regulatory sequences have been known since the late 1960s. the first identification of regulatory sequences in the human genome relied on recombinant dna technology. later with the advent of genomic sequencing, the identification of these sequences could be inferred by evolutionary conservation. the evolutionary branch between the primates and mouse, for example, occurred 70–90 million years ago. so computer comparisons of gene sequences that identify conserved non-coding sequences will be an indication of their importance in duties such as gene regulation. other genomes have been sequenced with the same intention of aiding conservation-guided methods, for exampled the pufferfish genome. however, regulatory sequences disappear and re-evolve during evolution at a high rate. as of 2012, the efforts have shifted toward finding interactions between dna and regulatory proteins by the technique chip-seq, or gaps where the dna is not packaged by histones (dnase hypersensitive sites), both of which tell where there are active regulatory sequences in the investigated cell type. repetitive dna sequences repetitive dna sequences comprise approximately 50% of the human genome. about 8% of the human genome consists of tandem dna arrays or tandem repeats, low complexity repeat sequences that have multiple adjacent copies (e.g. "cagcagcag..."). the tandem sequences may be of variable lengths, from two nucleotides to tens of nucleotides. these sequences are highly variable, even among closely related individuals, and so are used for genealogical dna testing and forensic dna analysis. repeated sequences of fewer than ten nucleotides (e.g. the