human genome human genome the human genome is a complete set of nucleic acid sequences for humans, encoded as dna within the 23 chromosome pairs in cell nuclei and in a small dna molecule found within individual mitochondria. these are usually treated separately as the nuclear genome and the mitochondrial genome. human genomes include both protein-coding dna sequences and various types of dna that does not encode proteins. the latter is a diverse category that includes dna coding for non-translated rna, such as that for ribosomal rna, transfer rna, ribozymes, small nuclear rnas, and several types of regulatory rnas. it also includes promoters and their associated gene-regulatory elements, dna playing structural and replicatory roles, such as scaffolding regions, telomeres, centromeres, and origins of replication, plus large numbers of transposable elements, inserted viral dna, non-functional pseudogenes and simple, highly-repetitive sequences. introns make up a large percentage of non-coding dna. some of this non-coding dna is non-functional junk dna, such as pseudogenes, but there is no firm consensus on the total amount of junk dna. for a non-technical introduction to the topic, see introduction to genetics. genomic informationschematic representation of the human diploid karyotype, showing the organization of the genome into chromosomes, as well as annotated bands and sub-bands as seen on g banding. this drawing shows both the female (xx) and male (xy) versions of the 23rd chromosome pair. chromosomal changes during the cell cycle are displayed at top center. the mitochondrial genome is shown to scale at bottom left.ncbi genome id51ploidydiploidgenome size3,117,275,501 base pairs (bp)number of chromosomes23 pairs haploid human genomes, which are contained in germ cells (the egg and sperm gamete cells created in the meiosis phase of sexual reproduction before fertilization) consist of 3,054,815,472 dna base pairs (if x chromosome is used), while female diploid genomes (found in somatic cells) have twice the dna content. while there are significant differences among the genomes of human individuals (on the order of 0.1% due to single-nucleotide variants and 0.6% when considering indels), these are considerably smaller than the differences between humans and their closest living relatives, the bonobos and chimpanzees (~1.1% fixed single-nucleotide variants and 4% when including indels). size in basepairs can vary too; the telomere length decreases after every round of dna replication. although the sequence of the human genome has been completely determined by dna sequencing in 2022 (including methylation), it is not yet fully understood. most, but not all, genes have been identified by a combination of high throughput experimental and bioinformatics approaches, yet much work still needs to be done to further elucidate the biological functions of their protein and rna products (in particular, annotation of the complete chm13v2.0 sequence is still ongoing). and yet, overlapping genes are quite common, in some cases allowing two protein coding genes from each strand to reuse base pairs twice (for example, genes dcdc2 and kaag1). recent results suggest that most of the vast quantities of noncoding dna within the genome have associated biochemical activities, including regulation of gene expression, organization of chromosome architecture, and signals controlling epigenetic inheritance. there are also a significant number of retroviruses in human dna, at least 3 of which have been proven to possess an important function (i.e., hiv-like herv-k, herv-w, and herv-frd play a role in placenta formation by inducing cell-cell fusion). in 2003, scientists reported the sequencing of 85% of the entire human genome, but as of 2020 at least 8% was still missing. in 2021, scientists reported sequencing the complete female genome (i.e., without the y chromosome). this sequence identified 19,969 protein-coding sequences, accounting for approximately 1.5% of the genome, and 63,494 genes in total, most of them being non-coding rna genes. the genome consists of regulatory dna sequences, lines, sines, introns, and sequences for which as yet no function has been determined. the human y chromosome, consisting of 62,460,029 base pairs from a different cell line and found in all males, was sequenced completely in january 2022. in 2023, a draft human pangenome reference was published. it is based on 47 genomes from persons of varied ethnicity. plans are underway for an improved reference capturing still more biodiversity from a still wider sample. sequencing the first human genome sequences were published in nearly complete draft form in february 2001 by the human genome project and celera corporation. completion of the human genome project's sequencing effort was announced in 2004 with the publication of a draft genome sequence, leaving just 341 gaps in the sequence, representing highly-repetitive and other dna that could not be sequenced with the technology available at the time. the human genome was the first of all vertebrates to be sequenced to such near-completion, and as of 2018, the diploid genomes of over a million individual humans had been determined using next-generation sequencing. these data are used worldwide in biomedical science, anthropology, forensics and other branches of science. such genomic studies have led to advances in the diagnosis and treatment of diseases, and to new insights in many fields of biology, including human evolution. by 2018, the total number of genes had been raised to at least 46,831, plus another 2300 micro-rna genes. a 2018 population survey found another 300 million bases of human genome that was not in the reference sequence. prior to the acquisition of the full genome sequence, estimates of the number of human genes ranged from 50,000 to 140,000 (with occasional vagueness about whether these estimates included non-protein coding genes). as genome sequence quality and the methods for identifying protein-coding genes improved, the count of recognized protein-coding genes dropped to 19,000–20,000. in june 2016, scientists formally announced hgp-write, a plan to synthesize the human genome. in 2022 the telomere-to-telomere (t2t) consortium reported the complete sequence of a human female genome, filling all the gaps in the x chromosome (2020) and the 22 autosomes (may 2021). the previously unsequenced parts contain immune response genes that help to adapt to and survive infections, as well as genes that are important for predicting drug response. the completed human genome sequence will also provide better understanding of human formation as an individual organism and how humans vary both between each other and other species. achieving completeness although the 'completion' of the human genome project was announced in 2001, there remained hundreds of gaps, with about 5–10% of the total sequence remaining undetermined. the missing genetic information was mostly in repetitive heterochromatic regions and near the centromeres and telomeres, but also some gene-encoding euchromatic regions. there remained 160 euchromatic gaps in 2015 when the sequences spanning another 50 formerly-unsequenced regions were determined. only in 2020 was the first truly complete telomere-to-telomere sequence of a human chromosome determined, namely of the x chromosome. the first complete telomere-to-telomere sequence of a human autosomal chromosome, chromosome 8, followed a year later. the complete human genome (without y chromosome) was published in 2021, while with y chromosome in january 2022. in 2023, a draft human pangenome reference was published. it is based on 47 genomes from persons of varied ethnicity. plans are underway for an improved reference capturing still more biodiversity from a still wider sample. molecular organization and gene content the total length of the human reference genome does not represent the sequence of any specific individual. the genome is organized into 22 paired chromosomes, termed autosomes, plus the 23rd pair of sex chromosomes (xx) in the female and (xy) in the male. the haploid genome is 3 054 815 472 base pairs, when the x chromosome is included, and 2 963 015 935 base pairs when the y chromosome is substituted for the x chromosome. these chromosomes are all large linear dna molecules contained within the cell nucleus. the genome also includes the mitochondrial dna, a comparatively small circular molecule present in multiple copies in each mitochondrion. human reference data, by chromosome chromo-somelengthbasepairsvaria-tionsprotein-codinggenespseudo-genestotallongncrnatotalsmallncrnamirnarrnasnrnasnornamiscncrnalinkscentromereposition(mbp)cumu-lative(%) 18.5 cm248,387,32812,151,14620581220120049613466221145192ebi1257.9 28.3 cm242,696,75212,945,96513091023103737511540161117176ebi93.316.2 36.7 cm201,105,94810,638,7151078763711298992913887134ebi9123 46.5 cm193,574,94510,165,685752727657228922412056104ebi50.429.6 56.2 cm182,045,4399,519,995876721844235832510661119ebi48.435.8 65.8 cm172,126,6289,130,4761048801639234812611173105ebi6141.6 75.4 cm160,567,4288,613,29898988560520890249076143ebi59.947.1 85.0 cm146,259,3318,221,5206776137352148028865282ebi45.652 94.8 cm150,617,2476,590,8117866614911906919665196ebi4956.3 104.6 cm134,758,1347,223,9447335685792046432875689ebi40.260.9 114.6 cm135,127,7697,535,37012988217102336324747697ebi53.765.4 124.5 cm133,324,5487,228,1291034617848227722710662115ebi35.870 133.9 cm113,566,6865,082,5743273723971044216453475ebi17.973.4 143.6 cm101,161,4924,865,9508305235332399210659779ebi17.676.4 153.5 cm99,753,1954,515,07661351063925078136313693ebi1979.3 163.1 cm96,330,3745,101,7028734657991875232535851ebi36.682 172.8 cm84,276,8974,614,97211975318342356115807199ebi2484.8 182.7 cm80,542,5384,035,9662702474531093213513641ebi17.287.4 192.0 cm61,707,3643,858,269147251262817911013293161ebi26.589.3 202.1 cm66,210,2553,439,6215442493841315715463768ebi27.591.4 211.6 cm45,090,6822,049,69723418530571165211924ebi13.292.6 221.7 cm51,324,9262,135,31148832435778315232362ebi14.793.8 x5.3 cm154,259,5665,753,881842874271258128228564100ebi60.699.1 y2.0 cm62,460,029211,6437138871301571738ebi10.4100 mtdna5.4 μm16,56992913002402000ebin/a100 hapl 1-23 + x104 cm3,054,815,47220328142121465649831741523192715182205 hapl 1-23 + y101 cm2,963,015,93519557137261445647551628508185914572113 dipl + mt♀208.23 cm6,109,647,513406692842429312999034821048385430364410 dipl + mt♂205.00 cm6,017,847,976398982793829112976233691033378629754318 original analysis published in the ensembl database at the european bioinformatics institute (ebi) and wellcome trust sanger institute. chromosome lengths estimated by multiplying the number of base pairs (of older reference genome, not chm13v2.0) by 0.34 nanometers (distance between base pairs in the most common structure of the dna double helix; a recent estimate of human chromosome lengths based on updated data reports 205.00 cm for the diploid male genome and 208.23 cm for female, corresponding to weights of 6.41 and 6.51 picograms (pg), respectively). number of proteins is based on the number of initial precursor mrna transcripts, and does not include products of alternative pre-mrna splicing, or modifications to protein structure that occur after translation. variations are unique dna sequence differences that have been identified in the individual human genome sequences analyzed by ensembl as of december 2016. the number of identified variations is expected to increase as further personal genomes are sequenced and analyzed. in addition to the gene content shown in this table, a large number of non-expressed functional sequences have been identified throughout the human genome (see below). links open windows to the reference chromosome sequences in the ebi genome browser. small non-coding rnas are rnas of as many as 200 bases that do not have protein-coding potential. these include: micrornas, or mirnas (post-transcriptional regulators of gene expression), small nuclear rnas, or snrnas (the rna components of spliceosomes), and small nucleolar rnas, or snorna (involved in guiding chemical modifications to other rna molecules). long non-coding rnas are rna molecules longer than 200 bases that do not have protein-coding potential. these include: ribosomal rnas, or rrnas (the rna components of ribosomes), and a variety of other long rnas that are involved in regulation of gene expression, epigenetic modifications of dna nucleotides and histone proteins, and regulation of the activity of protein-coding genes. small discrepancies between total-small-ncrna numbers and the numbers of specific types of small ncnras result from the former values being sourced from ensembl release 87 and the latter from ensembl release 68. the number of genes in the human genome is not entirely clear because the function of numerous transcripts remains unclear. this is especially true for non-coding rna. the number of protein-coding genes is better known but there are still on the order of 1,400 questionable genes which may or may not encode functional proteins, usually encoded by short open reading frames. discrepancies in human gene number estimates among different databases, as of july 2018 gencode ensembl refseq chess protein-coding genes 19,901 20,376 20,345 21,306 lncrna genes 15,779 14,720 17,712 18,484 antisense rna 5501 28 2694 miscellaneous rna 2213 2222 13,899 4347 pseudogenes 14,723 1740 15,952 total transcripts 203,835 203,903 154,484 328,827 number of genes (orange) and base pairs (green, in millions) on each chromosome information content the haploid human genome (23 chromosomes) is about 3 billion base pairs long and contains around 30,000 genes. since every base pair can be coded by 2 bits, this is about 750 megabytes of data. an individual somatic (diploid) cell contains twice this amount, that is, about 6 billion base pairs. males have fewer than females because the y chromosome is about 62 million base pairs whereas the x is about 154 million. since individual genomes vary in sequence by less than 1% from each other, the variations of a given human's genome from a common reference can be losslessly compressed to roughly 4 megabytes. the entropy rate of the genome differs significantly between coding and non-coding sequences. it is close to the maximum of 2 bits per base pair for the coding sequences (about 45 million base pairs), but less for the non-coding parts. it ranges between 1.5 and 1.9 bits per base pair for the individual chromosome, except for the y chromosome, which has an entropy rate below 0.9 bits per base pair. coding vs. noncoding dna the content of the human genome is commonly divided into coding and noncoding dna sequences. coding dna is defined as those sequences that can be transcribed into mrna and translated into proteins during the human