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Table 1 Molecular genetic differences between humans and chimpanzees

From: Differences between human and chimpanzee genomes and their implications in gene expression, protein functions and biochemical properties of the two species

Human Chimpanzee
Karyotype
46 chromosomes. Chromosome 2 was formed by fusion of two ancestral chromosomes [9]. 48 chromosomes, including chromosomes 2a and 2b [9].
Large pericentric inversions in chromosomes 1 and 18 [10,11,12]. Large pericentric inversions in chromosomes 4, 5, 9, 12, 15–17 [10,11,12].
Two pseudoautosomal regions, PAR2 and PAR3 on Y chromosome [13,14,15].  
Different amounts of pericentric, paracentric, intercalary and Y type heterochromatin [9].
Deletions, insertions, copy number variations (~ 3% of genomes differences)
Several hundreds of species-specific processed pseudogenes [8, 16].
134 genes increased copy numbers, 6 decreased [17]. SRGAP2 duplicated with the formation of two truncated homologs SRGAP2B and SRGAP2C [18]. 37 genes increased copy numbers, 15 – decreased [17].
Deletion of 510 conserved regions. Among them: androgen receptor (AR) enhancer, tumor suppressor GADD45G enhancer, CMAHP exon, etc. [19, 20].
Human-specific mobile elements recombination/insertion-associated deletions: at least 492 Alu-associated deletions(~ 400 kb of excised DNA) [21], at least 73 LINE-associated deletions (~ 450 kb of excised DNA) [22, 23], at least 26 SVA-associated deletions (~ 46 kb of excised DNA) [24].
Deletion of 334 conserved regions [19].
Chimpanzee-specific mobile elements recombination/insertion- associated deletions: at least 663 Alu-associated deletions(~ 771 kb of excised DNA) [25].
Mobile elements
• Alu: ~ 5000 unique copies, AluYa5 и AluYb8 families prevail [8, 26, 27]
• LINE L1: ≥ 2000 of unique insertions [26, 28]
• SVA (SINE-VNTR-Alu): several thousands of specific insertions, two times more active retrotransposition [26, 27]. New family emerged - CpG-SVA or SVAF1 [29, 30].
• HERVs: ~ 140 unique insertions of HERV-K (HML-2) [31,32,33,34]. Several hundred copies of HERV-K (HML-2) К111 and several dozen copies of HERV-K (HML-2) K222 emerged due to recombination in centromeric and pericentromeric regions [35, 36].
• Alu: ~ 1500 unique copies, Alu Y and Yc1 families prevail [8, 26, 27]
• LINE L1: ≥ 2000 of unique insertions [26, 28]
• SVA: several thousands of specific insertions [26, 27]
• HERVs: ~ 45 unique insertions of HERV-K (HML-2) [37, 38]
• Two new families emerged – PtERV1 and PtERV2 (totally around 250 copies) [8, 39]
Single nucleotide alterations (substitutions, insertions, deletions): ~ 1.23% of genomes differences
Protein-coding sequences
• Different repertoires of olfactory receptor genes and pseudogenes, 25% out of ~ 400 active genes are species-specific [40].
• Highly diverged genes relate to immunity and cell recognition. Point mutations inactivated genes of T-cell gamma-receptor TCRGV10, caspase 12, mannose-binding lectin gene MBL1P, etc. [8, 41, 42].
• Species-specific mutations in genes responsible for sialic acids metabolism: ST6GAL1, ST6GALNAC3, ST6GALNAC4, ST8SIA2, HF1. Point mutations in genes SIGLEC11 and SIGLEC12 abrogated their sialic-binding activities [8, 43,44,45,46]
• Substitutions in language-associated gene FOXP2: Thr303Asn and Asn325Ser [43, 44].
• Quickly evolving brain size-related genes MCPH1 and ASPM [46, 47].
• Different repertoires of olfactory receptor genes and pseudogenes, 25% out of ~ 400 active genes are species-specific [40].
• Highly diverged genes relate to immunity and cell recognition [8, 41, 42]
• Species-specific mutations in genes responsible for sialic acids metabolism: ST6GAL1, ST6GALNAC3, ST6GALNAC4, ST8SIA2, HF1 [8]
Non-coding sequences
~  3000 of human accelerated regions: HARs and HACNs [48, 49]. HARS and HACNs are enriched in genes related to DNA interaction, transcriptional regulation and neuronal development [50]. NPAS3 (neuronal PAS domain-containing protein) gene contains 14 HARs. The most rapidly evolving regions HAR1 and HARE5 are located in brain-related genes: HAR1F/HAR1R-overlap and FZD8 [48, 49, 51].
~ 100 of human-specific enhancers activated in nervous tissues (hEANTs) [52]