Research Article

A Draft Sequence of the Neandertal Genome

Science  07 May 2010:
Vol. 328, Issue 5979, pp. 710-722
DOI: 10.1126/science.1188021
Table 2

Amino acid changes that are fixed in present-day humans but ancestral in Neandertals. The table is sorted by Grantham scores (GS). Based on the classification proposed by Li et al. in (87), 5 amino acid substitutions are radical (>150), 7 moderately radical (101 to 150), 33 moderately conservative (51 to 100) and 32 conservative (1 to 50). One substitution creates a stop codon. Genes showing multiple substitutions have bold SwissProt identifiers. (Table S15 shows the human and chimpanzee genome coordinates, additional database identifiers, and the respective bases.) Genes with two fixed amino acids are indicated in bold.

RPTN785*/RMultifunctional epidermal matrix protein
GREB11164R/C180Response gene in estrogen receptor–regulated pathway
OR1K1267R/C180Olfactory receptor, family 1, subfamily K, member 1
SPAG17431Y/D160Involved in structural integrity of sperm central apparatus axoneme
NLRX1330Y/D160Modulator of innate immune response
NSUN378S/F155Protein with potential SAM-dependent methyl-transferase activity
RGS16197D/A126Retinally abundant regulator of G-protein signaling
BOD1L2684G/R125Biorientation of chromosomes in cell division 1-like
CF170505S/C112Uncharacterized protein: C6orf170
STEA1336C/S112Metalloreductase, six transmembrane epithelial antigen of prostate 1
F16A2630R/S110Uncharacterized protein: family with sequence similarity 160, member A2
LTK569R/S110Leukocyte receptor tyrosine kinase
BEND2261V/G109Uncharacterized protein: BEN domain-containing protein 2
O52W151P/L98Olfactory receptor, family 52, subfamily W, member 1
CAN15427L/P98Small optic lobes homolog, linked to visual system development
SCAP140I/T89Escort protein required for cholesterol as well as lipid homeostasis
TTF1474I/T89RNA polymerase I termination factor
OR5K4175H/D81Olfactory receptor, family 5, subfamily K, member 4
SCML1202T/M81Putative polycomb group (PcG) protein
TTL10394K/T78Probable tubulin polyglutamylase, forming polyglutamate side chains on tubulin
AFF3516S/P74Putative transcription activator, function in lymphoid development/oncogenesis
EYA2131S/P74Tyrosine phosphatase, dephosphorylating “Tyr-142” of histone H2AX
NOP14493T/R71Involved in nucleolar processing of pre-18S ribosomal RNA
PRDM101129N/T65PR domain containing 10, may be involved in transcriptional regulation
BTLA197N/T65B and T lymphocyte attenuator
O2AT4224V/A64Olfactory receptor, family 2, subfamily AT, member 4
CAN15356V/A64Small optic lobes homolog, linked to visual system development
ACCN4160V/A64Amiloride-sensitive cation channel 4, expressed in pituitary gland
PUR8429V/A64Adenylsuccinate lyase (purine synthesis)
MCHR2324A/V64Receptor for melanin-concentrating hormone, coupled to G proteins
AHR381V/A64Aromatic hydrocarbon receptor, a ligand-activated transcriptional activator
FAAH1476A/G60Fatty acid amide hydrolase
SPAG171415T/A58Involved in structural integrity of sperm central apparatus axoneme
ZF106697A/T58Zinc finger protein 106 homolog / SH3-domain binding protein 3
CAD16342T/A58Calcium-dependent, membrane-associated glycoprotein (cellular recognition)
K1C16306T/A58Keratin, type I cytoskeletal 16 (expressed in esophagus, tongue, hair follicles)
LIMS2360T/A58Focal adhesion protein, modulates cell spreading and migration
ZN502184T/A58Zinc finger protein 502, may be involved in transcriptional regulation
MEPE391A/T58Matrix extracellular phosphoglycoprotein, putative role in mineralization
FSTL4791T/A58Follistatin-related protein 4 precursor
SNTG1241T/S58Syntrophin, gamma 1; binding/organizing subcellular localization of proteins
RPTN735K/E56Multifunctional epidermal matrix protein
BCL9L543S/G56Nuclear cofactor of beta-catenin signaling, role in tumorigenesis
SSH21033S/G56Protein phosphatase regulating actin filament dynamics
PEG31521S/G56Apoptosis induction in cooperation with SIAH1A
DJC28290K/Q53DnaJ (Hsp40) homolog, may have role in protein folding or as a chaperone
CLTR250F/V50Receptor for cysteinyl leukotrienes, role in endocrine and cardiovascular systems
KIF15827N/S46Putative kinesin-like motor enzyme involved in mitotic spindle assembly
SPOC1355Q/R43Uncharacterized protein: SPOC domain containing 1
TTF1229R/Q43RNA polymerase I termination factor
F166A134T/P38Uncharacterized protein: family with sequence similarity 166, member A
CL066426V/L32Uncharacterized protein: chromosome 12 open reading frame 66
PCD16763E/Q29Calcium-dependent cell-adhesion protein, fibroblasts expression
TRPM51088I/V29Voltage-modulated cation channel (VCAM), central role in taste transduction
S36A4330H/R29Solute carrier family 36 (proton/amino acid symporter)
GP132328E/Q29High-affinity G-protein couple receptor for lysophosphatidylcholine (LPC)
ZFY26237H/R29Zinc finger FYVE domain-containing, associated with spastic paraplegia-15
CALD1671I/V29Actin- and myosin-binding protein, regulation of smooth muscle contraction
CDCA2606I/V29Regulator of chromosome structure during mitosis
GPAA1275E/Q29Glycosylphosphatidylinositol anchor attachment protein
ARSF200I/V29Arylsulfatase F precursor, relevant for composition of bone and cartilage matrix
OR4D9303R/K26Olfactory receptor, family 4, subfamily D, member 9
EMIL2155R/K26Elastin microfibril interface-located protein (smooth muscle anchoring)
PHLP216K/R26Putative modulator of heterotrimeric G proteins
TKTL1317R/K26Transketolase-related protein
MIIP280H/Q24Inhibits glioma cells invasion, down-regulates adhesion and motility genes
SPTA1265N/D23Constituent of cytoskeletal network of the erythrocyte plasma membrane
PCD16777D/N23Calcium-dependent cell-adhesion protein, fibroblasts expression
CS028326L/F22Uncharacterized protein: chromosome 19 open reading frame 28
PIGZ425L/F22Mannosyltransferase for glycosylphosphatidylinositol-anchor biosynthesis
DISP11079V/M21Segment-polarity gene required for normal Hedgehog (Hh) signaling
RNAS744M/V21Protein with RNase activity for broad-spectrum of pathogenic microorganisms
KR241205V/M21Keratin-associated protein, formation of a rigid and resistant hair shaft
SPLC3108I/M10Short palate, lung, and nasal epithelium carcinoma-associated protein
NCOA6823I/M10Hormone-dependent coactivation of several receptors
WWC2479M/I10Uncharacterized protein: WW, C2, and coiled-coil domain containing 2
ASCC1301E/D0Enhancer of NF-kappa-B, SRF, and AP1 transactivation
PROM2458D/E0Plasma membrane protrusion in epithelial and nonepithelial cells