Supplementary Table 5: Analysis of sequence divergence in gene-gene and gene-pseudogene pairs

Gene pair Chr Ks (+/-s.d.) Ka (+/-s.d.) Ks/Ka DNA
divergence
(coding
region, %)
Protein
divergence
(%)
Sequence
compared
(bp)
GenBank
accession
numbers
X gene/Y gene: GYG2/GYG2P X 0.11 (+/-0.04) 0.053 (+/-0.021) 2 7.0 11.0 522 U94362/Yseq
ARSD/ARSDP X 0.092 (+/-0.022) 0.079 (+/-0.013) 1 7.9 14.2 1200 X83572/Yseq
ARSE/ARSEP X 0.043 (+/-0.017) 0.042 (+/-0.013) 1 4.4 9.0 636 X83573/Yseq
ARSF/ARSFP X 0.070 (+/-0.040) 0.070 (+/-0.020) 1 6.9 14.8 447 X97868/Yseq
ADLICAN/ADLICANP X 0.080 (+/-0.008) 0.050 (+/-0.004) 2 5.4 9.7 7953 AF245505/Yseq
PRKX/PRKY X 0.071 (+/-0.020) 0.034 (+/-0.010) 2 4.7 7.7 1017 X85545/Y15801
NLGN4X/NLGN4Y X 0.070 (+/-0.016) 0.006 (+/-0.002) 12 2.1 0.9 1947 AB033086/AB023168
STS/STSP X 0.15 (+/-0.03) 0.094 (+/-0.018) 2 10.7 18.6 1017 M16505/Yseq
VCX/VCY X 0.000 (+/-0.006) 0.045 (+/-0.021) 0 3.1 6.9 354 AF159127/AF000979
KAL1/KALP X 0.081 (+/-0.020) 0.062 (+/-0.011) 1 6.6 12.5 1659 M97252/Yseq
TBL1X/TBL1Y X 0.23 (+/-0.03) 0.045 (+/-0.010) 5 8.9 8.8 1569 Y12781/AF332220
OA1/OA1P X 0.13 (+/-0.06) 0.11 (+/-0.04) 1 10.8 17.0 267 Z48804/Yseq
APXL/APXLP X 0.26 (+/-0.03) 0.16 (+/-0.01) 2 16.5 27.9 2358 X83543/Yseq
AMELX/AMELY X 0.061 (+/-0.023) 0.058 (+/-0.018) 1 6.1 11.5 576 M86932/M86933
TMSB4X/TMSB4Y X 0.29 (+/-0.17) 0.036 (+/-0.021) 8 7.4 6.7 135 M17733/AF000989
OFD1/OFD1P2 X 0.19 (+/-0.03) 0.16 (+/-0.01) 1 15.6 29.7 2727 Y15164/Yseq
CXorf15/CYorf15A,B X 0.18 (+/-0.04) 0.17 (+/-0.03) 1 15.3 28.6 630 AK002071/AF332224/
AF332225
EIF1AX/EIF1AY X 0.32 (+/-0.08) 0.006 (+/-0.006) 53 8.0 1.4 435 L18960/AF000987
ZFX/ZFY X 0.19 (+/-0.03) 0.035 (+/-0.006) 5 6.9 7.0 2397 X59739/M30607
BCoR/BCoRP X 0.35 (+/-0.03) 0.20 (+/-0.01) 2 19.9 32.2 4722 NM_020926/Yseq
USP9X/USP9Y X 0.33 (+/-0.02) 0.045 (+/-0.004) 7 10.3 8.8 7641 X98296/AF000986
DBX/DBY X 0.40 (+/-0.05) 0.043 (+/-0.008) 9 11.4 7.7 1980 AF000982/AF000984
CASK/CASKP X 0.35 (+/-0.11) 0.24 (+/-0.05) 1 21.5 34.0 297 AF032119/Yseq
UTX/UTY X 0.26 (+/-0.02) 0.076 (+/-0.008) 3 11.2 13.6 4035 AF000992/AF000994
UBE1X/UBE1Y X 0.57 (+/-0.10) 0.068 (+/-0.017) 8 15.8 12.9 696 M58028/AJ003105
SMCX/SMCY X 0.47 (+/-0.03) 0.075 (+/-0.007) 6 15.4 13.1 4575 L25270/U52191
RPS4X/RPS4Y1 X 0.97 (+/-0.17) 0.047 (+/-0.012) 21 17.9 7.2 792 M58458/M58459
RPS4X/RPS4Y2 X 0.98 (+/-0.17) 0.051 (+/-0.014) 19 18.3 8.3 792 M58458/AF497481
TGIF2LX/TGIF2LY X 0.017 (+/-0.014) 0.008 (+/-0.005) 2 1.0 1.7 723 AF497480/AF332223
PCDH11X/PCDH11Y
short
X 0.010 (+/-0.045) 0.008 (+/-0.003) 1 0.9 1.9 3072 AB026187/AF332216
PCDH11X/PCDH11Y
long
X 0.010 (+/-0.036) 0.009 (+/-0.003) 1 1.0 1.8 3921 AF332218/AF332217
RBMX/RBMY1 X 0.93 (+/-0.16) 0.25 (+/-0.03) 4 28.4 39.3 1131 Z23064/X76059
SOX3/SRY X 1.25 (+/-0.41) 0.20 (+/-0.05) 6 27.4 28.7 264 X71135/X53772
Autosomal gene/
Y gene:
PPP1R12B/PPP1R12BP 1 0.034 (+/-0.014) 0.025 (+/-0.006) 1 2.8 5.8 1668 AB003062/Yseq
GOLGA2L/GOLGA2LY 15 0.035 (+/-0.017) 0.050 (+/-0.015) 1 4.5 9.4 510 AC010725/AF332229
CSPG4L/CSPG4LY 15 0.048 (+/-0.023) 0.032 (+/-0.014) 2 3.8 7.3 660 AC010725/AF332228
TPTE/TPTEP 21 0.047 (+/-0.017) 0.082 (+/-0.013) 1 6.8 15.8 1650 NM_013315/Yseq
ADPRTL1/ADPRTL1P 13 0.069 (+/-0.015) 0.074 (+/-0.011) 1 7.1 14.7 2313 NM_006437/Yseq
SLC25A15/SLC25A15P 13 0.070 (+/-0.037) 0.034 (+/-0.020) 2 4.4 7.1 339 NM_014252/Yseq
DAZL/DAZ 3 0.13 (+/-0.05) 0.084 (+/-0.024) 2 8.8 14.5 498 U65918/AF248480
KIAA0084/KIAA0084P 3 0.15 (+/-0.04) 0.01 (+/-0.02) 2 10.8 19.6 981 D42043/Yseq
ZNF43/ZNF381P 19 0.37 (+/-0.07) 0.39 (+/-0.04) 1 29.9 53.1 1236 NM_003423/Yseq
TSPYL/TSPY 6 0.71 (+/-0.16) 0.42 (+/-0.07) 2 35.4 52.7 495 AF042181/M98525
CDYL/CDY 6 0.75 (+/-0.09) 0.22 (+/-0.02) 3 26.5 35.4 1542 AF081259/AF000981
Y gene/Y gene RPS4Y1/RPS4Y2 Y 0.16 (+/-0.04) 0.031 (+/-0.011) 5 6.4 6.1 792 M58459/AF497481
TBL1Y/TBLY1P Y 0.17 (+/-0.04) 0.73 (+/-0.015) 2 9.5 14.9 927 AF332220/Yseq
SMCY/SMCYP Y 0.28 (+/-0.09) 0.30 (+/-0.06) 1 24.3 45.5 336 U52191/Yseq