Supplementary Table 3: MSY pseudogenes*

Functional gene (progenitor) MSY pseudogene (derivative)
Name of functional gene Genbank accession # Chromosome of origin& Name of pseudogene
(if named)
Copy # on Y Processed (yes/no) MSY sequence class
18SrRNA X03205 21   1 unknown Other
ADPRTL1 AF057160 13 ADPRTL1P 1 no Other
AL080119 AL080119 1 1 yes X-transposed
AL110183 AL110183 21 1 unknown X-degenerate
APXL X83543 X APXLP 1 no X-degenerate
ARSD NM_009589 X ARSDP 1 no X-degenerate
ARSE X83573 X ARSEP 1 no X-degenerate
ARSF X97868 X ARSFP 1 no X-degenerate
ASS NM_000050 9 1 unknown X-degenerate
ADLICAN AF245505 X ADLICANP 1 no X-degenerate
Alpha7 AF029839 15 2 unknown Ampliconic
BCoR NM_020926 X BCoRP 1 no X-degenerate
BPY2 AF000980 Y 26 no Ampliconic
CASK AF032119 X CASKP 1 no X-degenerate
CDY AF000981 Y 27 no AZFa, ampliconic
CGI-137 AF151895 5 2 unknown Ampliconic
CRSP2 AB006651 X 1 no X-degenerate
CTBP2 AF016507 10 1 yes Other
EIF4A1 D13748 17 1 yes X-transposed
FAM8A1 AF097027 6 5 yes 5' end is in AZFa, 3' end in ampliconic
FLJ10842 NM_018238 7 1 unknown X-degenerate
FLJ20167 AK000174 5 1 unknown X-degenerate
FLJ21191 AK024844 X 1 unknown X-degenerate
GA X04098 3 2 yes Ampliconic
GADPH AF261085 12 1 unknown X-degenerate
GYG2 AF179615 X GYG2P 1 no X-degenerate
HS7 (HCS) M22877 7 1 unknown X-degenerate
HepG2 D16888 2 1 unknown Other
KAL1 M97252 X KALP 1 no X-degenerate
KIAA0008 D13633 14 1 yes X-transposed
KIAA0084 D42043 3 1 no Ampliconic
KIAA0306 AB002304 19 2 yes Ampliconic
KIAA0855 AB020662 15 2 no Ampliconic
KIAA1096 AB029019 1 1 unknown X-transposed
KRT18 NM_000224 12 1 yes X-transposed
LCC AF055479 3 1 unknown X-transposed
NF-L X05608 8 1 unknown X-degenerate
OA1 Z48804 X OA1P 1 no X-degenerate
OFD1 Y15164 X OFD1P2 15 no Ampliconic
PPP1R12B AB003062 1 PPP1R12BP 2 no Ampliconic
PRY AF000988 Y 4 no Ampliconic
PSIP1 AF063020 9 1 unknown X-degenerate
PSMA6 X59417 14 1 yes X-degenerate
RBMY1 X76060 Y 22 no Ampliconic
RBMY2 AF026564 Y 4 no Ampliconic
RPL26 NM_000987 17 1 yes X-transposed
RPL41 AB010874 12 2 unknown Ampliconic
RPS24 U12202 10 1 unknown X-degenerate
SFPQ X70944 1 1 yes X-degenerate
SH3P18 U61167 2 4 unknown Ampliconic
SLC25A15 NM_014252 13 SLC25A15P 1 no Other
SMCY U52191 Y 1 no X-degenerate
STS M16505 X STSP 1 no X-degenerate
TBL1Y AF332220 Y 1 no X-degenerate
TPTE AF007118 21 TPTEP 1 no Other
TSPY M98525 Y 5 no Ampliconic
TUB4q U83668 4 2 unknown Ampliconic
UBE2V1 U49278 20 1 yes X-transposed
UBH1 AF022789 13 1 yes X-transposed
USP9Y AF000986 Y 29 no Ampliconic
VDAC1 L06132 5 1 yes X-transposed
XG Z48519 X XGPY 1 no X-degenerate
XKRY AF000997 Y 6 no Ampliconic
ZNF43 NM_003423 19 ZNF381P 16 no Ampliconic
* Pseudogenes are defined as sequence showing significant homology to known genes, but lacking
   any evidence for transcription. For all listed pseudogenes at least one of the following is observed:
   mutations in splice sites, disrupted and shifted reading frame, partial loss of exons.
&Chromosomal assignment from GenBank annotations (when available) or from BLAST results against
   the non-redundant and high throughput GenBank databases.