| Linkage Group | Locus /Gene Name | Probe, Gene or Gene Product | References | Accession # |
| XII / XIII | GAPC | glyceraldehyde-3-phosphate dehydrogenase, (NAD) cytosolic, subunit C | Kersanach et al. (1994) | L27669 |
| XII / XIII | PF9/IDA1 | dynein heavy chain 1 | Myster et al. (1997) | U61364 |
| XII / XIII | CNC54 | cDNA fragment | This study | AF174532 |
| XII / XIII | CNB20 | cDNA fragment | This study | AF486824 |
| XII / XIII | CNA10 | cDNA fragment | This study | |
| XII / XIII | PSR1 | phosphorus metabolism regulatory protein | Wykoff et al. (1999) | AF174532 |
| XII / XIII | IDA4 | p28, dynein inner arm light chain | Ledizet and Piperno (1995) | Z48059 |
| XII / XIII | LF2 | LF2 / ULF2 gene | C. Amundsen and P. Lefebvre, unpublished results | |
| XII / XIII | CNC8 | cDNA corresponding to EST 963109F12 | This study | BI873562 |
| XII / XIII | CNC53 | cDNA corresponding to EST 894081D12 | This study | BE725171 |
| XII / XIII | M63 | gene involved in cytokinesis | J. Larson, L.-W. Tam and C. Silflow, unpublished results | |
| XII / XIII | GP330 | random genomic fragment | This study | |
| XII / XIII | GP31 | random genomic fragment | This study | |
| XII / XIII | ODA6 | IC70 dynein intermediate chain | Mitchell and Kang (1991) | X55382 |
| XII / XIII | PTX4 | gene involved in phototaxis | G. Pazour, unpublished results | |
| XII / XIII | EYE2 | gene required for eyespot assembly | Roberts et al. (2001) | AF233430 |
| XII / XIII | SAC3 | kinase regulating response to sulfur limitation | Davies et al. (1999) | AF100162 |
| XII / XIII | GP399 | random genomic fragment | This study | |
| XII / XIII | GP346D | random genomic fragment | This study | |
| XII / XIII | IC138 | inner arm dynein I1 subunit | P.Yang and W. Sale, unpublished results | |
| XII / XIII | GP227 | random genomic fragment | This study | |
| XII / XIII | ODA12 | LC2, 19 kDa outer arm dynein light chain | Pazour et al. (1999) | U89649 |
| XII / XIII | LC3 | LC3, 17 kDa dynein light chain | Patel - King et al. (1996) | U43610 |
| XII / XIII | GS2 | glutamine synthetase 2 (GS2) | Chen and Silflow (1996) | U46208 |
| XII / XIII | CALK | Chlamydomonas aurora-like kinase | Pan and Snell (2000) | AF199021 |
| XII / XIII | CNA38A | cDNA fragment | This study | |
| XII / XIII | ODA9 | IC78 dynein intermediate chain | Wilkerson et al. (1995) | U19120 |
| XII / XIII | 14-3-3 | 14-3-3 protein | Liebich and Voigt (1995) | X79445 |
| XII / XIII | LAO1 | L-amino acid oxidase catalytic subunit | Vallon and Wollman (1997) | U78797 |
| XII / XIII | TUB2 | beta2-tubulin | Youngblom et al. (1984) | K03281 |
| XII / XIII | RDB | roadblock protein; EST 1024060G02 | S. King, unpublished results | BG858985 |
| XII / XIII | GP114 | random genomic fragment | This study | |
| XII / XIII | CNC63 | cDNA fragment | This study | |
| XII / XIII | TUB1 | beta1-tubulin | Youngblom et al. (1984) | M10064 |