Table 1.
Oyster Homeobox Genes
| Classes | Gene Family | Gene Name | Gene Model |
|---|---|---|---|
| ANTP | Cdx | Cdx | CGI_10023003 |
| Evx | Evx1 | CGI_10013056 | |
| Evx | Evx2 | CGI_10013058 | |
| Gbx | Gbx | CGI_10012203 | |
| Gsx | Gsx | CGI_10015548 | |
| Hox1 | Hox1 | CGI_10024083 | |
| Hox2 | Hox2 | CGI_10024086 | |
| Hox3 | Hox3 | CGI_10024087 | |
| Hox4 | Hox4 | CGI_10024091 | |
| Hox5 | Hox5 | scaffold801_482925 _483164 | |
| Hox6-8 | Lox5 | CGI_10026565 | |
| Hox6-8 | Lox2 | CGI_10018592 | |
| Hox6-8 | Lox4 | CGI_10026562 | |
| Hox9-13(15) | Post1 | CGI_10027385 | |
| Hox9-13(15) | Post2 | CGI_10027388 | |
| Meox | Hrox | CGI_10014888 | |
| Mnx | Mnx1 | CGI_10026625 | |
| Mnx | Mnx2 | scaffold313_810611 _810757 | |
| Pdx | Xlox | CGI_10015546 | |
| Barhl | BarH1 | CGI_10009941 | |
| Barhl | BarH2 | CGI_10009942 | |
| Barhl | BarH3 | CGI_10009943 | |
| Barx | Barx | CGI_10004014 | |
| Bsx | Bsx | CGI_10008107 | |
| Dbx | Dbx | CGI_10002480 | |
| Dlx | Dlx | CGI_10016653 | |
| Emx | Emx1 | CGI_10018603 | |
| Emx | Emx2 | CGI_10025052 | |
| Emx | Emx3 | CGI_10025053 | |
| En | En1 | CGI_10012208 | |
| En | En2 | CGI_10012209 | |
| Hbn | Hbn | CGI_10011181 | |
| Hhex | Hex | CGI_10025054 | |
| Hlx | Hlx | CGI_10013972 | |
| Lbx | Lbx | CGI_10010398 | |
| Msx | Msx | CGI_10023979 | |
| Msxlx | Msxlx | CGI_10013606 | |
| Nk1 | Nk1 | CGI_10025189 | |
| Nk2.1 | Nkx2.1 | CGI_10021129 | |
| Nk2.2 | Nk2.2 | CGI_10026839 | |
| Nk3 | Nk3 | CGI_10023919 | |
| Nk4 | Nk4 | CGI_10019417 | |
| Nk5/Hmx | Hmx1 | CGI_10013448 | |
| Nk5/Hmx | Hmx2 | CGI_10027035 | |
| Nk6 | Nk6 | CGI_10028825 | |
| Nk7 | Nk7 | CGI_10027184 | |
| Noto | Noto | CGI_10013404 | |
| Ro | Ro | CGI_10005958 | |
| Tlx | Tlx1 | CGI_10020596 | |
| Tlx | Tlx2 | CGI_10020599 | |
| Vax | Vax | CGI_10020700 | |
| ANTP_NKL Clade I | Cgi_NKL | CGI_10028802 | |
| PRD | Arx | Arx | CGI_10028810 |
| Dmbx | Dmbx | CGI_10011833 | |
| Drgx | Drgx | CGI_10007626 | |
| Gsc | Gsc1 | CGI_10007832 | |
| Gsc | Gsc2 | CGI_10026711 | |
| Gsc | Gsc3 | scaffold42840_31020 _31181 | |
| Hopx | Hopx | CGI_10009529 | |
| Otp | Otp | CGI_10021751 | |
| Otx | Otx | CGI_10015784 | |
| Pax3/7 | Pax3/7 | CGI_10026438 | |
| Pax4/6 | Pax4/6 | CGI_10020873 | |
| Pax4/6 | Pax6 | CGI_10027695 | |
| Pitx | Pitx | CGI_10018398 | |
| Prop | Prop | CGI_10006125 | |
| Prrx | Prxx | CGI_10021523 | |
| Rax | Rax | CGI_10028663 | |
| Repo | Repo | CGI_10005826 | |
| Shox | Shox | CGI_10012343 | |
| Uncx | Uncx | CGI_10007529 | |
| Vsx | Vsx1 | CGI_10010562 | |
| Vsx | Vsx2 | CGI_10010563 | |
| PRD Clade IV | Cgi_PRD1 | CGI_10017003 | |
| n.d. | Cgi_PRD2 | CGI_10012650 | |
| PRD Clade VI | Cgi_PRD3 | CGI_10009720 | |
| PRD Clade V | Cgi_PRD4 | CGI_10003333 | |
| PRD Clade V | Cgi_PRD5 | CGI_10013213 | |
| PRD Clade I | Cgi_PRD6 | CGI_10015407 | |
| PRD Clade III | Cgi_PRD7 | CGI_10025814 | |
| PRD Clade II | Cgi_PRD8 | CGI_10026008 | |
| n.d. | Cgi_PRD9 | CGI_10026078 | |
| LIM | Isl | Islet | CGI_10028355 |
| Lhx1/5 | Lhx1/5 | CGI_10025343 | |
| Lhx2/9 | Lhx2/9 | CGI_10015423 | |
| Lhx3/4 | Lhx3/4 | CGI_10028171 | |
| Lhx6/8 | Awh1 | CGI_10025669 | |
| Lhx6/8 | Awh2 | CGI_10020871 | |
| Lmx | Lmx1 | CGI_10019449 | |
| Lmx | Lmx2 | CGI_10019450 | |
| POU | Pou2 | Pou2 | CGI_10006547 |
| Pou3 | Pou3 | CGI_10005968 | |
| Pou4 | Pou4 | CGI_10023764 | |
| Pou6 | Pou6 | CGI_10028901 | |
| SINE | Six1/2 | Six1/2 | CGI_10009922 |
| Six3/6 | Six3/6 | CGI_10027570 | |
| Six4/5 | Six4/5 | CGI_10022945 | |
| TALE | Irx | Irx1 | CGI_10011883 |
| Irx | Irx2 | CGI_10028533 | |
| Irx | Irx3 | CGI_10020098 | |
| Irx | Irx4 | CGI_10004700 | |
| Meis | Meis | CGI_10019589 | |
| Mkx | Mkx | CGI_10011802 | |
| Pbx | Pbx | CGI_10026001 | |
| Pknox | Pknox | CGI_10011944 | |
| Tgif | Tgif | CGI_10023491 | |
| TALE Clade II | Cgi_TALE1 | CGI_10000035 | |
| TALE Clade I | Cgi_TALE2 | CGI_10008335 | |
| TALE Clade III | Cgi_TALE3 | CGI_10011283 | |
| TALE Clade VII | Cgi_TALE4 | CGI_10013112 | |
| n.d. | Cgi_TALE5 | CGI_10014640 | |
| TALE Clade V | Cgi_TALE6 | CGI_10019516 | |
| TALE Clade IV | Cgi_TALE7 | CGI_10015054 | |
| TALE Clade IV | Cgi_TALE8 | CGI_10015055 | |
| TALE Clade VI | Cgi_TALE9 | CGI_10015742 | |
| TALE Clade VI | Cgi_TALE10 | CGI_10019518 | |
| TALE Clade VI | Cgi_TALE11 | CGI_10021477 | |
| TALE Clade VI | Cgi_TALE12 | CGI_10021478 | |
| TALE Clade VI | Cgi_TALE13 | CGI_10015317 | |
| TALE Clade IV | Cgi_TALE14 | CGI_10021576 | |
| CUT | Cmp | Cmp1 | CGI_10015221 |
| Cmp | Cmp2 | CGI_10015220 | |
| Cux | Cux | CGI_10022123 | |
| Onecut | Onecut | CGI_10019668 | |
| Cut Clade I | Cgi_CUT1 | CGI_10006727 | |
| Cut Clade I | Cgi_CUT2 | CGI_10022104 | |
| PROS | Prox | Prox | CGI_10022026 |
| ZF | Zeb | Zeb | scaffold42570_54922 _55110 |
| Zfhx | Zfhx | CGI_10012804 | |
| Zhx/Homez | Homez | CGI_10009971 | |
| n.d. | Cgi_ZF | CGI_10018873 | |
| CERS | Cers | Cers | CGI_10021077 |
| Others | n.d. | Cgi_Hbx_1 | CGI_10004542 |
| n.d. | Cgi_Hbx_2 | CGI_10016179 | |
| n.d. | Cgi_Hbx_3 | CGI_10007234 | |
| n.d. | Cgi_Hbx_4 | scaffold1627_218521 _218706 |
Note.—The homeobox gene complement of Crassostrea gigas, classified into gene classes and gene families. Protein models for each gene are indicated. n.d. denotes that the gene family cannot be determined, usually due to divergence of the homeodomain sequence and presence only in oyster.