------------------------------------------------------------------------------ SWISS-PROT Protein Sequence Data Bank. Release 31.0, February 1995 ------------------------------------------------------------------------------ Vertebrate homeobox proteins: nomenclature and index ------------------------------------------------------------------------------ Amos Bairoch Email: bairoch@cmu.unige.ch Medical Biochemistry Department University of Geneva Switzerland ------------------------------------------------------------------------------ Document name: HOXLIST.TXT ------------------------------------------------------------------------------ Background information The homeotic Hox proteins are sequence-specific transcription factor which are part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior (A-P) axis [1]. The hox proteins contain an `homeobox' domain. In Drosophila and other insects there are eight different Hox genes that are encoded in two gene complexes: ANT-C and BX-C; while in vertebrates there are 38 genes organized in four complexes. Recently [2,3] a new nomenclature system has been proposed for Hox genes. The four gene complexes are assigned the letters A to D. Based on sequence similarities the genes can be sorted into 13 `paralog' groups. The order of the paralogs along the chromosomes are conserved in the four complexes. The gene name is obtained by concatenating the gene complex letter designation with the group number; examples: HOXA1, HOXB4, HOXC8, HOXD13, etc. In several cases a representative of a paralog group is absent from a complex, in such cases that gene number is omitted. For example: HOXA8, HOXC1 and HOXD2 do not exist. We have fully implemented this nomenclature system in SWISS-PROT. [ 1] McGinnis W., Krumlauf R. Cell 68:283-302(1992). [ 2] Scott M.P. Cell 71:551-553(1992). [ 3] Scott M.P. Nucleic Acids res. 21:1687-1688(1993). ======================================= Table of the nomenclature for HOX genes ======================================= New Previous Previous Other Other Other previous names used gene Human Mouse Mouse Human in various species name name name names names ------ ------ -------- ------------ --------- ------------------------- HOXA1 HOX1F HOX-1.6 era-1 HOXA2 HOX1K HOX-1.11 NvHbox-2.8 HOXA3 HOX1E HOX-1.5 mo-10 HOXA4 HOX1D HOX-1.4 mh-3 R2; Chox-1.4 HOXA5 HOX1C HOX-1.3 m2 s12-B HOXA6 HOX1B HOX-1.2 m5-4 HOXA7 HOX1A HOX-1.1 m6-12; m6 R5; Quox-1; XlHbox-3; Xhox-36 HOXA9 HOX1G HOX-1.7 HOXA10 HOX1H HOX-1.8 PL HOXA11 HOX1I HOX-1.9 Ghox-1i HOXA12 HOX1J HOX-1.10 HOXB1 HOX2I HOX-2.9 Ghox-lab; AHox1 HOXB2 HOX2H HOX-2.8 K8 s6 HOXB3 HOX2G HOX-2.7 mh-23 Chox-2.7; XlHox-2.7 HOXB4 HOX2F HOX-2.6 Chox-Z; Xhox-1A HOXB5 HOX2A HOX-2.1 Mu-1; H24.1 Hu-1; c10 Ohox-2.1; Ghox-2.1; XlHbox-4; Xhox-1B; zf-21 HOXB6 HOX2B HOX-2.2 mh-22A Hu-2 Ghox-2.2; XlHox-2.2; zf-22 HOXB7 HOX2C HOX-2.3 mh-22B; mub1 c1 R1b; XlHbox-2; MM3 HOXB8 HOX2D HOX-2.4 R1a; Chox-2.4 HOXB9 HOX2E HOX-2.5 XlHbox-6 HOXC4 HOX3E HOX-3.5 cp19 R3 HOXC5 HOX3D HOX-3.4 Hox-6.2 cp11 XlHbox-5; NvHbox-3.4; zf-25 HOXC6 HOX3C HOX-3.3 Hox-6.1 c8; cp25 NvHox-1; FH-2; XlHbox-1; AC1; zf-61 HOXC8 HOX3A HOX-3.1 m31 R4 HOXC9 HOX3B HOX-3.2 HOXC10 HOX3I HOX-3.6 HOXC11 HOX3H HOX-3.7 HOXC12 HOX3F HOX-3.8 HOXC13 HOX3G HOX-3.9 HOXD1 HOX4G HOX-4.9 HOXD3 HOX4A HOX-4.1 mh-19 R6 HOXD4 HOX4B HOX-4.2 Hox-5.1 c13 Chox-A; zf-13 HOXD8 HOX4E HOX-4.3 Hox-5.4 Chox-M HOXD9 HOX4C HOX-4.4 Hox-5.2 Chox-4.4 HOXD10 HOX4D HOX-4.5 Hox-5.3 Hox4E Chox-4.5; Chox-4d HOXD11 HOX4F HOX-4.6 Hox-5.5 Chox-4.6; Ghox-4.6; Chox-4e; NvHox-2 HOXD12 HOX4H HOX-4.7 Hox-5.6 Chox-4.7; Chox-4f HOXD13 HOX4I HOX-4.8 Hox-5.7 Chox-4.8; Chox-4g ================================ SWISS-PROT entries for HOX genes ================================ Hox sequences in vertebrates ---------------------------- A1 P09022; HXA1_MOUSE A2 P31245; HXA2_MOUSE P31246; HXA2_RAT Q08727; HXA2_CHICK P31261; HXA2_NOTVI A3 P02831; HXA3_MOUSE A4 Q00056; HXA4_HUMAN P06798; HXA4_MOUSE P09635; HXA4_RAT P17277; HXA4_CHICK A5 P20719; HXA5_HUMAN P09021; HXA5_MOUSE P09637; HXA5_SALSA A6 P31267; HXA6_HUMAN P09092; HXA6_MOUSE A7 P31268; HXA7_HUMAN P02830; HXA7_MOUSE P09634; HXA7_RAT P24061; HXA7_COTJA P09071; HXA7_XENLA A9 P31269; HXA9_HUMAN P09631; HXA9_MOUSE A10 P31260; HXAA_HUMAN P31310; HXAA_MOUSE A11 P31270; HXAB_HUMAN P31311; HXAB_MOUSE P31258; HXAB_CHICK A13 P31271; HXAD_HUMAN B1 P14653; HXB1_HUMAN P17919; HXB1_MOUSE P31259; HXB1_CHICK P31357; HXB1_AMBME B2 P14652; HXB2_HUMAN P09638; HXB2_SALSA B3 P14651; HXB3_HUMAN P09026; HXB3_MOUSE P23682; HXB3_CHICK P31247; HXB3_XENLA B4 P17483; HXB4_HUMAN P10284; HXB4_MOUSE P14840; HXB4_CHICK P09070; HXB4_XENLA B5 P09067; HXB5_HUMAN P09079; HXB5_MOUSE P14157; HXB5_SHEEP P14838; HXB5_CHICK P09014; HXB5_BRARE P09019; HXB5_XENLA B6 P17509; HXB6_HUMAN P09023; HXB6_MOUSE P14839; HXB6_CHICK P15861; HXB6_BRARE P31256; HXB6_XENLA B7 P09629; HXB7_HUMAN P09024; HXB7_MOUSE P18864; HXB7_RAT P04476; HXB7_XENLA B8 P17481; HXB8_HUMAN P09632; HXB8_MOUSE P18863; HXB8_RAT P09078; HXB8_PIG P23681; HXB8_CHICK B9 P17482; HXB9_HUMAN P20615; HXB9_MOUSE P31272; HXB9_XENLA C4 P09017; HXC4_HUMAN Q08624; HXC4_MOUSE P18865; HXC4_RAT C5 Q00444; HXC5_HUMAN P32043; HXC5_MOUSE P31262; HXC5_NOTVI P09074; HXC5_BRARE P09020; HXC5_XENLA C6 P09630; HXC6_HUMAN P10629; HXC6_MOUSE P14858; HXC6_NOTVI P15862; HXC6_BRARE P02832; HXC6_XENLA C8 P31273; HXC8_HUMAN P09025; HXC8_MOUSE P18866; HXC8_RAT C9 P31274; HXC9_HUMAN P09633; HXC9_MOUSE C10 P31257; HXCA_MOUSE C11 P31312; HXCB_MOUSE C12 P31275; HXCC_HUMAN P31313; HXCC_MOUSE C13 P31276; HXCD_HUMAN D1 Q01822; HXD1_MOUSE D3 P31249; HXD3_HUMAN P09027; HXD3_MOUSE P18867; HXD3_RAT D4 P09016; HXD4_HUMAN P10628; HXD4_MOUSE P17278; HXD4_CHICK P22574; HXD4_BRARE D8 P13378; HXD8_HUMAN P23463; HXD8_MOUSE P23459; HXD8_CHICK D9 P28356; HXD9_HUMAN P28357; HXD9_MOUSE P24340; HXD9_CHICK D10 P28358; HXDA_HUMAN P28359; HXDA_MOUSE P24341; HXDA_CHICK D11 P31277; HXDB_HUMAN P23813; HXDB_MOUSE P24342; HXDB_CHICK P31263; HXDB_NOTVI D12 P35452; HXDC_HUMAN P23812; HXDC_MOUSE P24343; HXDC_CHICK D13 P35453; HXDD_HUMAN P24344; HXDD_CHICK Hox sequences in Drosophila and other insects --------------------------------------------- Abd-A P29555; HMAA_DROME P29552; HMAA_AEDAE P15856; HMAA_APIME P29556; HMAA_SCHGR Abd-B P09087; HMAB_DROME AntP P02833; HMAN_DROME Dfd P07548; HMDF_DROME lab P10105; HMLA_DROME pb P31264; HMPB_DROME Scr P09077; HMSC_DROME P15859; HMSC_APIME Ubx P02834; HMUX_DROME P05048; HMUX_DROFU P20822; HMUX_DROPS