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PRD Class
Families List  Genes List
The PRD class is the second largest of the homeobox gene classes in animal genomes; like the ANTP class these genes have only been found in animals. The PRD class derives its name from (but is not an abbreviation for) the Paired (Prd) gene of Drosophila. PRD class genes are defined phylogenetically - they form a robust monophyletic group in evolutionary trees of homeodomain sequences. The PRD homeobox class overlaps with the Pax gene class - some but not all Pax genes are in the PRD homeobox gene class, while the vast majority of PRD class homeobox genes are not Pax genes.

There are 9 Pax genes in the human or mouse genomes, defined by presence of a 128 amino acid Paired domain, and of these 7 are members of the PRD homeobox class by virtue of possessing a homeobox: complete homeobox for PAX3, 4, 6 and 7; partial homeobox for PAX2, 5 and 8 (the two human Pax genes lacking a homeobox entirely are PAX1 and PAX9; these are not included in this database). In addition to these 7 homeobox-containing Pax genes, there are a further 43 PRD class genes in the human genome. These 50 genes can be divided into 31 gene families. There are also 24 human pseudogenes generated from these genes, plus an unknown number of DUX repetitive sequences (Holland et al. 2007).

In amphioxus there are 5 Pax genes, and of these 3 are have a partial or complete homeobox (Pax-1/9 and Pon are the two lacking homeobox sequence and therefore excluded; Pon is present in Drosophila and amphioxus, but not human). In addition to these genes, there are a further 27 PRD class genes in amphioxus (Takatori et al. 2008).

Reference(s):
Holland PWH, Booth HAF, Bruford EA (2007) BMC Biology 5:47.
Takatori N et al (2008) Dev Genes Evol 218: 579-590.
 
Families List of Class PRD :
Alx(5)Arx(1)Dmbx(3)Drgx(1)Gsc(2)Hesx(1)Mix(3)Nobox(1)Otp(2)
Otx(5)Pax2/5/8(1)Pax3/7(4)Pax4/6(4)Phox(4)Pitx(3)Prop(1)Prrx(2)Rax(3)
Shox(2)Uncx(3)Vsx(2)       
 
Loci in PRD of Zebrafish back to top..
Symbol/LocusNameFamilyOrganismRegulator
Alx3-lAlx3 likeAlxZebrafish 
alx4aaristaless-like homeobox 4aAlxZebrafish 
alx4baristaless-like homeobox 4bAlxZebrafish 
arxaristaless related homeoboxArxZebrafish 
bonbonnie and clydeMixZebrafish 
cart1cartilage paired-class homeoprotein 1AlxZebrafish 
chr04.1Alx likeAlxZebrafish 
chr05.1Gsc likeGscZebrafish 
crxcone-rod homeoboxOtxZebrafish 
Dmbx1-lDmbx1 likeDmbxZebrafish 
dmbx1adiencephalon/mesencephalon homeobox 1aDmbxZebrafish 
dmbx1bdiencephalon/mesencephalon homeobox 1bDmbxZebrafish 
drgxdorsal root ganglia homeoboxDrgxZebrafish 
gscgoosecoidGscZebrafish 
hesx1homeo box (expressed in ES cells) 1HesxZebrafish 
LOC100330956bonnie and clyde-likeMixZebrafish 
og9xOG9 homeobox geneMixZebrafish 
otpaorthopedia homolog aOtpZebrafish 
otpborthopedia homolog bOtpZebrafish 
otx1aorthodenticle homolog 1aOtxZebrafish 
otx1borthodenticle homolog 1bOtxZebrafish 
otx2orthodenticle homolog 2OtxZebrafish 
otx5orthodenticle homolog 5OtxZebrafish 
pax2bpaired box gene 2bPax2/5/8Zebrafish 
pax3apaired box gene 3aPax3/7Zebrafish 
pax3bpaired box gene 3bPax3/7Zebrafish 
pax4paired box 4Pax4/6Zebrafish 
Pax6-lPax6 likePax4/6Zebrafish 
pax6apaired box gene 6aPax4/6Zebrafish 
pax6bpaired box gene 6bPax4/6Zebrafish 
pax7apaired box gene 7aPax3/7Zebrafish 
pax7bpaired box gene 7bPax3/7Zebrafish 
Phox-lPhox likePhoxZebrafish 
phox2apaired-like homeobox 2aPhoxZebrafish 
phox2bpaired-like homeobox 2bPhoxZebrafish 
phox2b-lphox2b like PhoxZebrafish 
pitx1paired-like homeodomain transcription factor 1PitxZebrafish 
pitx2paired-like homeodomain transcription factor 2PitxZebrafish 
pitx3paired-like homeodomain transcription factor 3PitxZebrafish 
prop1PROP paired-like homeobox 1PropZebrafish 
prrx1apaired related homeobox 1aPrrxZebrafish 
prrx1bpaired related homeobox 1bPrrxZebrafish 
rx1retinal homeobox gene 1RaxZebrafish 
rx2retinal homeobox gene 2RaxZebrafish 
rx3retinal homeobox gene 3RaxZebrafish 
shoxshort stature homeoboxShoxZebrafish 
shox2short stature homeobox 2ShoxZebrafish 
uncxUNC homeoboxUncxZebrafish 
uncx4.1Unc4.1 homeoboxUncxZebrafish 
Uncxl-2Uncx like 2UncxZebrafish 
vsx1visual system homeobox 1 homolog, chx10-likeVsxZebrafish 
vsx2visual system homeobox 2VsxZebrafish 
wu:fi69e09wu:fi69e09NoboxZebrafish